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[{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2020 EpiForecasts Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/articles/quickstart.html","id":"quick-start-to-covidregionaldata","dir":"Articles","previous_headings":"","what":"Quick start to covidregionaldata","title":"Quick start","text":"covidregionaldata designed extract national subnational Covid-19 data publicly available sources, daily aggregated time. example, : Get Covid-19 cases deaths countries day since reporting began. Get total Covid-19 cases deaths countries today. Get number new cases state United States time. Get total number deaths local authorities United Kingdom. demonstrate examples , well useful data manipulation visualisation.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/articles/quickstart.html","id":"retrieving-national-cases-and-deaths-over-time","dir":"Articles","previous_headings":"Quick start to covidregionaldata","what":"Retrieving national cases and deaths over time","title":"Quick start","text":"Let’s say want see evolution pandemic time countries. , need get number cases (positive test results) deaths country date since pandemic started. Firstly load covidregionaldata, call get_national_data(): can take look data printing console: can see provides information number cases deaths country time. tibble returned, can easily manipulate plot using tidyverse packages. example, can plot total deaths Italy time. also filtered country using get_national_data(countries = \"Italy\") achieve result. plot evolution cases several countries since start pandemic, perform something like following:","code":"library(covidregionaldata) all_countries <- get_national_data() #> Downloading data from https://covid19.who.int/WHO-COVID-19-global-data.csv #> Rows: 212589 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (3): Country_code, Country, WHO_region #> dbl (4): New_cases, Cumulative_cases, New_deaths, Cumulative_deaths #> date (1): Date_reported #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Cleaning data #> #> Processing data all_countries #> # A tibble: 212,589 × 15 #> date un_region who_region country iso_code cases_new cases_total #> <date> <chr> <chr> <chr> <chr> <dbl> <dbl> #> 1 2020-01-03 Asia EMRO Afghanistan AF 0 0 #> 2 2020-01-03 Europe EURO Albania AL 0 0 #> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 #> 4 2020-01-03 Oceania WPRO American Samoa AS 0 0 #> 5 2020-01-03 Europe EURO Andorra AD 0 0 #> 6 2020-01-03 Africa AFRO Angola AO 0 0 #> 7 2020-01-03 Americas AMRO Anguilla AI 0 0 #> 8 2020-01-03 Americas AMRO Antigua & Bar… AG 0 0 #> 9 2020-01-03 Americas AMRO Argentina AR 0 0 #> 10 2020-01-03 Asia EURO Armenia AM 0 0 #> # … with 212,579 more rows, and 8 more variables: deaths_new <dbl>, #> # deaths_total <dbl>, recovered_new <dbl>, recovered_total <dbl>, #> # hosp_new <dbl>, hosp_total <dbl>, tested_new <dbl>, tested_total <dbl> library(dplyr) library(ggplot2) all_countries %>% filter(country == \"Italy\") %>% ggplot() + aes(x = date, y = deaths_total) + geom_line() + labs(x = NULL, y = \"All reported Covid-19 deaths, Italy\") + theme_minimal() all_countries %>% filter(country %in% c( \"Italy\", \"United Kingdom\", \"Spain\", \"United States\" )) %>% ggplot() + aes(x = date, y = cases_total, colour = country) + geom_line() + labs(x = NULL, y = \"All reported Covid-19 cases\", colour = \"Country\") + theme_minimal() + theme(legend.position = \"bottom\")"},{"path":"https://epiforecasts.io/covidregionaldata/articles/quickstart.html","id":"retrieving-total-cases-and-deaths-for-all-countries","dir":"Articles","previous_headings":"Quick start to covidregionaldata","what":"Retrieving total cases and deaths for all countries","title":"Quick start","text":"Using get_national_data(totals = TRUE) can obtain total cases deaths nations latest date reported. useful get snapshot current running total country. Note data sorted total number cases:","code":"all_countries_totals <- get_national_data(totals = TRUE, verbose = FALSE) all_countries_totals #> # A tibble: 236 × 7 #> country iso_code cases_total deaths_total recovered_total hosp_total #> <chr> <chr> <dbl> <dbl> <dbl> <dbl> #> 1 United States US 85007630 1005385 0 0 #> 2 India IN 43270582 524817 0 0 #> 3 Brazil BR 31612342 668693 0 0 #> 4 France FR 29114200 145700 0 0 #> 5 Germany DE 27124689 140118 0 0 #> 6 United Kingdom GB 22460453 179472 0 0 #> 7 Russia RU 18391797 380333 0 0 #> 8 South Korea KR 18263643 24416 0 0 #> 9 Italy IT 17773764 167648 0 0 #> 10 Turkey TR 15085742 98996 0 0 #> # … with 226 more rows, and 1 more variable: tested_total <dbl>"},{"path":"https://epiforecasts.io/covidregionaldata/articles/quickstart.html","id":"retrieving-subnational-region-data","dir":"Articles","previous_headings":"Quick start to covidregionaldata","what":"Retrieving subnational region data","title":"Quick start","text":"well national data, can also retrieve subnational data, states counties US, regions local authorities UK, perform similar manipulations. See README current list countries subnational data. , use get_regional_data() (also use underlying method follows us <- USA$new(get = TRUE); us$return()). ’ll get state-level data United States time: retrieves new total cases deaths states time United States. Note country argument get_regional_data() function must specified. Let’s plot number cases evolved selection states: totals argument can also used get_regional_data return cumulative number cases deaths time. Let’s plot total deaths state, ordered total deaths: countries hierarchy political subdivisions. data available, use level = \"2\" argument get_regional_data. can dig US state looking data county: returns data county day reported data. 3,000 counties US, reporting data since 21st January, makes large download. method work different countries data available, returning relevant sub-national units country. example, Germany data available Bundesland (federated state) Kreise (district) areas. Additional subnational data supported via JHU() Google() classes. Use available_regions() method data downloaded cleaned (see examples) subnational data internally support.","code":"usa_states <- get_regional_data(country = \"USA\") #> Downloading data from https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv #> Rows: 46430 Columns: 5 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (2): state, fips #> dbl (2): cases, deaths #> date (1): date #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Cleaning data #> #> Processing data usa_states %>% filter(state %in% c(\"New York\", \"Texas\", \"Florida\")) %>% ggplot() + aes(x = date, y = cases_total, colour = state) + geom_line() + labs(x = NULL, y = \"All reported Covid-19 cases\", colour = \"U.S. state\") + theme_minimal() + theme(legend.position = \"bottom\") usa_states_totals <- get_regional_data( country = \"USA\", totals = TRUE, verbose = FALSE ) usa_states_totals %>% ggplot() + aes(x = reorder(state, -deaths_total), y = deaths_total) + geom_bar(stat = \"identity\") + labs(x = \"U.S. states\", y = \"All reported Covid-19 deaths\") + theme_minimal() + theme( axis.text.x = element_text(angle = 90), axis.title.y = element_text(hjust = 1), legend.position = \"bottom\" ) usa_counties <- get_regional_data(country = \"USA\", level = \"2\", verbose = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/articles/quickstart.html","id":"mapping-data","dir":"Articles","previous_headings":"Quick start to covidregionaldata","what":"Mapping data","title":"Quick start","text":"provide relevant national subnational ISO codes, local alternatives, enable mapping. can map Covid-19 data national subnational level, using standard shapefile. R, rnaturalearth package already provides shapefiles country borders, largest (administrative level 1) subnational units countries. simplicity use rworldmap package, uses data rnaturalearth national country borders inbuilt mapping. can join Covid-19 data map using iso_code.","code":"# Get latest worldwide WHO data map_data <- get_national_data(totals = TRUE, verbose = FALSE) %>% rworldmap::joinCountryData2Map( joinCode = \"ISO2\", nameJoinColumn = \"iso_code\" ) #> 225 codes from your data successfully matched countries in the map #> 11 codes from your data failed to match with a country code in the map #> 16 codes from the map weren't represented in your data # Produce map rworldmap::mapCountryData(map_data, nameColumnToPlot = \"deaths_total\", catMethod = \"fixedWidth\", mapTitle = \"Total Covid-19 deaths to date\", addLegend = TRUE )"},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"installing-and-loading-the-package","dir":"Articles","previous_headings":"","what":"Installing and loading the package","title":"Package overview","text":"package can either installed CRAN, r-universe repository, GitHub. See README details. installed load package using following,","code":"library(covidregionaldata)"},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"accessing-national-data","dir":"Articles","previous_headings":"Worldwide data","what":"Accessing national data","title":"Package overview","text":"World Health Organisation () European Centre Disease Control (ECDC) provide worldwide national data. Access national level data country using: returns daily new cumulative (total) cases, available, deaths, hospitalisations, tests. complete list variables returned, see section 5, “Data glossary” . See documentation (?get_national_data) details optional arguments. Data returned gaps structure data country time, NAs fill data available.","code":"get_national_data()"},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"accessing-sub-national-data","dir":"Articles","previous_headings":"Sub-national time-series data","what":"Accessing sub-national data","title":"Package overview","text":"Access sub-national level data specific country time using get_regional_data(). Use get_available_datasets() explore currently supported sub-national datasets select data set interest using country (selects country interest), level (selects spatial scale data) arguments get_regional_data. function returns daily new cumulative (total) cases, available, deaths, hospitalisations, tests. complete list variables returned, see section 5, “Data glossary” . See documentation (?get_regional_data) details optional arguments. national level data gaps reported data filled NAs. example, data Lithuania Level 1 regions time can accessed using: data following format: Alternatively, data can accessed using underlying class follows (Lithuania object now contains data processing step methods used step),","code":"get_regional_data(country = \"lithuania\") lithuania <- Lithuania$new(get = TRUE) lithuania$return()"},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"level-1-and-level-2-regions","dir":"Articles","previous_headings":"Sub-national time-series data","what":"Level 1 and Level 2 regions","title":"Package overview","text":"countries included package (see ,“Coverage”) data regions admin-1 level, largest administrative unit country (e.g. state USA). countries also data smaller areas admin-2 level (e.g. county USA). Data Level 2 units can returned using level = \"2\" argument. dataset still show corresponding Level 1 region. example country Level 2 units Lithuania, Level 2 units Lithuanian municipalities: data following format:","code":"get_regional_data(country = \"lithuania\", level = \"2\")"},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"totals","dir":"Articles","previous_headings":"Sub-national time-series data","what":"Totals","title":"Package overview","text":"totalled data recent date available, use totals argument. data now date variable reflects latest total:","code":"get_regional_data(\"lithuania\", totals = TRUE)"},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"subnational-data","dir":"Articles","previous_headings":"Data glossary","what":"Subnational data","title":"Package overview","text":"data columns returned get_regional_data() listed . standardise across countries regions, columns returned country always . corresponding data missing original source data field filled NA values (0 accessing totals data). Note Date included totals argument set TRUE. Level 2 region/level 2 region code included level = \"1\". date: date counts reported (YYYY-MM-DD). level_1_region: level 1 region name. column named differently different countries (e.g. state, province). level_1_region_code: standard code level 1 region. column name reflects specific administrative code used. Typically data returns iso_3166_2 standard, although available column named differently reflect source. level_2_region: level 2 region name. column named differently different countries (e.g. city, county). level_2_region_code: standard code level 2 region. column named differently different countries (e.g. fips USA). cases_new: new reported cases day. cases_total: total reported cases including day. deaths_new: new reported deaths day. deaths_total: total reported deaths including day. recovered_new: new reported recoveries day. recovered_total: total reported recoveries including day. hosp_new: new reported hospitalisations day. hosp_total: total reported hospitalisations including day (note cumulative total new reported, total currently hospital). tested_new: tests day. tested_total: total tests completed including day.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/articles/slowstart.html","id":"national-data","dir":"Articles","previous_headings":"Data glossary","what":"National data","title":"Package overview","text":"addition , following columns included using get_national_data(). un_region: country geographical region defined United Nations. who_region: included source = \"\". Country geographical region defined . population_2019: included source = \"ECDC\". Total country population estimate 2019.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/articles/supported-countries.html","id":"countries-with-subnational-data","dir":"Articles","previous_headings":"","what":"Countries with subnational data","title":"Supported countries and their support status","text":"map shows countries level 1 level 2 subregion data directly official source within country. Please note countries may provided interface external data sources, () JHU().","code":""},{"path":"https://epiforecasts.io/covidregionaldata/articles/supported-countries.html","id":"status","dir":"Articles","previous_headings":"","what":"Status","title":"Supported countries and their support status","text":"Dataset status shown table . Please see hosted page date information CRAN status data sets. Please note due release schedule datasets may remain non-functional broken using CRAN version time even fixed GitHub. Also note transient issues may affect testing datasets checks may occasionally show spurious failure.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/articles/testing.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Testing","text":"PR moves testing class methods, allowing tests ran interactively within country class object, within existing testing infrastructure. DataClass parent class country classes, Italy, UK, USA, etc. generic testing function method test within DataClass. Interactively, tests can ran following: , break different components function walk tests run. given country, UK, make calling something like ukdata <- UK$new(level = \"1\") can run steps one one calling respective methods: ukdata$download(); ukdata$clean(); ukdata$process(). run tests call ukdata$test(shapshot_dir = \"place/2/save/snapshots\") default, snapshot_dir given use generic snapsots directory. snapshot_dir argument specifies directory save data snapshots doesn’t exist make . file constructed internally object testing data level, e.g. Uk_level_1.rds. Rather running tests active class, code first makes clone class used tests: self_copy <- self$clone() snapshot path path rds file either stored raw downloaded data test, want downloaded snapshot data end . handled function test_download(). cloned class passed function, along download parameter, dictates whether overwrite snapshot file provided. shown code, data downloaded (either requesting download parameter providing path none existent file) download method called class copy (DataClass_obj): DataClass_obj$download(). downloaded code tests data data.frame, empty least 2 columns. code takes first 250 rows work , using whole data set slow purpose testing needed. sliced data saved snapshot file provided use later . data downloaded, snapshot data saved snapshot path loaded raw data DataClass_obj$data$raw. data downloaded, cleaning methods tested test_cleaning(). function takes copied class argument runs tests clean data. tests check data data.frame, empty, 2 columns method avaliable_regions returns list characters. addition, expect_clean_cols checks date column s3 class region level column character cleaned data (data$clean). cleaning tested test_processing() called process data run tests check works. function takes clone class work , clone called preceding functions. tests check data data.frame, empty, 2 columns. addition expect_processed_cols checks processed data columns date, cases_new, cases_total, deaths_new, deaths_total region level correct types. processing extra parameter called . parameter, TRUE runs processing step localised TRUE FALSE, making another copy object check localised data influence tests. FALSE processing ran localised set whatever set prior test() invoked. processing return method tested test_return check data data.frame, empty, 2 columns columns contain data just composed NAs. tests form generic tests applied classes. However, country specific tests called calling method specific_tests country specific tests defined. Italy, specific tests, specific tests called, UK, ECDC specific tests ran though, defined country class. functions take clone class argument (self_copy ) additional arguments may need, path NHS included data UK.","code":"library(covidregionaldata) ukdata <- UK$new(level = \"1\", verbose = FALSE) # could use anything but I used the acutal test one here for simplicity ukdata$test(snapshot_dir = \"../tests/testthat/custom_data/\") #> Test passed 😸 #> Test passed 🎊 #> Test passed 🎉 #> Test passed 🎊 #> Test passed 😸 #> Test passed 🎉 #> Test passed 🎊 #> Test passed 🎉 #> Test passed 🎉 #> Test passed 🌈 ukdata$test #> function (download = FALSE, snapshot_dir = paste0(tempdir(), #> \"/snapshots\"), all = FALSE, ...) #> { #> snapshot_file_name <- paste0(class(self)[1], \"_level_\", self$level, #> \".rds\") #> dir.create(snapshot_dir, showWarnings = FALSE) #> message_verbose(verbose = self$verbose, paste(\"snapshot to be saved at\", #> snapshot_dir)) #> snapshot_path <- file.path(snapshot_dir, snapshot_file_name) #> self_copy <- self$clone() #> test_download(DataClass_obj = self_copy, download = download, #> snapshot_path = snapshot_path) #> test_cleaning(DataClass_obj = self_copy) #> test_processing(DataClass_obj = self_copy, all = all) #> test_return(DataClass_obj = self_copy) #> if (\"specific_tests\" %in% names(self_copy)) { #> specific <- paste0(\"self$specific_tests(\\n self_copy = self_copy,\\n download = download,\\n all = all,\\n snapshot_path = snapshot_path,\\n ...\\n )\") #> eval(parse(text = specific)) #> } #> } #> <environment: 0x560367084938> test_download #> function (DataClass_obj, download, snapshot_path) #> { #> if (!file.exists(snapshot_path)) { #> download <- TRUE #> } #> if (download) { #> testthat::test_that(paste0(DataClass_obj$data_name, \" downloads sucessfully\"), #> { #> DataClass_obj$download() #> walk(DataClass_obj$data$raw, function(data) { #> testthat::expect_s3_class(data, \"data.frame\") #> testthat::expect_true(nrow(data) > 0) #> testthat::expect_true(ncol(data) >= 2 || typeof(data[[1]]) == #> \"list\") #> }) #> }) #> DataClass_obj$data$raw <- map(DataClass_obj$data$raw, #> slice_tail, n = 250) #> DataClass_obj$data$raw <- map(DataClass_obj$data$raw, #> ~.[, seq_len(min(100, ncol(.)))]) #> saveRDS(DataClass_obj$data$raw, snapshot_path) #> } #> else { #> DataClass_obj$data$raw <- readRDS(snapshot_path) #> } #> } #> <bytecode: 0x56036747ce28> #> <environment: namespace:covidregionaldata> test_cleaning #> function (DataClass_obj) #> { #> testthat::test_that(paste0(DataClass_obj$data_name, \" can be cleaned as expected\"), #> { #> DataClass_obj$clean() #> testthat::expect_s3_class(DataClass_obj$data$clean, #> \"data.frame\") #> testthat::expect_true(nrow(DataClass_obj$data$clean) > #> 0) #> testthat::expect_true(ncol(DataClass_obj$data$clean) >= #> 2) #> expect_clean_cols(DataClass_obj$data$clean, DataClass_obj$level) #> }) #> testthat::test_that(paste(DataClass_obj$data_name, \"highlights available regions as expected\"), #> { #> testthat::expect_error(DataClass_obj$available_regions(), #> NA) #> testthat::expect_true(class(DataClass_obj$available_regions()) %in% #> \"character\") #> }) #> } #> <bytecode: 0x5603674765c8> #> <environment: namespace:covidregionaldata> test_processing #> function (DataClass_obj, all = FALSE) #> { #> testthat::test_that(paste0(DataClass_obj$data_name, \" can be processed as expected\"), #> { #> DataClass_obj$process() #> testthat::expect_s3_class(DataClass_obj$data$processed, #> \"data.frame\") #> testthat::expect_true(nrow(DataClass_obj$data$processed) > #> 0) #> testthat::expect_true(ncol(DataClass_obj$data$processed) >= #> 2) #> expect_processed_cols(DataClass_obj$data$processed, #> level = DataClass_obj$level, localised = DataClass_obj$localise) #> if (all) { #> local_region <- DataClass_obj$clone() #> local_region$localise <- FALSE #> local_region$process() #> expect_processed_cols(local_region$data$processed, #> level = local_region$level, localised = local_region$localise) #> } #> }) #> } #> <bytecode: 0x560369aae350> #> <environment: namespace:covidregionaldata> test_return #> function (DataClass_obj) #> { #> testthat::test_that(paste0(DataClass_obj$data_name, \" can be returned as expected\"), #> { #> returned <- DataClass_obj$return() #> if (any(class(returned) %in% \"data.frame\")) { #> testthat::expect_s3_class(returned, \"data.frame\") #> testthat::expect_true(nrow(returned) > 0) #> testthat::expect_true(ncol(returned) >= 2) #> } #> }) #> expect_columns_contain_data(DataClass_obj) #> } #> <bytecode: 0x56036e790a50> #> <environment: namespace:covidregionaldata>"},{"path":"https://epiforecasts.io/covidregionaldata/articles/testing.html","id":"integration-with-testthat","dir":"Articles","previous_headings":"","what":"Integration with testthat","title":"Testing","text":"well interactive tests test() method also used testthat conducting package level tests argument = TRUE. done file tests/testthat/custom_tests/test_regional_dataset.R","code":""},{"path":"https://epiforecasts.io/covidregionaldata/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joseph Palmer. Author. Katharine Sherratt. Author. Richard Martin-Nielsen. Author. https://github.com/RichardMN Jonnie Bevan. Author. Hamish Gibbs. Author. Hugo Gruson. Author. Sophie Meakin. Contributor. Joel Hellewell. Contributor. Patrick Barks. Contributor. Paul Campbell. Contributor. Flavio Finger. Contributor. Richard Boyes. Contributor. https://github.com/rboyes Vang Le. Contributor. https://github.com/biocyberman Sebastian Funk. Author. Sam Abbott. Author, maintainer.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Joseph Palmer, Katharine Sherratt, Richard Martin-Nielsen, Jonnie Bevan, Hamish Gibbs, Sebastian Funk Sam Abbott (2021). covidregionaldata: Subnational data COVID-19 epidemiology, DOI: 10.21105/joss.03290","code":"@Article{, title = {covidregionaldata: Subnational data for COVID-19 epidemiology}, author = {Joseph Palmer and Katharine Sherratt and Richard Martin-Nielsen and Jonnie Bevan and Hamish Gibbs and Sebastian Funk and Sam Abbott}, journal = {Journal of Open Source Software}, year = {2021}, volume = {6}, number = {63}, pages = {3290}, doi = {10.21105/joss.03290}, }"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"subnational-data-for-the-covid-19-outbreak-","dir":"","previous_headings":"","what":"Subnational Data for COVID-19 Epidemiology","title":"Subnational Data for COVID-19 Epidemiology","text":"Interface subnational national level COVID-19 data sourced official sources, Public Health England UK, COVID-19 data collections, including World Health Organisation (), European Centre Disease Prevention Control (ECDC), John Hopkins University (JHU), Google Open Data others. package designed streamline COVID-19 data extraction, cleaning, processing range data sources open transparent way. allows users inspect scrutinise data, tools used process , every step. countries supported, data includes daily time-series cases , wherever available, data deaths, hospitalisations, tests. National level data also supported using range data sources.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Subnational Data for COVID-19 Epidemiology","text":"Install CRAN: Install stable development version package : Install unstable development version package :","code":"install.packages(\"covidregionaldata\") install.packages(\"covidregionaldata\", repos = \"https://epiforecasts.r-universe.dev\" ) remotes::install_github(\"epiforecasts/covidregionaldata\")"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick start","title":"Subnational Data for COVID-19 Epidemiology","text":"Load covidregionaldata, dplyr, scales, ggplot2 (used quick start),","code":"library(covidregionaldata) library(dplyr) library(ggplot2) library(scales)"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"setup-data-caching","dir":"","previous_headings":"Quick start","what":"Setup data caching","title":"Subnational Data for COVID-19 Epidemiology","text":"package can optionally use data cache memoise locally cache downloads. can enabled using following (use temporary directory default), stop using memoise use, reset cache (required download new data),","code":"start_using_memoise() #> Using a cache at: /var/folders/68/22ndk9854tq394wl_n1cxzlr0000gn/T//RtmpylL81U stop_using_memoise() reset_cache()"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"national-data","dir":"","previous_headings":"Quick start","what":"National data","title":"Subnational Data for COVID-19 Epidemiology","text":"get worldwide time-series data country (sourced World Health Organisation () default also optionally European Centre Disease Control (ECDC), John Hopkins University, Google COVID-19 open data project), use: can also filtered country interest, Using data can compare case information countries, example number deaths time country G7:","code":"nots <- get_national_data() #> Downloading data from https://covid19.who.int/WHO-COVID-19-global-data.csv #> Cleaning data #> Processing data nots #> # A tibble: 182,253 × 15 #> date un_region who_region country iso_code cases_new cases_total deaths_new deaths_total recovered_new #> <date> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 2020-01-03 Asia EMRO Afghan… AF 0 0 0 0 NA #> 2 2020-01-03 Europe EURO Albania AL 0 0 0 0 NA #> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 0 0 NA #> 4 2020-01-03 Oceania WPRO Americ… AS 0 0 0 0 NA #> 5 2020-01-03 Europe EURO Andorra AD 0 0 0 0 NA #> 6 2020-01-03 Africa AFRO Angola AO 0 0 0 0 NA #> 7 2020-01-03 Americas AMRO Anguil… AI 0 0 0 0 NA #> 8 2020-01-03 Americas AMRO Antigu… AG 0 0 0 0 NA #> 9 2020-01-03 Americas AMRO Argent… AR 0 0 0 0 NA #> 10 2020-01-03 Asia EURO Armenia AM 0 0 0 0 NA #> # … with 182,243 more rows, and 5 more variables: recovered_total <dbl>, hosp_new <dbl>, hosp_total <dbl>, #> # tested_new <dbl>, tested_total <dbl> g7 <- c( \"United States\", \"United Kingdom\", \"France\", \"Germany\", \"Italy\", \"Canada\", \"Japan\" ) g7_nots <- get_national_data(countries = g7, verbose = FALSE) g7_nots %>% ggplot() + aes(x = date, y = deaths_new, col = country) + geom_line(alpha = 0.4) + labs(x = \"Date\", y = \"Reported Covid-19 deaths\") + scale_y_continuous(labels = comma) + theme_minimal() + theme(legend.position = \"top\") + guides(col = guide_legend(title = \"Country\"))"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"subnational-data","dir":"","previous_headings":"Quick start","what":"Subnational data","title":"Subnational Data for COVID-19 Epidemiology","text":"get time-series data subnational regions specific country, example level 1 region UK, use: Now data can create plots, example time-series number cases region: See get_available_datasets() supported regions subregional levels. view datasets currently subnational data , along current status, check supported countries page build supported countries vignette. examples see quick start vignette. Additional subnational data supported via JHU() Google() classes. Use available_regions() method data downloaded cleaned (see examples) subnational data internally support.","code":"uk_nots <- get_regional_data(country = \"UK\", verbose = FALSE) uk_nots #> # A tibble: 9,893 × 26 #> date region region_code cases_new cases_total deaths_new deaths_total recovered_new recovered_total #> <date> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 2020-01-11 North Ea… E12000001 NA NA NA NA NA NA #> 2 2020-01-11 North We… E12000002 NA NA NA NA NA NA #> 3 2020-01-11 Yorkshir… E12000003 NA NA NA NA NA NA #> 4 2020-01-11 East Mid… E12000004 NA NA NA NA NA NA #> 5 2020-01-11 West Mid… E12000005 NA NA NA NA NA NA #> 6 2020-01-11 East of … E12000006 NA NA NA NA NA NA #> 7 2020-01-11 London E12000007 NA NA NA NA NA NA #> 8 2020-01-11 South Ea… E12000008 NA NA NA NA NA NA #> 9 2020-01-11 South We… E12000009 NA NA NA NA NA NA #> 10 2020-01-11 England E92000001 NA NA NA NA NA NA #> # … with 9,883 more rows, and 17 more variables: hosp_new <dbl>, hosp_total <dbl>, tested_new <dbl>, #> # tested_total <dbl>, areaType <chr>, cumCasesByPublishDate <dbl>, cumCasesBySpecimenDate <dbl>, #> # newCasesByPublishDate <dbl>, newCasesBySpecimenDate <dbl>, cumDeaths28DaysByDeathDate <dbl>, #> # cumDeaths28DaysByPublishDate <dbl>, newDeaths28DaysByDeathDate <dbl>, newDeaths28DaysByPublishDate <dbl>, #> # newPillarFourTestsByPublishDate <lgl>, newPillarOneTestsByPublishDate <dbl>, #> # newPillarThreeTestsByPublishDate <dbl>, newPillarTwoTestsByPublishDate <dbl> uk_nots %>% filter(!(region %in% \"England\")) %>% ggplot() + aes(x = date, y = cases_new, col = region) + geom_line(alpha = 0.4) + labs(x = \"Date\", y = \"Reported Covid-19 cases\") + scale_y_continuous(labels = comma) + theme_minimal() + theme(legend.position = \"top\") + guides(col = guide_legend(title = \"Region\"))"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Subnational Data for COVID-19 Epidemiology","text":"using covidregionaldata work please consider citing using following,","code":"#> #> To cite covidregionaldata in publications use: #> #> Joseph Palmer, Katharine Sherratt, Richard Martin-Nielsen, Jonnie Bevan, Hamish Gibbs, Sebastian #> Funk and Sam Abbott (2021). covidregionaldata: Subnational data for COVID-19 epidemiology, DOI: #> 10.21105/joss.03290 #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {covidregionaldata: Subnational data for COVID-19 epidemiology}, #> author = {Joseph Palmer and Katharine Sherratt and Richard Martin-Nielsen and Jonnie Bevan and Hamish Gibbs and Sebastian Funk and Sam Abbott}, #> journal = {Journal of Open Source Software}, #> year = {2021}, #> volume = {6}, #> number = {63}, #> pages = {3290}, #> doi = {10.21105/joss.03290}, #> }"},{"path":"https://epiforecasts.io/covidregionaldata/index.html","id":"development","dir":"","previous_headings":"","what":"Development","title":"Subnational Data for COVID-19 Epidemiology","text":"package result work number contributors (see contributors list ). like thank CMMID COVID-19 working group insightful comments feedback. welcome contributions new contributors! particularly appreciate help adding new data sources countries sub-national level, work priority problems issues. Please check add issues, /add pull request. details, start contributing guide. details steps required add support dataset see adding data guide.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":null,"dir":"Reference","previous_headings":"","what":"Belgium Class for downloading, cleaning and processing notification data — Belgium","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"Information downloading, cleaning processing COVID-19 region level 1 2 data Belgium.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"https://epistat.sciensano./Data/COVID19BE_CASES_AGESEX.csv","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"covidregionaldata::DataClass -> Belgium","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. ISO 3166-2 codes used region province levels Belgium, provinces marked iso_3166_2_province common_data_urls List named links raw data common across levels. level_data_urls List named links raw data specific level regions. Belgium, additional data level 1 regions. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$clean_common() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"Belgium$set_region_codes() Belgium$download() Belgium$clean_level_1() Belgium$clean_level_2() Belgium$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"","code":"Belgium$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"Downloads data source (Belgium) applies initial data patch.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"","code":"Belgium$download()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"Region-level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"","code":"Belgium$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"Province-level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"","code":"Belgium$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"","code":"Belgium$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Belgium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Belgium Class for downloading, cleaning and processing notification data — Belgium","text":"","code":"if (FALSE) { region <- Belgium$new(verbose = TRUE, steps = TRUE, get = TRUE, level = \"2\") region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":null,"dir":"Reference","previous_headings":"","what":"Brazil Class for downloading, cleaning and processing notification data — Brazil","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"Information downloading, cleaning processing COVID-19 region data Brazil. Data available Github, curated Wesley Cota: DOI 10.1590/SciELOPreprints.362","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"https://github.com/wcota/covid19br","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"covidregionaldata::DataClass -> Brazil","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. Data available city level aggregated provide state data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"Brazil$set_region_codes() Brazil$clean_common() Brazil$clean_level_1() Brazil$clean_level_2() Brazil$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"","code":"Brazil$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"Common data cleaning levels","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"","code":"Brazil$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"State Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"","code":"Brazil$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"City Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"","code":"Brazil$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"","code":"Brazil$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Brazil.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Brazil Class for downloading, cleaning and processing notification data — Brazil","text":"","code":"if (FALSE) { region <- Brazil$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":null,"dir":"Reference","previous_headings":"","what":"Canada Class containing origin specific attributes and methods — Canada","title":"Canada Class containing origin specific attributes and methods — Canada","text":"Information downloading, cleaning processing COVID-19 region data Canada.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Canada Class containing origin specific attributes and methods — Canada","text":"https://health-infobase.canada.ca","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Canada Class containing origin specific attributes and methods — Canada","text":"covidregionaldata::DataClass -> Canada","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Canada Class containing origin specific attributes and methods — Canada","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data common across levels. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Canada Class containing origin specific attributes and methods — Canada","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Canada Class containing origin specific attributes and methods — Canada","text":"Canada$set_region_codes() Canada$clean_common() Canada$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Canada Class containing origin specific attributes and methods — Canada","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Canada Class containing origin specific attributes and methods — Canada","text":"","code":"Canada$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Canada Class containing origin specific attributes and methods — Canada","text":"Provincial Level Data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Canada Class containing origin specific attributes and methods — Canada","text":"","code":"Canada$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Canada Class containing origin specific attributes and methods — Canada","text":"... pass additional arguments","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Canada Class containing origin specific attributes and methods — Canada","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Canada Class containing origin specific attributes and methods — Canada","text":"","code":"Canada$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Canada Class containing origin specific attributes and methods — Canada","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Canada.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Canada Class containing origin specific attributes and methods — Canada","text":"","code":"if (FALSE) { region <- Canada$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":null,"dir":"Reference","previous_headings":"","what":"Colombia Class for downloading, cleaning and processing notification data — Colombia","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"Information downloading, cleaning processing COVID-19 region data Colombia","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"https://www.datos.gov.co/Salud-y-Protecci-n-Social/Casos-positivos-de-COVID-19-en-Colombia/gt2j-8ykr","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"covidregionaldata::DataClass -> Colombia","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"Colombia$set_region_codes() Colombia$download() Colombia$clean_common() Colombia$clean_level_1() Colombia$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"","code":"Colombia$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"Colombia specific download using Socrata API uses RSocrata package installed downloads much larger csv file package available.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"","code":"Colombia$download()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"Colombia specific data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"","code":"Colombia$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"Colombia Specific Department Level Data Cleaning Aggregates data level 1 (department) regional level. Data provided source level 2 (municipality) regional level.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"","code":"Colombia$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"","code":"Colombia$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Colombia.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Colombia Class for downloading, cleaning and processing notification data — Colombia","text":"","code":"if (FALSE) { region <- Colombia$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing national level methods — CountryDataClass","title":"R6 Class containing national level methods — CountryDataClass","text":"Acts parent class national data classes, allowing access general methods defined DataClass() additional","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R6 Class containing national level methods — CountryDataClass","text":"top methods documented DataClass(), class implements custom filter function supports partial matching English country names using countrycode package.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"R6 Class containing national level methods — CountryDataClass","text":"covidregionaldata::DataClass -> CountryDataClass","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing national level methods — CountryDataClass","text":"filter_level Character level data filter . Defaults country level data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing national level methods — CountryDataClass","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$clean_common() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$set_region_codes() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing national level methods — CountryDataClass","text":"CountryDataClass$filter() CountryDataClass$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"method-filter-","dir":"Reference","previous_headings":"","what":"Method filter()","title":"R6 Class containing national level methods — CountryDataClass","text":"Filter method country level data. Uses countryname match input countries known names.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing national level methods — CountryDataClass","text":"","code":"CountryDataClass$filter(countries, level)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing national level methods — CountryDataClass","text":"countries character vector target countries. Overrides current class setting target_regions. filter_level field level argument set anything level 1 passed directly parent DataClass() filter() method alteration. level Character level data filter . Defaults conuntry level specified.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing national level methods — CountryDataClass","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing national level methods — CountryDataClass","text":"","code":"CountryDataClass$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/CountryDataClass.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing national level methods — CountryDataClass","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"Attributes methods COVID-19 data provided Covid19 Data Hub","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"https://covid19datahub.io/articles/data.html","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"dataset supports national subnational data sources national level data returned default. National data sourced John Hopkins University recommend using JHU class included package. Subnational data supported subset countries can found cleaning using available_regions() method, see examples details. data sets minimally cleaned data files hosted team COVID19 Data Hub please see source repository details (https://github.com/covid19datahub/COVID19/#data-sources) using analysis checking source details strongly advised. using class please cite: \"Guidotti et al., (2020). COVID-19 Data Hub Journal Open Source Software, 5(51), 2376, https://doi.org/10.21105/joss.02376\"","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"covidregionaldata::DataClass -> covidregionaldata::CountryDataClass -> Covid19DataHub","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"origin name country fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. level_data_urls List named links raw data. first, entry, named main. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$set_region_codes() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test() covidregionaldata::CountryDataClass$filter()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"Covid19DataHub$clean_common() Covid19DataHub$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"Covid19 Data Hub specific data cleaning. takes raw data, renames columns checks types.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"","code":"Covid19DataHub$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"","code":"Covid19DataHub$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Covid19DataHub.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class containing specific attributes and methods for Covid19 Data Hub — Covid19DataHub","text":"","code":"# nolint start if (FALSE) { # set up a data cache start_using_memoise() # get all countries data cv19dh <- Covid19DataHub$new(level = \"1\", get = TRUE) cv19dh$return() # show available regions with data at the second level of interest cv19dh_level_2 <- Covid19DataHub$new(level = \"2\") cv19dh_level_2$download() cv19dh_level_2$clean() cv19dh$available_regions() # get all region data for the uk cv19dh_level_2$filter(\"uk\") cv19dh_level_2$process() cv19dh_level_2$return() # get all regional data for the UK uk <- Covid19DataHub$new(regions = \"uk\", level = \"2\", get = TRUE) uk$return() # get all subregional data for the UK uk <- Covid19DataHub$new(regions = \"uk\", level = \"3\", get = TRUE) uk$return() } # nolint end"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":null,"dir":"Reference","previous_headings":"","what":"Cuba Class for downloading, cleaning and processing notification data — Cuba","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"Information downloading, cleaning processing COVID-19 region data Cuba","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"https://covid19cubadata.github.io/","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"covidregionaldata::DataClass -> Cuba","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"Cuba$set_region_codes() Cuba$clean_common() Cuba$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"","code":"Cuba$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"Cuba specific state level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"","code":"Cuba$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"","code":"Cuba$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Cuba.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cuba Class for downloading, cleaning and processing notification data — Cuba","text":"","code":"if (FALSE) { region <- Cuba$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing non-dataset specific methods — DataClass","title":"R6 Class containing non-dataset specific methods — DataClass","text":"parent class containing non-dataset specific methods.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R6 Class containing non-dataset specific methods — DataClass","text":"data sets shared methods extracting geographic codes, downloading, processing, returning data. functions contained within parent class accessible data sets inherit . Individual data sets can overwrite functions fields providing define method name, can extended additional functionality. See individual method documentaion details.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing non-dataset specific methods — DataClass","text":"origin origin data source. regional data sources usually name country. data initialised, list named data frames: raw (list named raw data frames) clean (cleaned data) processed (processed data). Data accessed using $data. supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. region_name string Name region column, e.g. 'region'. field filled initialisation region name specified level (supported_region_names$level). code_name string Name codes column, e.g. 'iso_3166_2' Filled initialisation code name associated requested level (supported_region_codes$level). codes_lookup string tibble Region codes target origin filled origin specific codes set_region_codes() data_urls List named common shared url links raw data. Prefers shared name conflict. common_data_urls List named links raw data common across levels. first entry named main. level_data_urls List named links raw data level specific. urls share name url common_data_urls selected preferentially. top level list named supported level. source_data_cols existing columns within raw data level target region level. field filled initialisation using user inputs defaults $new() data_name string. country name followed level. E.g. \"Italy level 1\" totals Boolean. TRUE, returns totalled data per region today's date. field filled initialisation using user inputs defaults $new() localise Boolean. region names localised. field filled initialisation using user inputs defaults $new() verbose Boolean. Display information various stages. field filled initialisation. using user inputs defaults $new() steps Boolean. Keep data processing step. field filled initialisation.using user inputs defaults $new() target_regions character vector regions filter . Used filter method. process_fns array, additional, user supplied functions process data. filter_level Character level data filter . Defaults target level.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing non-dataset specific methods — DataClass","text":"DataClass$set_region_codes() DataClass$new() DataClass$download() DataClass$download_JSON() DataClass$clean() DataClass$clean_common() DataClass$available_regions() DataClass$filter() DataClass$process() DataClass$get() DataClass$return() DataClass$summary() DataClass$test() DataClass$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Place holder custom country specific function load region codes.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Initialize function used DataClass objects. Set DataClass class attributes set input parameters. called DataClass class object.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$new( level = \"1\", filter_level, regions, totals = FALSE, localise = TRUE, verbose = TRUE, steps = FALSE, get = FALSE, process_fns )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing non-dataset specific methods — DataClass","text":"level character string indicating target administrative level data default \"1\". Currently supported options level 1 (\"1) level 2 (\"2\"). filter_level character string indicating level filter . Defaults level data specified otherwise defined class. Use get_available_datasets() supported options dataset. regions character vector target regions assigned thetarget_regions field present. totals Logical, defaults FALSE. TRUE, returns totalled data per region today's date. FALSE, returns full dataset stratified date region. localise Logical, defaults TRUE. region names localised. verbose Logical, defaults TRUE. verbose processing steps Logical, defaults FALSE. processing cleaning steps kept output list. get Logical, defaults FALSE. class get method called (download, clean, process data initialisation). process_fns Array, additional functions process data. Users can supply functions act clean data called alongside default processing functions. default optional function added set_negative_values_to_zero. process_fns set (see process_fns field defaults). want keep supplying processing functions remember add list also. feel created cool processing function others benefit please submit Pull Request github repository consider adding package.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Download raw data data_urls, stores named list data_url name corresponding raw data table data$raw","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$download()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-download-json-","dir":"Reference","previous_headings":"","what":"Method download_JSON()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Download raw data data_urls, stores named list data_url name corresponding raw data table data$raw. Designed drop-replacement download can used sub-classes.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$download_JSON()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-clean-","dir":"Reference","previous_headings":"","what":"Method clean()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Cleans raw data (corrects format, converts column types, etc). Works raw data called download() Calls specific class specific cleaning method (clean_common) followed level specific cleaning methods. clean_level_[1/2]. Cleaned data stored data$clean","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$clean()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Cleaning methods common across class. default method empty code required defined child class specific clean_common method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-available-regions-","dir":"Reference","previous_headings":"","what":"Method available_regions()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Show regions available used filtering operations. Can called clean() called. Filtering level determined checking filter_level field.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$available_regions(level)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing non-dataset specific methods — DataClass","text":"level character string indicating level filter . Defaults using filter_level field specified","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-filter-","dir":"Reference","previous_headings":"","what":"Method filter()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Filter cleaned data specific region called clean()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$filter(regions, level)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing non-dataset specific methods — DataClass","text":"regions character vector target regions. Overrides current class setting target_regions. level Character level data filter . Defaults lowest level data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-process-","dir":"Reference","previous_headings":"","what":"Method process()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Processes data adding calculating absent columns. Called clean data (clean()). countries may data new events (e.g. number new cases day) whilst others running total date. Processing calculates based data comes via functions region_dispatch() process_internal(), following: Adds columns present data add_extra_na_cols() Ensures negative values set_negative_values_to_zero() Removes NA dates fill_empty_dates_with_na() Calculates cumulative data complete_cumulative_columns() Calculates missing columns existing ones calculate_columns_from_existing_data()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$process(process_fns)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing non-dataset specific methods — DataClass","text":"process_fns Array, additional functions process data. Users can supply functions act clean data called alongside default processing functions. default optional function added set_negative_values_to_zero. process_fns set (see process_fns field defaults).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-get-","dir":"Reference","previous_headings":"","what":"Method get()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Get data related data class. runs distinct step workflow order. Internally calls download(), clean(), filter() process() download, clean, filter process methods.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$get()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-return-","dir":"Reference","previous_headings":"","what":"Method return()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Return data. Designed called process() uses steps argument return either list data preserved step just processed data. datasets custom method needed.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$return()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-summary-","dir":"Reference","previous_headings":"","what":"Method summary()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Create table summary information data set processed.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$summary()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Returns single row summary tibble containing origin data source, class, level 1 2 region names, type data, urls raw data columns present raw data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-test-","dir":"Reference","previous_headings":"","what":"Method test()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"Run tests country class instance. Calling test() class instance runs tests settings use. example, set level = \"1\" localise = FALSE tests run level 1 data localised. Rather downloading data test users can provide path snapshot file data test instead. Tests run clone class. method calls generic tests country class objects. also calls country specific tests can defined individual country class method called specific_tests(). snapshots contain first 1000 rows data. details see 'testing' vignette: vignette(testing).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$test( download = FALSE, snapshot_dir = paste0(tempdir(), \"/snapshots\"), all = FALSE, ... )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing non-dataset specific methods — DataClass","text":"download logical. download data (TRUE) use snapshot (FALSE). Defaults FALSE. snapshot_dir character_array name directory save downloaded data read . defined directory called 'snapshots' created temp directory. Snapshots saved rds files class name level: e.g. Italy_level_1.rds. logical. Run tests settings (TRUE) defined current class instance (FALSE). Defaults FALSE. ... Additional parameters pass specific_tests","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing non-dataset specific methods — DataClass","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing non-dataset specific methods — DataClass","text":"","code":"DataClass$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/DataClass.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing non-dataset specific methods — DataClass","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"Information downloading, cleaning processing European Centre Disease Prevention Control COVID-19 data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"covidregionaldata::DataClass -> covidregionaldata::CountryDataClass -> ECDC","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$set_region_codes() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test() covidregionaldata::CountryDataClass$filter()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"ECDC$clean_common() ECDC$return() ECDC$specific_tests() ECDC$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"ECDC specific state level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"","code":"ECDC$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"method-return-","dir":"Reference","previous_headings":"","what":"Method return()","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"Specific return settings ECDC dataset.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"","code":"ECDC$return()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"method-specific-tests-","dir":"Reference","previous_headings":"","what":"Method specific_tests()","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"Run additional tests ECDC class. Tests ECDC required additional columns one row per country. Designed run test run directly.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"","code":"ECDC$specific_tests(self_copy, ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"self_copy R6class object test ... Extra params passed specific download functions","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"","code":"ECDC$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/ECDC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class containing specific attributes and methods for the European Centre\nfor Disease Prevention and Control dataset — ECDC","text":"","code":"if (FALSE) { national <- ECDC$new(verbose = TRUE, steps = TRUE, get = TRUE) national$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":null,"dir":"Reference","previous_headings":"","what":"Estonia Class for downloading, cleaning and processing notification data — Estonia","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"Information downloading, cleaning processing COVID-19 region data Estonia","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"https://www.terviseamet.ee/et/koroonaviirus/avaandmed","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"covidregionaldata::DataClass -> Estonia","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"Estonia$set_region_codes() Estonia$clean_common() Estonia$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"","code":"Estonia$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"Estonia specific state level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"","code":"Estonia$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"","code":"Estonia$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Estonia.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estonia Class for downloading, cleaning and processing notification data — Estonia","text":"","code":"if (FALSE) { region <- Estonia$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":null,"dir":"Reference","previous_headings":"","what":"France Class containing origin specific attributes and methods — France","title":"France Class containing origin specific attributes and methods — France","text":"Information downloading, cleaning processing COVID-19 region data France.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"France Class containing origin specific attributes and methods — France","text":"https://www.data.gouv.fr/fr/datasets/r/406c6a23-e283-4300-9484-54e78c8ae675 https://www.data.gouv.fr/fr/datasets/r/6fadff46-9efd-4c53-942a-54aca783c30c https://www.data.gouv.fr/fr/datasets/r/001aca18-df6a-45c8-89e6-f82d689e6c01","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"France Class containing origin specific attributes and methods — France","text":"covidregionaldata::DataClass -> France","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"France Class containing origin specific attributes and methods — France","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. level_data_urls List named links raw data level specific. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"France Class containing origin specific attributes and methods — France","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$clean_common() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"France Class containing origin specific attributes and methods — France","text":"France$set_region_codes() France$clean_level_1() France$clean_level_2() France$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"France Class containing origin specific attributes and methods — France","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"France Class containing origin specific attributes and methods — France","text":"","code":"France$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"France Class containing origin specific attributes and methods — France","text":"Region Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"France Class containing origin specific attributes and methods — France","text":"","code":"France$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"France Class containing origin specific attributes and methods — France","text":"Department Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"France Class containing origin specific attributes and methods — France","text":"","code":"France$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"France Class containing origin specific attributes and methods — France","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"France Class containing origin specific attributes and methods — France","text":"","code":"France$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"France Class containing origin specific attributes and methods — France","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/France.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"France Class containing origin specific attributes and methods — France","text":"","code":"if (FALSE) { region <- France$new(level = \"2\", verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":null,"dir":"Reference","previous_headings":"","what":"Germany Class for downloading, cleaning and processing notification data — Germany","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"Information downloading, cleaning processing COVID-19 region level 1 2 data Germany.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"https://opendata.arcgis.com/datasets/dd4580c810204019a7b8eb3e0b329dd6_0.csv","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"covidregionaldata::DataClass -> Germany","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. first, entry, named main. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"Germany$set_region_codes() Germany$clean_common() Germany$clean_level_1() Germany$clean_level_2() Germany$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"","code":"Germany$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"Common Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"","code":"Germany$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"Bundesland Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"","code":"Germany$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"Landkreis Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"","code":"Germany$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"","code":"Germany$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Germany.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Germany Class for downloading, cleaning and processing notification data — Germany","text":"","code":"if (FALSE) { region <- Germany$new(verbose = TRUE, steps = TRUE, level = \"2\", get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing specific attributes and methods for Google data — Google","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"Google specific information downloading, cleaning processing covid-19 region data example Country. function works national data sources, however, data Google supports three subregions (country, subregion subregion2) can accessed using 'level' argument. also data available, hospitalisations data. raw data comes three seperate data sets, \"epidemiology\" comprised cases, tests deaths, \"index\", holds information countries linking data sets, \"hospitalizations\" holds data number people hospital, ICU, etc.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"https://github.com/GoogleCloudPlatform/covid-19-open-data","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"covidregionaldata::DataClass -> covidregionaldata::CountryDataClass -> Google","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"origin name country fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$set_region_codes() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test() covidregionaldata::CountryDataClass$filter()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"Google$clean_common() Google$clean_level_1() Google$clean_level_2() Google$new() Google$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"GoogleData specific subregion2 level data cleaning. takes raw data, puts single data frame, renames columns checks types.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"","code":"Google$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"Google specific subregion level data cleaning. Takes data cleaned clean_common aggregates country level (level 1).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"","code":"Google$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"Google specific subregion2 level data cleaning. Takes data cleaned clean_common aggregates subregion level (level 2).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"","code":"Google$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"custom initialize Google","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"","code":"Google$new(...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"... arguments passed DataClass initialize Google","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"","code":"Google$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Google.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class containing specific attributes and methods for Google data — Google","text":"","code":"# nolint start if (FALSE) { # set up a data cache start_using_memoise() # get all countries national <- Google$new(level = \"1\", get = TRUE) national$return() # show available regions with data at the second level of interest google_level_2 <- Google$new(level = \"2\") google_level_2$download() google_level_2$clean() google$available_regions() # get all region data for the uk google_level_2$filter(\"uk\") google_level_2$process() google_level_2$return() # get all regional data for the UK uk <- Google$new(regions = \"uk\", level = \"2\", get = TRUE) uk$return() # get all subregional data for the UK uk <- Google$new(regions = \"uk\", level = \"3\", get = TRUE) uk$return() } # nolint end"},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":null,"dir":"Reference","previous_headings":"","what":"India Class for downloading, cleaning and processing notification data — India","title":"India Class for downloading, cleaning and processing notification data — India","text":"Information downloading, cleaning processing COVID-19 region data India.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"India Class for downloading, cleaning and processing notification data — India","text":"https://www.covid19india.org","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"India Class for downloading, cleaning and processing notification data — India","text":"covidregionaldata::DataClass -> India","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"India Class for downloading, cleaning and processing notification data — India","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"India Class for downloading, cleaning and processing notification data — India","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"India Class for downloading, cleaning and processing notification data — India","text":"India$set_region_codes() India$clean_common() India$get_desired_status() India$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"India Class for downloading, cleaning and processing notification data — India","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"India Class for downloading, cleaning and processing notification data — India","text":"","code":"India$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"India Class for downloading, cleaning and processing notification data — India","text":"India state level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"India Class for downloading, cleaning and processing notification data — India","text":"","code":"India$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"method-get-desired-status-","dir":"Reference","previous_headings":"","what":"Method get_desired_status()","title":"India Class for downloading, cleaning and processing notification data — India","text":"Extract data raw table","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"India Class for downloading, cleaning and processing notification data — India","text":"","code":"India$get_desired_status(status)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"India Class for downloading, cleaning and processing notification data — India","text":"status data extract","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"India Class for downloading, cleaning and processing notification data — India","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"India Class for downloading, cleaning and processing notification data — India","text":"","code":"India$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"India Class for downloading, cleaning and processing notification data — India","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/India.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"India Class for downloading, cleaning and processing notification data — India","text":"","code":"if (FALSE) { region <- India$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":null,"dir":"Reference","previous_headings":"","what":"Italy Class for downloading, cleaning and processing notification data — Italy","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"Information downloading, cleaning processing COVID-19 region data Italy.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"https://github.com/pcm-dpc/COVID-19/","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"covidregionaldata::DataClass -> Italy","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. first, entry, named main. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"Italy$set_region_codes() Italy$clean_common() Italy$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"","code":"Italy$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"State level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"","code":"Italy$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"","code":"Italy$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Italy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Italy Class for downloading, cleaning and processing notification data — Italy","text":"","code":"if (FALSE) { region <- Italy$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"Attributes methods COVID-19 data used 2019 Novel Coronavirus Visual Dashboard operated Johns Hopkins University Center Systems Science Engineering (JHU CSSE). Supported ESRI Living Atlas Team Johns Hopkins University Applied Physics Lab (JHU APL)","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"dataset support national subnational data sources national level data returned default. Subnational data supported subset countries can found cleaning using available_regions() method, see examples details. data sets sourced, cleaned, standardised JHU team please see source repository details. Note unlike many data sets means methods applied source applied raw surveillance data instead already cleaned data. using analysis checking JHU source details advisable. using data please cite: \"Dong E, Du H, Gardner L. interactive web-based dashboard track COVID-19 real time. Lancet Inf Dis. 20(5):533-534. doi: 10.1016/S1473-3099(20)30120-1\"","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"covidregionaldata::DataClass -> covidregionaldata::CountryDataClass -> JHU","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"origin name country fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. first, entry, named main. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test() covidregionaldata::CountryDataClass$filter()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"JHU$set_region_codes() JHU$clean_common() JHU$clean_level_1() JHU$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"","code":"JHU$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"JHU specific data cleaning. Joins raw data sets, checks column types renames needed.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"","code":"JHU$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"JHU specific country level data cleaning. Aggregates data country (level 2) level.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"","code":"JHU$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"","code":"JHU$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class containing specific attributes and methods for John Hopkins\nUniversity data — JHU","text":"","code":"# nolint start if (FALSE) { # set up a data cache start_using_memoise() # get all countries data jhu <- JHU$new(level = \"1\", get = TRUE) jhu$return() # show available regions with data at the second level of interest jhu_level_2 <- JHU$new(level = \"2\") jhu_level_2$download() jhu_level_2$clean() jhu$available_regions() # get all region data for the uk jhu_level_2$filter(\"uk\") jhu_level_2$process() jhu_level_2$return() } # nolint end"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for JHU Dataset. Taken from the region codes provided as\npart of the WHO dataset. — JHU_codes","title":"Region Codes for JHU Dataset. Taken from the region codes provided as\npart of the WHO dataset. — JHU_codes","text":"region codes JHU","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for JHU Dataset. Taken from the region codes provided as\npart of the WHO dataset. — JHU_codes","text":"","code":"JHU_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for JHU Dataset. Taken from the region codes provided as\npart of the WHO dataset. — JHU_codes","text":"object class spec_tbl_df (inherits tbl_df, tbl, data.frame) 4193 rows 2 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JHU_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for JHU Dataset. Taken from the region codes provided as\npart of the WHO dataset. — JHU_codes","text":"tibble region codes related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"Class downloading, cleaning processing COVID-19 region data European Commission's Joint Research Centre. Subnational data (admin level 1) numbers contagious fatalities COVID-19, collected directly National Authoritative sources (National monitoring websites, available). details see https://github.com/ec-jrc/COVID-19","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"https://github.com/ec-jrc/COVID-19","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"covidregionaldata::DataClass -> covidregionaldata::CountryDataClass -> JRC","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. level_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$set_region_codes() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test() covidregionaldata::CountryDataClass$filter()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"JRC$clean_common() JRC$clean_level_1() JRC$clean_level_2() JRC$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"JRC specific data cleaning. raw source data columns converted correct type renamed appropriately match standard general processing.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"","code":"JRC$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"JRC specific country level data cleaning. Selects country level (level 1) columns data ready processing.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"","code":"JRC$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"JRC specific region level data cleaning. Selects country (level 1) region (level 2) columns data ready processing.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"","code":"JRC$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"","code":"JRC$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/JRC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class containing specific attributes and methods for European Commission's\nJoint Research Centre data — JRC","text":"","code":"if (FALSE) { # get country level data jrc_level_1 <- JRC$new(level = \"1\", verbose = TRUE, steps = TRUE, get = TRUE) jrc_level_1$return() # show available regions with data at the first level of interest (country) jrc_level_1$available_regions() # get region level data jrc_level_2 <- JRC$new(level = \"2\", verbose = TRUE, steps = TRUE, get = TRUE) jrc_level_2$return() # show available regions with data at the second level of interest (region) jrc_level_2$available_regions() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":null,"dir":"Reference","previous_headings":"","what":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Information downloading, cleaning processing COVID-19 region level 1 2 data Lithuania.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"https://hub.arcgis.com/datasets/d49a63c934be4f65a93b6273785a8449_0","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"osp-data-fields","dir":"Reference","previous_headings":"","what":"OSP Data fields","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Official Statistics Portal (OSP) provides many data series table. full range vectors can returned setting all_osp_fields TRUE. following describes data provided OSP. * municipality_code discarded since correspond ISO-3166:2 codes used elsewhere package. + fields renamed returned unmodified. # Lithuania offers counts according three different definitions whether death attributable COVID-19. $ field recalculated counties deleted.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"criteria-for-attributing-deaths","dir":"Reference","previous_headings":"","what":"Criteria for attributing deaths","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Beginning February 2021 OSP publishes death counts according three different criteria, least strictly attributed COVID-19. Number deaths COVID-19 (coronavirus infection) leading cause death. indicator calculated summing registered records medical form E106 (unique persons), main cause death IPC disease codes U07.1 U07.2. Deaths due external causes included (ICD disease codes V00-Y36, Y85-Y87, Y89, S00-T79, T89-T98). Number deaths COVID-19 (coronavirus infection) cause death. indicator calculated summing registered records medical form E106 (unique persons), ICD disease codes U07.1, U07.2, U07.3, U07.4, U07.5 indicated main, direct, intermediate cause death important pathological condition, identified related COVID-19 disease (coronavirus infection). Deaths due external causes included (ICD disease codes V00-Y36, Y85-Y87, Y89, S00-T79, T89-T98). Number deaths cause COVID-19 COVID-19 deaths due non-external causes within 28 days. indicator calculated summing registered records medical form E106 (unique persons), ICD disease codes U07.1, U07.2, U07.3, U07.4, U07 indicated main, direct, intermediate cause death important pathological condition, identified related COVID-19 disease (coronavirus infection) records medical form E106 (unique individuals) person died within last 28 days receiving positive diagnostic response SARS-CoV-2 test entry medical form E025 ICD disease code U07.2 U07.1. Deaths due external causes included (ICD disease codes V00-Y36, Y85-Y87, Y89, S00-T79, T89-T98). number deaths reported last day preliminary increases 20-40% days. \"delay\" data natural: example, died last night, death certificate likely issued soon report published morning.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"de-jure-and-statistical-counts","dir":"Reference","previous_headings":"","what":"De jure and statistical counts","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Beginning February 2021 OSP makes statistical estimates number recovered active cases, since review data showed cases individuals still considered active cases recovered, documented registered . listed OSP active_de_jure recovered_de_jure (officially still considered sick), active_sttstcl recovered_sttstcl (estimate many still ill).","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"covidregionaldata::DataClass -> Lithuania","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data common across levels. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data death_definition criteria deaths attributed COVID use recovered_definition whether use official counts recovered cases statistical estimates provided OSP all_osp_fields whether return data vectors provided OSP national_data whether return data rows national results","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Lithuania$set_region_codes() Lithuania$clean_common() Lithuania$clean_level_1() Lithuania$new() Lithuania$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"","code":"Lithuania$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Common data cleaning levels","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"","code":"Lithuania$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Lithuania Specific County Level Data Cleaning Aggregates data level 1 (county) regional level. Data provided source level 2 (municipality) regional level.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"","code":"Lithuania$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"Initialize country","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"","code":"Lithuania$new( death_definition = \"of\", recovered_definition = \"official\", all_osp_fields = FALSE, national_data = FALSE, ... )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"death_definition character string. Determines criteria attributing deaths COVID used. \"\", \"\", \"\". Can also \"daily_deaths_def1\", \"daily_deaths_def2\", \"daily_deaths_def3\". (Defaults \"\", strictest definition.) recovered_definition character string. Determines whether count officially-recovered (de jure) cases used, statistical estimate provided OSP. \"official\" \"statistical\". (Defaults \"official\".) all_osp_fields logical scalar. meaningful data fields OSP source returned? (Defaults FALSE) national_data logical scalar. national values returned? (Defaults FALSE) ... Parameters passed DataClass() initalize","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"","code":"Lithuania$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Lithuania.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lithuania Class for downloading, cleaning and processing notification data — Lithuania","text":"","code":"if (FALSE) { region <- Lithuania$new(verbose = TRUE, steps = TRUE, get = TRUE) }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":null,"dir":"Reference","previous_headings":"","what":"Meixco Class for downloading, cleaning and processing notification data — Mexico","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Information downloading, cleaning processing COVID-19 region data Mexico. Notes region codes: Level 1 codes = ISO-3166-2, source: https://en.wikipedia.org/wiki/ISO_3166-2:MX Level 2 codes = INEGI Mexican official statistics geocoding, source: raw data Level 1 INEGI codes first 2 characters Level 2 INEGI codes","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"https://datos.covid-19.conacyt.mx/","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"covidregionaldata::DataClass -> Mexico","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. level_data_urls List named links raw data level specific. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Mexico$set_region_codes() Mexico$download() Mexico$clean_common() Mexico$clean_level_1() Mexico$clean_level_2() Mexico$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"Mexico$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Data download() function Mexico data. replaces generic download function DataClass(). get latest data use PHP script website.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"Mexico$download()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Common Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"Mexico$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Estados Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"Mexico$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"Municipality Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"Mexico$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"Mexico$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Mexico.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Meixco Class for downloading, cleaning and processing notification data — Mexico","text":"","code":"if (FALSE) { region <- Mexico$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":null,"dir":"Reference","previous_headings":"","what":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"Class downloading, cleaning processing COVID-19 sub-regional data Netherlands, provided RVIM (English: National Institute Public Health Environment). data contains number newly reported cases (tested positive), number newly reported hospital admissions number newly reported deaths going back 27/02/2020. Data provided province municipality level.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"https://data.rivm.nl/geonetwork/srv/dut/catalog.search#/metadata/5f6bc429-1596-490e-8618-1ed8fd768427?tab=relations","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"covidregionaldata::DataClass -> Netherlands","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. first, entry, named main. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"Netherlands$set_region_codes() Netherlands$clean_common() Netherlands$clean_level_1() Netherlands$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"","code":"Netherlands$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"Common cleaning steps applied raw data, regardless level (province municipality) raw Netherlands data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"","code":"Netherlands$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"Netherlands specific province level data cleaning. Takes data cleaned clean_common aggregates Province level (level 1).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"","code":"Netherlands$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"","code":"Netherlands$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Netherlands.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Netherlands Class for downloading, cleaning and processing notification data — Netherlands","text":"","code":"if (FALSE) { region <- Netherlands$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":null,"dir":"Reference","previous_headings":"","what":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"Information downloading, cleaning processing COVID-19 region data South Africa.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"https://github.com/dsfsi/covid19za/","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"covidregionaldata::DataClass -> SouthAfrica","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"SouthAfrica$set_region_codes() SouthAfrica$clean_common() SouthAfrica$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"","code":"SouthAfrica$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"Province level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"","code":"SouthAfrica$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"","code":"SouthAfrica$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/SouthAfrica.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"SouthAfrica Class for downloading, cleaning and processing notification data — SouthAfrica","text":"","code":"if (FALSE) { region <- SouthAfrica$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":null,"dir":"Reference","previous_headings":"","what":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"Information downloading, cleaning processing COVID-19 region data Switzerland","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"covidregionaldata::DataClass -> Switzerland","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. url links JSON file provides addresses recently-updated CSV files, downloaded. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"Switzerland$set_region_codes() Switzerland$download() Switzerland$clean_common() Switzerland$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"","code":"Switzerland$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"Download function get raw data. Downloads updated list CSV files using download_JSON, filters identify required CSV files, uses parent method download download CSV files.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"","code":"Switzerland$download()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"Switzerland specific state level data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"","code":"Switzerland$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"","code":"Switzerland$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/Switzerland.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Switzerland Class for downloading, cleaning and processing notification data — Switzerland","text":"","code":"if (FALSE) { region <- Switzerland$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":null,"dir":"Reference","previous_headings":"","what":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Extracts daily COVID-19 data UK, stratified region nation. Additional options class : return subnational English regions using NHS region boundaries instead PHE boundaries (nhsregions = TRUE), release date download (release_date) geographical resolution (resolution).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"https://coronavirus.data.gov.uk/details/download https://coronavirus.data.gov.uk/details/download","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"covidregionaldata::DataClass -> UK","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. first, entry, named main. level_data_urls List named links raw data level specific. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data query_filters Set filters use query data nhsregions Whether include NHS regions data release_date release date data resolution resolution data return authority_data raw data creating authority lookup tables","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$clean_common() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"UK$set_region_codes() UK$download() UK$clean_level_1() UK$clean_level_2() UK$new() UK$download_filter() UK$set_filters() UK$download_nhs_regions() UK$add_nhs_regions() UK$specific_tests() UK$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Specific function getting region codes UK .","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-download-","dir":"Reference","previous_headings":"","what":"Method download()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"UK specific download() function.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$download()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Region Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Level 2 Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Initalize UK Class","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$new(nhsregions = FALSE, release_date = NULL, resolution = \"utla\", ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"nhsregions Return subnational English regions using NHS region boundaries instead PHE boundaries. release_date Date data released. Default extract latest release. Dates format \"yyyy-mm-dd\". resolution \"utla\" (default) \"ltla\", depending geographical resolution preferred ... Optional arguments passed DataClass() initalize.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"\\dontrun{ UK$new( level = 1, localise = TRUE, verbose = True, steps = FALSE, nhsregions = FALSE, release_date = NULL, resolution = \"utla\" ) }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-download-filter-","dir":"Reference","previous_headings":"","what":"Method download_filter()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Helper function downloading data API","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$download_filter(filter)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"filter region filters","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-set-filters-","dir":"Reference","previous_headings":"","what":"Method set_filters()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Set filters UK data api query.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$set_filters()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-download-nhs-regions-","dir":"Reference","previous_headings":"","what":"Method download_nhs_regions()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Download NHS data level 1 regions Separate NHS data available \"first\" admissions, excluding readmissions. available England + English regions . Data available separately periods 2020-08-01 2021-04-06, 2021-04-07 - present. See: https://www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/ Section 2, \"2. Estimated new hospital cases\"","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$download_nhs_regions()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"nhs data.frame nhs regions","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-add-nhs-regions-","dir":"Reference","previous_headings":"","what":"Method add_nhs_regions()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Add NHS data level 1 regions Separate NHS data available \"first\" admissions, excluding readmissions. available England + English regions . See: https://www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/ Section 2, \"2. Estimated new hospital cases\"","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$add_nhs_regions(clean_data, nhs_data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"clean_data Cleaned UK covid-19 data nhs_data NHS region data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-specific-tests-","dir":"Reference","previous_headings":"","what":"Method specific_tests()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"Specific tests UK data. addition generic tests ran DataClass$test() data NHS regions downloaded ran generic checks (test_cleaning, test_processing, test_return). download = TRUE snapshot file found, nhs data downloaded saved snapshot location provided. existing snapshot file found data used next tests. Tests data can downloaded, cleaned, processed returned. Designed ran test ran directly.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$specific_tests( self_copy, download = FALSE, all = FALSE, snapshot_path = \"\", ... )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"self_copy R6class object test. download logical. download data (TRUE) use snapshot (FALSE). Defaults FALSE. logical. Run tests settings (TRUE) defined current class instance (FALSE). Defaults FALSE. snapshot_path character_array path save downloaded snapshot . Works snapshot path constructed test adds ... Additional parameters pass specific_tests","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"UK$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/UK.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"United Kingdom Class for downloading, cleaning and processing notification\ndata. — UK","text":"","code":"if (FALSE) { # setup a data cache start_using_memoise() # download, clean and process level 1 UK data with hospital admissions region <- UK$new(level = \"1\", nhsregions = TRUE) region$return() # initialise level 2 data utla <- UK$new(level = \"2\") # download UTLA data utla$download() # clean UTLA data utla$clean() # inspect available level 1 regions utla$available_regions(level = \"1\") # filter data to the East of England utla$filter(\"East of England\") # process UTLA data utla$process() # return processed and filtered data utla$return() # inspect all data steps utla$data } ## ------------------------------------------------ ## Method `UK$new` ## ------------------------------------------------ if (FALSE) { UK$new( level = 1, localise = TRUE, verbose = True, steps = FALSE, nhsregions = FALSE, release_date = NULL, resolution = \"utla\" ) }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":null,"dir":"Reference","previous_headings":"","what":"USA Class for downloading, cleaning and processing notification data — USA","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"Information downloading, cleaning processing COVID-19 region data USA.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"https://github.com/nytimes/covid-19-data/","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"covidregionaldata::DataClass -> USA","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. level_data_urls List named links raw data level specific. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$clean_common() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$filter() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$return() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"USA$set_region_codes() USA$clean_level_1() USA$clean_level_2() USA$clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"method-set-region-codes-","dir":"Reference","previous_headings":"","what":"Method set_region_codes()","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"Set table region codes clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"","code":"USA$set_region_codes()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"method-clean-level-","dir":"Reference","previous_headings":"","what":"Method clean_level_1()","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"State Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"","code":"USA$clean_level_1()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"method-clean-level--1","dir":"Reference","previous_headings":"","what":"Method clean_level_2()","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"County Level Data Cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"","code":"USA$clean_level_2()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"","code":"USA$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/USA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"USA Class for downloading, cleaning and processing notification data — USA","text":"","code":"if (FALSE) { region <- USA$new(verbose = TRUE, steps = TRUE, get = TRUE) region$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"Information downloading, cleaning processing COVID-19 region data World Health Organisation","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"https://covid19..int/","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"covidregionaldata::DataClass -> covidregionaldata::CountryDataClass -> ","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"origin name origin fetch data supported_levels list supported levels. supported_region_names list region names order level. supported_region_codes list region codes order level. common_data_urls List named links raw data. first, entry, named main. source_data_cols existing columns within raw data source_text Plain text description source data source_url Website address explanation/introduction data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"covidregionaldata::DataClass$available_regions() covidregionaldata::DataClass$clean() covidregionaldata::DataClass$download() covidregionaldata::DataClass$download_JSON() covidregionaldata::DataClass$get() covidregionaldata::DataClass$initialize() covidregionaldata::DataClass$process() covidregionaldata::DataClass$set_region_codes() covidregionaldata::DataClass$summary() covidregionaldata::DataClass$test() covidregionaldata::CountryDataClass$filter()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"$clean_common() $return() $specific_tests() $clone()","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"method-clean-common-","dir":"Reference","previous_headings":"","what":"Method clean_common()","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"specific data cleaning","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"","code":"WHO$clean_common()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"method-return-","dir":"Reference","previous_headings":"","what":"Method return()","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"Specific return settings dataset.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"","code":"WHO$return()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"method-specific-tests-","dir":"Reference","previous_headings":"","what":"Method specific_tests()","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"Run additional tests data. Tests one row per country. Designed ran test ran directly.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"","code":"WHO$specific_tests(self_copy, ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"self_copy R6class object test ... Extra params passed specific download functions","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"objects class cloneable method.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"","code":"WHO$clone(deep = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"deep Whether make deep clone.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/WHO.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class containing specific attributes and methods for World Health\nOrganisation data — WHO","text":"","code":"if (FALSE) { national <- WHO$new(verbose = TRUE, steps = TRUE, get = TRUE) national$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/add_extra_na_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Add extra columns filled with NA values to a dataset. — add_extra_na_cols","title":"Add extra columns filled with NA values to a dataset. — add_extra_na_cols","text":"Adds extra columns filled NAs dataset. ensures datasets covidregionaldata package return datasets underlying structure (.e. columns).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/add_extra_na_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add extra columns filled with NA values to a dataset. — add_extra_na_cols","text":"","code":"add_extra_na_cols(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/add_extra_na_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add extra columns filled with NA values to a dataset. — add_extra_na_cols","text":"data data frame","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/add_extra_na_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add extra columns filled with NA values to a dataset. — add_extra_na_cols","text":"tibble relevant NA columns added","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/all_country_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Table of available datasets along with level and other information.\nRendered from the individual R6 class objects included in this package. — all_country_data","title":"Table of available datasets along with level and other information.\nRendered from the individual R6 class objects included in this package. — all_country_data","text":"Available datasets","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/all_country_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Table of available datasets along with level and other information.\nRendered from the individual R6 class objects included in this package. — all_country_data","text":"","code":"all_country_data"},{"path":"https://epiforecasts.io/covidregionaldata/reference/all_country_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Table of available datasets along with level and other information.\nRendered from the individual R6 class objects included in this package. — all_country_data","text":"object class tbl_df (inherits tbl, data.frame) 23 rows 10 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/all_country_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Table of available datasets along with level and other information.\nRendered from the individual R6 class objects included in this package. — all_country_data","text":"tibble available datasets related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/calculate_columns_from_existing_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative counts from daily counts or daily counts from cumulative,\ndependent on which columns already exist — calculate_columns_from_existing_data","title":"Cumulative counts from daily counts or daily counts from cumulative,\ndependent on which columns already exist — calculate_columns_from_existing_data","text":"Checks columns missing (cumulative/daily counts) one present calculates second first.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/calculate_columns_from_existing_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative counts from daily counts or daily counts from cumulative,\ndependent on which columns already exist — calculate_columns_from_existing_data","text":"","code":"calculate_columns_from_existing_data(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/calculate_columns_from_existing_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative counts from daily counts or daily counts from cumulative,\ndependent on which columns already exist — calculate_columns_from_existing_data","text":"data data frame","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/calculate_columns_from_existing_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative counts from daily counts or daily counts from cumulative,\ndependent on which columns already exist — calculate_columns_from_existing_data","text":"data frame extra columns required","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/check_level.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks a given level is supported — check_level","title":"Checks a given level is supported — check_level","text":"Checks given level supported","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/check_level.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks a given level is supported — check_level","text":"","code":"check_level(level, supported_levels)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/check_level.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks a given level is supported — check_level","text":"level character string indicating current level. supported_levels character vector supported levels","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/colombia_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for Colombia Dataset. — colombia_codes","title":"Region Codes for Colombia Dataset. — colombia_codes","text":"region codes Colombia","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/colombia_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for Colombia Dataset. — colombia_codes","text":"","code":"colombia_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/colombia_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for Colombia Dataset. — colombia_codes","text":"object class data.frame 1119 rows 4 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/colombia_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for Colombia Dataset. — colombia_codes","text":"tibble region codes related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/complete_cumulative_columns.html","id":null,"dir":"Reference","previous_headings":"","what":"Completes cumulative columns if rows were added with NAs. — complete_cumulative_columns","title":"Completes cumulative columns if rows were added with NAs. — complete_cumulative_columns","text":"dataset row NAs added (using fill_empty_dates_with_na) cumulative data columns NAs can cause issues later. function fills values previous non-NA value.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/complete_cumulative_columns.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Completes cumulative columns if rows were added with NAs. — complete_cumulative_columns","text":"","code":"complete_cumulative_columns(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/complete_cumulative_columns.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Completes cumulative columns if rows were added with NAs. — complete_cumulative_columns","text":"data data frame","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/complete_cumulative_columns.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Completes cumulative columns if rows were added with NAs. — complete_cumulative_columns","text":"data tibble NAs filled cumulative data columns.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/csv_reader.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom CSV reading function — csv_reader","title":"Custom CSV reading function — csv_reader","text":"Checks use memoise uses vroom::vroom.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/csv_reader.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom CSV reading function — csv_reader","text":"","code":"csv_reader(file, verbose = FALSE, guess_max = 1000, ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/csv_reader.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom CSV reading function — csv_reader","text":"file URL filepath CSV verbose Logical, defaults TRUE. verbose processing messages warnings returned. guess_max Maximum number records use guessing column types. Defaults 1000. ... extra parameters passed vroom::vroom","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/csv_reader.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom CSV reading function — csv_reader","text":"data table","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/download_excel.html","id":null,"dir":"Reference","previous_headings":"","what":"Download Excel Documents — download_excel","title":"Download Excel Documents — download_excel","text":"Download Excel Documents","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/download_excel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download Excel Documents — download_excel","text":"","code":"download_excel(url, archive, verbose = FALSE, transpose = TRUE, ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/download_excel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download Excel Documents — download_excel","text":"url Character string containing full URL Excel document. archive Character string naming file name assign temporary directory. verbose Logical, defaults TRUE. verbose processing messages warnings returned. transpose Logical, read data transposed ... Additional parameters pass read_excel().","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/download_excel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download Excel Documents — download_excel","text":"data.frame.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_clean_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Test clean columns contain the correct data and types — expect_clean_cols","title":"Test clean columns contain the correct data and types — expect_clean_cols","text":"Checks date column s3 class region level column character cleaned data (data$clean)","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_clean_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test clean columns contain the correct data and types — expect_clean_cols","text":"","code":"expect_clean_cols(data, level)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_clean_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test clean columns contain the correct data and types — expect_clean_cols","text":"data clean data check level character_array level data check","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_columns_contain_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Test that cleaned columns contain data/ — expect_columns_contain_data","title":"Test that cleaned columns contain data/ — expect_columns_contain_data","text":"Checks cleaned columns cases, deaths, recovered test (new total) entirely composed NAs.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_columns_contain_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test that cleaned columns contain data/ — expect_columns_contain_data","text":"","code":"expect_columns_contain_data(DataClass_obj)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_columns_contain_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test that cleaned columns contain data/ — expect_columns_contain_data","text":"DataClass_obj DataClass object (R6Class) perform checks . Must DataClass DataClass child object.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_processed_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Test that processed columns contain the correct data and types — expect_processed_cols","title":"Test that processed columns contain the correct data and types — expect_processed_cols","text":"Checks processed data columns date, cases_new, cases_total, deaths_new, deaths_total region level correct types.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_processed_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test that processed columns contain the correct data and types — expect_processed_cols","text":"","code":"expect_processed_cols(data, level = \"1\", localised = TRUE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/expect_processed_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test that processed columns contain the correct data and types — expect_processed_cols","text":"data data check level character_array level data check localised logical check localised data , defaults TRUE.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/fill_empty_dates_with_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Add rows of NAs for dates where a region does not have any data — fill_empty_dates_with_na","title":"Add rows of NAs for dates where a region does not have any data — fill_empty_dates_with_na","text":"points, particularly early data collection, data collected regions. function finds dates data regions, , adds rows NAs missing regions. mainly reasons completeness.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/fill_empty_dates_with_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add rows of NAs for dates where a region does not have any data — fill_empty_dates_with_na","text":"","code":"fill_empty_dates_with_na(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/fill_empty_dates_with_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add rows of NAs for dates where a region does not have any data — fill_empty_dates_with_na","text":"data data frame","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/fill_empty_dates_with_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add rows of NAs for dates where a region does not have any data — fill_empty_dates_with_na","text":"tibble rows NAs added.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/france_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for France Dataset. — france_codes","title":"Region Codes for France Dataset. — france_codes","text":"region codes France","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/france_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for France Dataset. — france_codes","text":"","code":"france_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/france_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for France Dataset. — france_codes","text":"object class data.frame 104 rows 5 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/france_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for France Dataset. — france_codes","text":"tibble region codes related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_available_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get supported data sets — get_available_datasets","title":"Get supported data sets — get_available_datasets","text":"Returns data countries available data provided package either using cached dataset built searching target namespace.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_available_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get supported data sets — get_available_datasets","text":"","code":"get_available_datasets(type, render = FALSE, namespace = \"covidregionaldata\")"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_available_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get supported data sets — get_available_datasets","text":"type character vector indicating types data return. Current options include \"national\" (datasets national level inherit CountryDataClass) \"regional\" (datasets regional level inherit directly DataClass()). render Logical TRUE supported data set table built available classes using summary methods. FALSE supported data set table taken package data. Defaults FALSE. namespace Character string name namespace search class objects. Defaults \"covidregionaldata\" package.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_available_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get supported data sets — get_available_datasets","text":"list available data sets spatial aggregation data available .","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_available_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get supported data sets — get_available_datasets","text":"","code":"# see all available datasets get_available_datasets() #> # A tibble: 23 × 10 #> origin class level_1_region level_2_region level_3_region type data_urls #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Belgium Belg… region province NA regi… https://… #> 2 Brazil Braz… state city NA regi… https://… #> 3 Canada Cana… province NA NA regi… https://… #> 4 Colombia Colo… departamento municipio NA regi… https://… #> 5 Covid-19 … Covi… country region subregion nati… https://… #> 6 Cuba Cuba provincia NA NA regi… https://… #> 7 European … ECDC country NA NA nati… https://… #> 8 Estonia Esto… county NA NA regi… https://… #> 9 France Fran… region department NA regi… https://… #> 10 Germany Germ… bundesland landkreis NA regi… https://… #> # … with 13 more rows, and 3 more variables: source_data_cols <chr>, #> # source_text <chr>, source_url <chr> # see only national level datasets get_available_datasets(\"national\") #> # A tibble: 6 × 10 #> origin class level_1_region level_2_region level_3_region type data_urls #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Covid-19 D… Covi… country region subregion nati… https://… #> 2 European C… ECDC country NA NA nati… https://… #> 3 Google Goog… country subregion subregion2 nati… https://… #> 4 John Hopki… JHU country region NA nati… https://… #> 5 European C… JRC country region NA nati… https://… #> 6 World Heal… WHO country NA NA nati… https://… #> # … with 3 more variables: source_data_cols <chr>, source_text <chr>, #> # source_url <chr> # see only regional level datasets get_available_datasets(\"regional\") #> # A tibble: 17 × 10 #> origin class level_1_region level_2_region level_3_region type data_urls #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Belgium Belg… region province NA regi… https://… #> 2 Brazil Braz… state city NA regi… https://… #> 3 Canada Cana… province NA NA regi… https://… #> 4 Colombia Colo… departamento municipio NA regi… https://… #> 5 Cuba Cuba provincia NA NA regi… https://… #> 6 Estonia Esto… county NA NA regi… https://… #> 7 France Fran… region department NA regi… https://… #> 8 Germany Germ… bundesland landkreis NA regi… https://… #> 9 India India state NA NA regi… https://… #> 10 Italy Italy regioni NA NA regi… https://… #> 11 Lithuania Lith… county municipality NA regi… https://… #> 12 Mexico Mexi… estado municipio NA regi… Download… #> 13 Netherlan… Neth… province municipality NA regi… https://… #> 14 South Afr… Sout… province NA NA regi… https://… #> 15 Switzerla… Swit… canton NA NA regi… https://… #> 16 United Ki… UK region authority NA regi… https://… #> 17 United St… USA state county NA regi… https://… #> # … with 3 more variables: source_data_cols <chr>, source_text <chr>, #> # source_url <chr> # render the data get_available_datasets(render = TRUE) #> # A tibble: 23 × 10 #> origin class level_1_region level_2_region level_3_region type data_urls #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Belgium Belg… region province NA regi… https://… #> 2 Brazil Braz… state city NA regi… https://… #> 3 Canada Cana… province NA NA regi… https://… #> 4 Colombia Colo… departamento municipio NA regi… https://… #> 5 Covid-19 … Covi… country region subregion nati… https://… #> 6 Cuba Cuba provincia NA NA regi… https://… #> 7 European … ECDC country NA NA nati… https://… #> 8 Estonia Esto… county NA NA regi… https://… #> 9 France Fran… region department NA regi… https://… #> 10 Germany Germ… bundesland landkreis NA regi… https://… #> # … with 13 more rows, and 3 more variables: source_data_cols <chr>, #> # source_text <chr>, source_url <chr>"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_linelist.html","id":null,"dir":"Reference","previous_headings":"","what":"Get patient line list data — get_linelist","title":"Get patient line list data — get_linelist","text":"Provides public international patient line list January 2020 June 2020. version line list stopped updating. new version line list free requires login. See: https://global.health/","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_linelist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get patient line list data — get_linelist","text":"","code":"get_linelist(clean = TRUE, report_delay_only = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_linelist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get patient line list data — get_linelist","text":"https://github.com/beoutbreakprepared/nCoV2019","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_linelist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get patient line list data — get_linelist","text":"clean Logical, defaults TRUE. data returned cleaned use. report_delay_only Logical, defaults FALSE. certain variables (id, country, onset date, days' delay), observations (patients report delay) returned","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_linelist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get patient line list data — get_linelist","text":"line list reported cases COVID-19","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_linelist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get patient line list data — get_linelist","text":"","code":"if (FALSE) { # Get the complete linelist get_linelist() # Return the report delay only get_linelist(report_delay_only = TRUE) }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_national_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get national-level data for countries globally from a range of sources — get_national_data","title":"Get national-level data for countries globally from a range of sources — get_national_data","text":"Provides interface source specific classes support national level data. simple use cases allows downloading clean, standardised, national-level COVID-19 data sets. Internally uses CountryDataClass() parent class allows documented downloading, cleaning, processing. Optionally steps data processing can returned along functions used processing default just finalised processed data returned. See examples potential use cases links lower level functions details options.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_national_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get national-level data for countries globally from a range of sources — get_national_data","text":"","code":"get_national_data( countries, source = \"who\", level = \"1\", totals = FALSE, steps = FALSE, class = FALSE, verbose = TRUE, ... )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_national_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get national-level data for countries globally from a range of sources — get_national_data","text":"countries character vector specifying country names interest. Used filter data. source character string specifying data source (case dependent). Defaults (World Health Organisation). See get_available_datasets(\"national\") options. level character string indicating target administrative level data default \"1\". Currently supported options level 1 (\"1) level 2 (\"2\"). Use get_available_datasets() supported options dataset. totals Logical, defaults FALSE. TRUE, returns totalled data per region today's date. FALSE, returns full dataset stratified date region. steps Logical, defaults FALSE. processing cleaning steps kept output list. class Logical, defaults FALSE. TRUE returns DataClass object rather tibble list tibbles. Overrides steps. verbose Logical, defaults TRUE. verbose processing messages warnings returned. ... Additional arguments pass class specific functionality.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_national_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get national-level data for countries globally from a range of sources — get_national_data","text":"tibble data related cases, deaths, hospitalisations, recoveries testing.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_national_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get national-level data for countries globally from a range of sources — get_national_data","text":"","code":"if (FALSE) { # set up a data cache start_using_memoise() # download all national data from the WHO get_national_data(source = \"who\") # download data for Canada keeping all processing steps get_national_data(countries = \"canada\", source = \"ecdc\") # download data for Canada from the JHU and return the full class jhu <- get_national_data(countries = \"canada\", source = \"jhu\", class = TRUE) jhu # return the JHU data for canada jhu$return() # check which regions the JHU supports national data for jhu$available_regions() # filter instead for France (and then reprocess) jhu$filter(\"France\") jhu$process() # explore the structure of the stored JHU data jhu$data }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_regional_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get regional-level data — get_regional_data","title":"Get regional-level data — get_regional_data","text":"Provides interface source specific classes support regional level data. simple use cases allows downloading clean, standardised, regional-level COVID-19 data sets. Internally uses DataClass() parent class allows documented downloading, cleaning, processing. Optionally steps data processing can returned along functions used processing default just finalised processed data returned. See examples potential use cases links lower level functions details options.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_regional_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get regional-level data — get_regional_data","text":"","code":"get_regional_data( country, level = \"1\", totals = FALSE, localise = TRUE, steps = FALSE, class = FALSE, verbose = TRUE, regions, ... )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_regional_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get regional-level data — get_regional_data","text":"country character string specifying country get data . case dependent. Name English name. list options use get_available_datasets(). level character string indicating target administrative level data default \"1\". Currently supported options level 1 (\"1) level 2 (\"2\"). Use get_available_datasets() supported options dataset. totals Logical, defaults FALSE. TRUE, returns totalled data per region today's date. FALSE, returns full dataset stratified date region. localise Logical, defaults TRUE. region names localised. steps Logical, defaults FALSE. processing cleaning steps kept output list. class Logical, defaults FALSE. TRUE returns DataClass object rather tibble list tibbles. Overrides steps. verbose Logical, defaults TRUE. verbose processing messages warnings returned. regions character vector target regions assigned target_regions field used filter returned data. ... Additional arguments pass class specific functionality.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_regional_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get regional-level data — get_regional_data","text":"tibble data related cases, deaths, hospitalisations, recoveries testing stratified regions within given country.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/get_regional_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get regional-level data — get_regional_data","text":"","code":"if (FALSE) { # set up a data cache start_using_memoise() # download data for Italy get_regional_data(\"italy\") # return totals for Italy with no localisation get_regional_data(\"italy\", localise = FALSE, totals = TRUE) # download data for the UK but return the class uk <- get_regional_data(\"United Kingdom\", class = TRUE) uk # return UK data from the class object] uk$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/glue_level.html","id":null,"dir":"Reference","previous_headings":"","what":"Glue the spatial level into a variable name — glue_level","title":"Glue the spatial level into a variable name — glue_level","text":"Glue spatial level variable name","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/glue_level.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Glue the spatial level into a variable name — glue_level","text":"","code":"glue_level(level)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/glue_level.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Glue the spatial level into a variable name — glue_level","text":"level character string indicating current level.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/glue_level.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Glue the spatial level into a variable name — glue_level","text":"string form \"level_1_region\".","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/initialise_dataclass.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialise a child class of DataClass if it exists — initialise_dataclass","title":"Initialise a child class of DataClass if it exists — initialise_dataclass","text":"function initialises classes based DataClass() allows documented downloading, cleaning, processing. See examples potential use cases DataClass() documentation details.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/initialise_dataclass.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialise a child class of DataClass if it exists — initialise_dataclass","text":"","code":"initialise_dataclass( class = character(), level = \"1\", totals = FALSE, localise = TRUE, regions, verbose = TRUE, steps = FALSE, get = FALSE, type = c(\"national\", \"regional\"), ... )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/initialise_dataclass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialise a child class of DataClass if it exists — initialise_dataclass","text":"class character string specifying DataClass() initialise. case dependent matching based either class name country definition. list options use get_available_datasets(). level character string indicating target administrative level data default \"1\". Currently supported options level 1 (\"1) level 2 (\"2\"). Use get_available_datasets() supported options dataset. totals Logical, defaults FALSE. TRUE, returns totalled data per region today's date. FALSE, returns full dataset stratified date region. localise Logical, defaults TRUE. region names localised. regions character vector target regions assigned target_regions field used filter returned data. verbose Logical, defaults TRUE. verbose processing messages warnings returned. steps Logical, defaults FALSE. processing cleaning steps kept output list. get Logical, defaults FALSE. class get method called (download, clean, process data initialisation). type character vector indicating types data return. Current options include \"national\" (datasets national level inherit CountryDataClass) \"regional\" (datasets regional level inherit directly DataClass()). ... Additional arguments pass class specific functionality.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/initialise_dataclass.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialise a child class of DataClass if it exists — initialise_dataclass","text":"initialised version target class available, e.g. Italy()","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/initialise_dataclass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Initialise a child class of DataClass if it exists — initialise_dataclass","text":"","code":"if (FALSE) { # set up a cache to store data to avoid downloading repeatedly start_using_memoise() # check currently available datasets get_available_datasets() # initialise a data set in the United Kingdom # at the UTLA level utla <- UK$new(level = \"2\") # download UTLA data utla$download() # clean UTLA data utla$clean() # inspect available level 1 regions utla$available_regions(level = \"1\") # filter data to the East of England utla$filter(\"East of England\") # process UTLA data utla$process() # return processed and filtered data utla$return() # inspect all data steps utla$data # initialise Italian data, download, clean and process it italy <- initialise_dataclass(\"Italy\", get = TRUE) italy$return() # initialise ECDC data, fully process it, and return totals ecdc <- initialise_dataclass(\"ecdc\", get = TRUE, totals = TRUE) ecdc$return() }"},{"path":"https://epiforecasts.io/covidregionaldata/reference/json_reader.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom JSON reading function — json_reader","title":"Custom JSON reading function — json_reader","text":"Checks use memoise uses vroom::vroom.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/json_reader.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom JSON reading function — json_reader","text":"","code":"json_reader(file, verbose = FALSE, ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/json_reader.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom JSON reading function — json_reader","text":"file URL filepath JSON verbose Logical, defaults TRUE. verbose processing messages warnings returned. ... extra parameters passed jsonlite::fromJSON","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/json_reader.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom JSON reading function — json_reader","text":"data table","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/lithuania_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for Lithuania Dataset. — lithuania_codes","title":"Region Codes for Lithuania Dataset. — lithuania_codes","text":"region codes Lithuania","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/lithuania_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for Lithuania Dataset. — lithuania_codes","text":"","code":"lithuania_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/lithuania_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for Lithuania Dataset. — lithuania_codes","text":"object class spec_tbl_df (inherits tbl_df, tbl, data.frame) 61 rows 6 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/lithuania_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for Lithuania Dataset. — lithuania_codes","text":"tibble region codes related information, including ISO 3166:2 codes counties (apskritis) municipalities (savivaldybe), noting municipalities city municipalities regional municipalities.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/make_github_workflow.html","id":null,"dir":"Reference","previous_headings":"","what":"Create github action for a given source — make_github_workflow","title":"Create github action for a given source — make_github_workflow","text":"Makes github workflow yaml file given source used action check data github action.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/make_github_workflow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create github action for a given source — make_github_workflow","text":"","code":"make_github_workflow( source, workflow_path = paste0(\".github/workflows/\", source, \".yaml\"), cron = \"36 12 * * *\" )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/make_github_workflow.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create github action for a given source — make_github_workflow","text":"source character_array name class create workflow . workflow_path character_array path workflow file saved. Defaults '.github/workflows/' cron character_array cron time run tests, defaults 36 12 * * *, following minute, hour, day(month), month day(week) format.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/make_new_data_source.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new country class for a given source — make_new_data_source","title":"Create new country class for a given source — make_new_data_source","text":"Makes new regional national country class name provided source. forms basic template user fill specific field values cleaning functions required. also creates github workflow file country.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/make_new_data_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new country class for a given source — make_new_data_source","text":"","code":"make_new_data_source( source, type = \"subnational\", newfile_path = paste0(\"R/\", source, \".R\") )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/make_new_data_source.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new country class for a given source — make_new_data_source","text":"source character_array name class create. Must start capital letter (upper camel case acronym caps ). type character_array type class create, subnational National defaults subnational. Regional classes individual countries, UK, Italy, India, etc. inherit DataClass, whilst national classes sources multiple countries data, JRC, JHU, Google, etc. inherit CountryDataClass. newfile_path character_array place save class file","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/message_verbose.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for message — message_verbose","title":"Wrapper for message — message_verbose","text":"wrapper message prints output verbose = TRUE.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/message_verbose.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for message — message_verbose","text":"","code":"message_verbose(verbose = TRUE, ...)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/message_verbose.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for message — message_verbose","text":"verbose Logical, defaults TRUE. verbose processing messages warnings returned. ... Additional arguments passed message.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/mexico_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for Mexico Dataset. — mexico_codes","title":"Region Codes for Mexico Dataset. — mexico_codes","text":"Details region codes used Mexico dataset.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/mexico_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for Mexico Dataset. — mexico_codes","text":"","code":"mexico_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/mexico_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for Mexico Dataset. — mexico_codes","text":"object class spec_tbl_df (inherits tbl_df, tbl, data.frame) 2489 rows 4 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/mexico_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for Mexico Dataset. — mexico_codes","text":"nested tibble region codes related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/process_internal.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal Shared Regional Dataset Processing — process_internal","title":"Internal Shared Regional Dataset Processing — process_internal","text":"Internal shared regional data cleaning designed called process.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/process_internal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal Shared Regional Dataset Processing — process_internal","text":"","code":"process_internal( clean_data, level, group_vars, totals = FALSE, localise = TRUE, verbose = TRUE, process_fns )"},{"path":"https://epiforecasts.io/covidregionaldata/reference/process_internal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal Shared Regional Dataset Processing — process_internal","text":"clean_data clean data class, e.g. Italy$data$clean level level data, e.g. 'level_1_region' group_vars Grouping variables, used grouping localise names. assumed first entry indicates main region variable second indicates geocode variable. totals Logical, defaults FALSE. `TRUE``, returns totalled data per region today's date. FALSE, returns full dataset stratified date region. localise Logical, defaults TRUE. region names localised. verbose Logical, defaults TRUE. verbose processing messages warnings returned. process_fns array, additional functions called default processing steps","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. dplyr %>%","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/region_dispatch.html","id":null,"dir":"Reference","previous_headings":"","what":"Control Grouping Variables used in process_internal — region_dispatch","title":"Control Grouping Variables used in process_internal — region_dispatch","text":"Controls grouping variables used process_internal based supported regions present class.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/region_dispatch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control Grouping Variables used in process_internal — region_dispatch","text":"","code":"region_dispatch(level, all_levels, region_names, region_codes)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/region_dispatch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control Grouping Variables used in process_internal — region_dispatch","text":"level character string indicating current level. all_levels character vector indicating levels supported. region_names named list region names named levels supported. region_codes named list region codes named levels supported.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/reset_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset Cache and Update all Local Data — reset_cache","title":"Reset Cache and Update all Local Data — reset_cache","text":"Reset Cache Update Local Data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/reset_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset Cache and Update all Local Data — reset_cache","text":"","code":"reset_cache()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/reset_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset Cache and Update all Local Data — reset_cache","text":"Null","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/return_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Control data return — return_data","title":"Control data return — return_data","text":"Controls data return get_reigonal_data get_national_data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/return_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control data return — return_data","text":"","code":"return_data(obj, class = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/return_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control data return — return_data","text":"obj Class based DataClass class Logical, defaults FALSE. TRUE returns DataClass object rather tibble list tibbles. Overrides steps.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/run_default_processing_fns.html","id":null,"dir":"Reference","previous_headings":"","what":"Default processing steps to run — run_default_processing_fns","title":"Default processing steps to run — run_default_processing_fns","text":"default processing steps always run. Runs clean data","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/run_default_processing_fns.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default processing steps to run — run_default_processing_fns","text":"","code":"run_default_processing_fns(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/run_default_processing_fns.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default processing steps to run — run_default_processing_fns","text":"data data table","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/run_optional_processing_fns.html","id":null,"dir":"Reference","previous_headings":"","what":"Optional processing steps to run — run_optional_processing_fns","title":"Optional processing steps to run — run_optional_processing_fns","text":"user supplied processing steps run default steps","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/run_optional_processing_fns.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Optional processing steps to run — run_optional_processing_fns","text":"","code":"run_optional_processing_fns(data, process_fns)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/run_optional_processing_fns.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Optional processing steps to run — run_optional_processing_fns","text":"data data table process_fns array, additional functions called default processing steps","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/set_negative_values_to_zero.html","id":null,"dir":"Reference","previous_headings":"","what":"Set negative data to 0 — set_negative_values_to_zero","title":"Set negative data to 0 — set_negative_values_to_zero","text":"Set data values 0 negative dataset. Data datasets always > 0.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/set_negative_values_to_zero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set negative data to 0 — set_negative_values_to_zero","text":"","code":"set_negative_values_to_zero(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/set_negative_values_to_zero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set negative data to 0 — set_negative_values_to_zero","text":"data data frame","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/set_negative_values_to_zero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set negative data to 0 — set_negative_values_to_zero","text":"data frame relevant data > 0.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/start_using_memoise.html","id":null,"dir":"Reference","previous_headings":"","what":"Add useMemoise to options — start_using_memoise","title":"Add useMemoise to options — start_using_memoise","text":"Adds useMemoise options meaning memoise used reading data .","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/start_using_memoise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add useMemoise to options — start_using_memoise","text":"","code":"start_using_memoise(path = tempdir(), verbose = TRUE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/start_using_memoise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add useMemoise to options — start_using_memoise","text":"path Path cache directory, defaults temporary directory. verbose Logical, defaults TRUE. verbose processing messages warnings returned.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/stop_using_memoise.html","id":null,"dir":"Reference","previous_headings":"","what":"Stop using useMemoise — stop_using_memoise","title":"Stop using useMemoise — stop_using_memoise","text":"Sets useMemoise options NULL, meaning memoise used reading data ","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/stop_using_memoise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stop using useMemoise — stop_using_memoise","text":"","code":"stop_using_memoise()"},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_cleaning.html","id":null,"dir":"Reference","previous_headings":"","what":"Test clean method works correctly — test_cleaning","title":"Test clean method works correctly — test_cleaning","text":"Test data can cleaned properly. clean method invoked generate clean data. data checked ensure data.frame, empty, least two columns columns clean calling expect_clean_cols. Also tests avaliable_regions() NA characters.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_cleaning.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test clean method works correctly — test_cleaning","text":"","code":"test_cleaning(DataClass_obj)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_cleaning.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test clean method works correctly — test_cleaning","text":"DataClass_obj R6Class object perform checks . Must DataClass DataClass child object.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_download.html","id":null,"dir":"Reference","previous_headings":"","what":"Test download method works correctly — test_download","title":"Test download method works correctly — test_download","text":"Test data can downloaded download = TRUE, requested snapshot file found, store snap shot snapshot_dir. existing snapshot file found load data use future tests","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test download method works correctly — test_download","text":"","code":"test_download(DataClass_obj, download, snapshot_path)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test download method works correctly — test_download","text":"DataClass_obj R6Class object perform checks . Must DataClass DataClass child object. download Logical check download use snapshot data snapshot_path character_array path save downloaded snapshot .","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_download_JSON.html","id":null,"dir":"Reference","previous_headings":"","what":"Test download method for JSON files works correctly — test_download_JSON","title":"Test download method for JSON files works correctly — test_download_JSON","text":"Test data can downloaded download = TRUE, requested snapshot file found, store snap shot snapshot_dir. existing snapshot file found load data use future tests","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_download_JSON.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test download method for JSON files works correctly — test_download_JSON","text":"","code":"test_download_JSON(DataClass_obj, download, snapshot_path)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_download_JSON.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test download method for JSON files works correctly — test_download_JSON","text":"DataClass_obj R6Class object perform checks . Must DataClass DataClass child object. download Logical check download use snapshot data snapshot_path character_array path save downloaded snapshot .","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_processing.html","id":null,"dir":"Reference","previous_headings":"","what":"Test process method works correctly — test_processing","title":"Test process method works correctly — test_processing","text":"Test data can processed correctly using process method. process invoked generate processed data checked ensure data.frame, empty, least 2 columns calls expect_processed_columns check column types.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_processing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test process method works correctly — test_processing","text":"","code":"test_processing(DataClass_obj, all = FALSE)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_processing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test process method works correctly — test_processing","text":"DataClass_obj R6Class object perform checks . Must DataClass DataClass child object. Logical. Run tests settings (TRUE) defined current class instance (FALSE). Defaults FALSE.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_return.html","id":null,"dir":"Reference","previous_headings":"","what":"Test return method works correctly — test_return","title":"Test return method works correctly — test_return","text":"Test data can returned correctly using return method. return invoked generate returned data checked ensure data.frame, empty least 2 columns. column checked ensure contains data just composed NAs.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_return.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test return method works correctly — test_return","text":"","code":"test_return(DataClass_obj)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/test_return.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test return method works correctly — test_return","text":"DataClass_obj R6Class object perform checks . Must DataClass DataClass child object.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/totalise_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get totals data given the time series data. — totalise_data","title":"Get totals data given the time series data. — totalise_data","text":"Get totals data given time series data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/totalise_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get totals data given the time series data. — totalise_data","text":"","code":"totalise_data(data)"},{"path":"https://epiforecasts.io/covidregionaldata/reference/totalise_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get totals data given the time series data. — totalise_data","text":"data data table","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/totalise_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get totals data given the time series data. — totalise_data","text":"data table, totalled ","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/reference/uk_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for UK Dataset. — uk_codes","title":"Region Codes for UK Dataset. — uk_codes","text":"uk authority look table providing region codes used level 2 UK data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/uk_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for UK Dataset. — uk_codes","text":"","code":"uk_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/uk_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for UK Dataset. — uk_codes","text":"object class tbl_df (inherits tbl, data.frame) 429 rows 4 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/uk_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for UK Dataset. — uk_codes","text":"tibble region codes related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/vietnam_codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Region Codes for Vietnam Dataset. — vietnam_codes","title":"Region Codes for Vietnam Dataset. — vietnam_codes","text":"region codes Viet Nam","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/vietnam_codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Region Codes for Vietnam Dataset. — vietnam_codes","text":"","code":"vietnam_codes"},{"path":"https://epiforecasts.io/covidregionaldata/reference/vietnam_codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Region Codes for Vietnam Dataset. — vietnam_codes","text":"object class data.frame 63 rows 2 columns.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/reference/vietnam_codes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Region Codes for Vietnam Dataset. — vietnam_codes","text":"tibble region codes related information.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-093","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.9.3","title":"covidregionaldata 0.9.3","text":"CRAN release: 2022-02-07 largely patch release dealing processing issues introduced recent release tidyr 1.2.0. addition support data Estonia Vietnam added. See full release notes details. Thanks @RichardMN, @biocyberman, @Bisaloo, @sbfnk, @kathsherratt contributing release.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"new-data-sets-0-9-3","dir":"Changelog","previous_headings":"","what":"New data sets","title":"covidregionaldata 0.9.3","text":"Support level 1 region data Estonia (thanks @RichardMN). See ?Estonia details. Support level 1 region data Vietnam (thanks @biocyberman). See ?Vietnam details. Note class available installing vietnam branch GitHub due API instability issues.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"other-changes-0-9-3","dir":"Changelog","previous_headings":"","what":"Other changes","title":"covidregionaldata 0.9.3","text":"Change data source Switzerland draw data Swiss Federal Office Public Health (FOPH) Updated package logo include newly supported data sets. Reduced number package dependencies (@bisaloo @RichardMN) Added tests JSON download code (@RichardMN).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"covidregionaldata 0.9.3","text":"Fixed bug fill_empty_dates_with_na() caused changes made version 1.2.0 tidyr. Fixed bug data sourced Germany instead treating line list individuals treated relatively finely resolved count data needs summed (@sbfnk). Fixed bug Vietnam class due stringr (#448 @RichardMN). Fixed bug Netherlands class lack Hospitalisation data source causing class fail (#446 @RichardMN). Fixed issue Colombia data reduced dependencies making RSocrata suggested package (#433 @RichardMN).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"depreciations-0-9-3","dir":"Changelog","previous_headings":"","what":"Depreciations","title":"covidregionaldata 0.9.3","text":"get_interventions_data() depreciated removed. get_info_covidregionaldata() depreciated removed. country argument get_national_data() depreciated removed. ’s functionality can replicated using countries argument. get_linelist() updated fail use vs warn use removed future versions package.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-092","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.9.2","title":"covidregionaldata 0.9.2","text":"CRAN release: 2021-07-05 release adds support Covid19 Data Hub includes Google Apple mobility data amongst large range data sets, data European Commission’s Joint Research Centre regional national level, individual sources regional data several countries. Package updates made line software review Journal Open Source Software. Finally, release exposes testing infrastructure users adds package hexsticker. Thanks @joseph-palmer, @RichardMN, @kathsherratt contributions towards release.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"new-features-0-9-2","dir":"Changelog","previous_headings":"","what":"New features","title":"covidregionaldata 0.9.2","text":"Support added data sets Covid19 Data Hub. source aggregates range data national subnational level provides keys link mobility data provided Apple Google (@joseph-palmer). Support added data European Commission’s Joint Research Centre (JRC). source aggregates incidence data country regional level 34 UCPM Participating States plus Switzerland (@joseph-palmer). Support added data Netherlands provided RVIM (English: National Institute Public Health Environment). source provides case, deaths hospital admission data province municipal levels (@joseph-palmer). Support added data Switzerland Liechtenstein collated Canton Zurich (@OpenZH). source provides case, deaths hospital admission data canton level (@RichardMN). Made package changes recomended JOSS review, including additional statements need README, updates manuscript (paper.md) fixes bug multiple sources countries. grateful detailed feedback given JOSS reviewers help improving package.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"changes-to-implemented-data-sources-0-9-2","dir":"Changelog","previous_headings":"","what":"Changes to implemented data sources","title":"covidregionaldata 0.9.2","text":"Increased robustness fetching UK NHS admissions region. Rather testing single date data now look last 7 days pick recent available data set (@kathsherratt).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"other-changes-0-9-2","dir":"Changelog","previous_headings":"","what":"Other changes","title":"covidregionaldata 0.9.2","text":"Testing classes updated allow least one common_data_urls level_data_urls present. previous default forced presence common_data_urls meant several classes define empty field (@joseph-palmer). Tests data sets now included method DataClass. test_regional-datasets now calls test function classes level. Data set specific tests (NHS regions UK) included specific_tests function within country class, called parent (DataClass) test performing standard checks. allows code country defined class. addition, users can run tests interactively calling test method (e.g. $test()) (@joseph-palmer) function create template class automatically add github workflow file added. makes adding new data source country even easier now can call function make_new_data_source() country / source name add set basic structure . also now github check make sure new sources workflow set (@joseph-palmer). Adds source_ fields data sets help users properly attribute data sources (@RichardMN).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"covidregionaldata 0.9.2","text":"issue Lithuania() data set ignore optional class specific arguments fixed (@RichardMN). issue JHU() source multiple region codes country fixed, giving just one region code per country (@joseph-palmer).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-091","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.9.1","title":"covidregionaldata 0.9.1","text":"CRAN release: 2021-05-07 release adds support data sets John Hopkins University Google open data project. sources aggregate range data national subnational levels. also contains range small fixes improvements documentation. Finally, release adds optional data processing extended future releases (contributions warmly welcomed). Thanks @joseph-palmer, @RichardMN, @kathsherratt contributions towards release.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"New features","title":"covidregionaldata 0.9.1","text":"Support data provided John Hopkins University (@joseph-palmer). Support data provided Google COVID-19 open data project (@joseph-palmer). Added available_regions method classes shows level 1 regions data available region interest. particular use combined JHU Google datasets processing large number regions required can take time. Adds support JHU Google data get_national_data(). may also now used access lower level data sources may better instead use classes directly via initialise_dataclass().","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"other-changes-0-9-1","dir":"Changelog","previous_headings":"","what":"Other changes","title":"covidregionaldata 0.9.1","text":"optional downloading NHS region data UK() improved include dynamic data previously supported archive document now produced (@kathsherratt). examples UK() class expanded better showcase package functionality. documentation examples get_regional_data(), get_national_data(), get_available_datasets() expanded focus increasing visibility underlying package structure. documentation examples initialise_dataclass(), DataClass(), CountryDataClass() expanded improved. Improvements linking documentation related functions classes. Improvements documentation contributors (@RichardMN). Improvements pkgdown documentation organise packages appropriate subcategories.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-090","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.9.0","title":"covidregionaldata 0.9.0","text":"CRAN release: 2021-04-24 release covidregionaldata substantially retooled robust, handle data transparent way. Adding new data sets functionality also made streamlined. update substantial package refactor breaking changes may inadvertently introduced. requiring old behaviour please install covidregionaldata@0.8.3 GitHub. Thanks @joseph-palmer, @RichardMN, @kathsherratt major contributions release. Thanks @RichardMN volunteering time.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"New features","title":"covidregionaldata 0.9.0","text":"Track data processing raw clean using step = TRUE argument get_regional_data(). Filter datasets regions countries interest. Access underlying methods data sets steps data processing pipeline.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"documentation-0-9-0","dir":"Changelog","previous_headings":"","what":"Documentation","title":"covidregionaldata 0.9.0","text":"vignettes updated readability. quickstart added package README.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"technical-improvements-0-9-0","dir":"Changelog","previous_headings":"","what":"Technical improvements","title":"covidregionaldata 0.9.0","text":"get_regional_data() get_national_data() now use R6 method dispatch. internal change minimal user impact users get_ functions. However, datasets now available used R6 methods (see get_available_datasets) may allow modular use cases. classes can also initialised using initialise_dataclass() used internally get_regional_data() get_national_data(). Unit testing separated data downloading now tested individually data set. allows contributors easily assess impact additions also allows us publish data status updates data sets (see README: https://github.com/epiforecasts/covidregionaldata#readme).","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"deprecated-functions-0-9-0","dir":"Changelog","previous_headings":"","what":"Deprecated functions","title":"covidregionaldata 0.9.0","text":"get_available_datasets() replaces get_info_covidregionaldata() view available data. get_info_covidregionaldata() deprecated. get_interventions_data() deprecated. data longer update December 2020. Check alternatives https://supertracker.spi.ox.ac.uk/policy-trackers/ get_linelist deprecated. Linelist stopped updating June 2020. date linelist data now behind login: access https://global.health/. working solution accessing covidregionaldata.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"data-changes-since-0-9-0","dir":"Changelog","previous_headings":"","what":"Data changes since 0.8.3","title":"covidregionaldata 0.9.0","text":"Colombia now capitalized region names. Germany level 2 region codes removed (previously NAs). India uses NA unknown region codes, change -UN previously. Italy column region now regioni. Mexico codes ‘inegi_code’ changed ‘inegi’. UK Level 1 ‘ons_region_code’ now ‘region_code’. UK level 2 “ltla_code” now “local_authority_code”. get_available_datasets() now return origin column rather country column type column rather get_data_function better reflect types data supported.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"new-data-sets-0-8-3","dir":"Changelog","previous_headings":"","what":"New data sets","title":"covidregionaldata 0.8.3","text":"Level 1 admin data Cuba Level 1 admin data South Africa","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"data-set-changes-0-8-3","dir":"Changelog","previous_headings":"","what":"Data set changes","title":"covidregionaldata 0.8.3","text":"UK data - added option get either lower tier upper tier local authorities (level 2 regions). Updated Northern Ireland case data specimen date default rather date report previously case. means UK data except data streams Wales Scotland date specimen. Switched source default national level data.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"new-features-0-8-3","dir":"Changelog","previous_headings":"","what":"New features","title":"covidregionaldata 0.8.3","text":"Relevant date package information can fetched using get_info_covidregionaldata(). Switched using vroom faster csv downloads.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"other-changes-0-8-3","dir":"Changelog","previous_headings":"","what":"Other changes","title":"covidregionaldata 0.8.3","text":"Replaced silently broken functions converting cumulative data daily vice versa. Removed integration Covid19R formatting. UK data - removed hospital admissions age, occupied mechanical ventilation beds. Currently, don’t fit existing data structure available lower level regions. Removed code required ECDC variables work. Update ECDC source pull data new weekly snapshots. Updated variables. later update downloading now archived daily data made possible.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-082","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.8.2","title":"covidregionaldata 0.8.2","text":"CRAN release: 2020-12-12 Updates API backend used extract UK data V2. Adds release date variable can used return data releases specified dates rather latest snapshot. Various fixes maintain compatibility data set sources. Adds quickstart vignette examples exploratory data analysis.","code":""},{"path":[]},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"breaking-changes-0-7-0","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"covidregionaldata 0.7.0","text":"get_linelist: argument clean changed clean_dates reflect slight change use case.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"changes-0-7-0","dir":"Changelog","previous_headings":"","what":"Changes","title":"covidregionaldata 0.7.0","text":"Added new option return UK data NHS region. also return “first admissions” hospital data (excludes readmissions). Specify ‘nhsregions = TRUE’. Default FALSE, returning ONS regions . Fixed inconsistent reference dates variables UK data. cases_new cases_total now “Specimen date” (date test), deaths_new deaths_total “Date death”, regions nations. Additional delays added get_linelist clean_dates = TRUE.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-060","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.6.0","title":"covidregionaldata 0.6.0","text":"CRAN release: 2020-08-27 Added whitespace trimming regional data functions. Fixed region codes Colombia. Fixed region name cleaning afghanistan. Updated UK data source expanded available variables based newly implemented API. Enabled regional localisation optional. Minor quality life changes.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-050","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.5.0","title":"covidregionaldata 0.5.0","text":"CRAN release: 2020-07-24 Release candidate.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-040","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.4.0","title":"covidregionaldata 0.4.0","text":"Added functions extract regional cases Spain, Japan, South Korea, United Kingdom, United States. Improved data extraction ECDC. Added minimal unit tests.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-030","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.3.0","title":"covidregionaldata 0.3.0","text":"Added function extract case counts region Italy. Function extract ECDC cases. Added function extract case counts region Germany. Fixed cache reset. Added covidregionaldata cache public linelist fall back option source available.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-020","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.2.0","title":"covidregionaldata 0.2.0","text":"Added memoise functionality automatically cache current directory remote resources. Added non-Hubei linelist function can extract country city linelists. Added function extract latest case counts. Added function summarise current total number cases.","code":""},{"path":"https://epiforecasts.io/covidregionaldata/news/index.html","id":"covidregionaldata-010","dir":"Changelog","previous_headings":"","what":"covidregionaldata 0.1.0","title":"covidregionaldata 0.1.0","text":"Added NEWS.md file track changes package. Added get_linelist function Added functions reparameterise Weibull Gamma distributions mean standard deviations.","code":""}]