diff --git a/DESCRIPTION b/DESCRIPTION index 7af5354..583a3b1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,5 +28,6 @@ Remotes: cmu-delphi/epiprocess Encoding: UTF-8 LazyData: true +Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.1 URL: https://cmu-delphi.github.io/epidatasets/ diff --git a/R/epipredict-data.R b/R/epipredict-data.R index 0663fb1..f9ff36c 100644 --- a/R/epipredict-data.R +++ b/R/epipredict-data.R @@ -73,7 +73,7 @@ #' reported #' by JHU-CSSE and downloaded from the CMU Delphi COVIDcast Epidata API. #' This data set covers the period from June 2021 to December 2021, and is -#' used in the [epipredict] Vignette on ... . +#' used in the epipredict Vignette on ... . #' #' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the #' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} @@ -94,7 +94,7 @@ #' which also reports vaccine-related signals. #' #' This dataset contains versioned data covering the period from April 2020 to -#' December 2021 and is used in the [epipredict] slide vignette. +#' December 2021 and is used in the epipredict slide vignette. #' #' @source This object contains a modified part of the COVID-19 Canada Open #' Data Working Group's diff --git a/R/epiprocess-data.R b/R/epiprocess-data.R index cf1b0d7..e0bf6ef 100644 --- a/R/epiprocess-data.R +++ b/R/epiprocess-data.R @@ -129,7 +129,7 @@ #' Data set for 2 states containing COVID-19 Incident Cases as reported #' by JHU-CSSE and Downloaded from the CMU Delphi COVIDcast Epidata API. #' This data set covers the period from June 2020 to May 2021, and is -#' used in the [epiprocess] Vignette on Outliers. +#' used in the epiprocess Vignette on Outliers. #' #' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the #' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} @@ -142,7 +142,7 @@ #' Data set for 4 states containing COVID-19 Cumulative Cases as reported #' by JHU-CSSE and downloaded from the CMU Delphi COVIDcast Epidata API. #' This data set covers the period from March 2020 to January 2022, and is -#' used in the [epiprocess] Vignette on ... . +#' used in the epiprocess Vignette on ... . #' #' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the #' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} diff --git a/man/archive_cases_dv_subset_dt.Rd b/man/archive_cases_dv_subset_dt.Rd index 7fb4cb5..50db359 100644 --- a/man/archive_cases_dv_subset_dt.Rd +++ b/man/archive_cases_dv_subset_dt.Rd @@ -5,13 +5,13 @@ \alias{archive_cases_dv_subset_dt} \title{Subset of daily doctor visits and cases in archive format} \format{ -An `epi_archive$DT` data format. The data table DT has 129,638 rows and 5 columns: +An \code{epi_archive$DT} data format. The data table DT has 129,638 rows and 5 columns: \describe{ - \item{geo_value}{the geographic value associated with each row of measurements.} - \item{time_value}{the time value associated with each row of measurements.} - \item{version}{the time value specifying the version for each row of measurements. } - \item{percent_cli}{percentage of doctor’s visits with CLI (COVID-like illness) computed from medical insurance claims} - \item{case_rate_7d_av}{7-day average signal of number of new confirmed deaths due to COVID-19 per 100,000 population, daily} +\item{geo_value}{the geographic value associated with each row of measurements.} +\item{time_value}{the time value associated with each row of measurements.} +\item{version}{the time value specifying the version for each row of measurements. } +\item{percent_cli}{percentage of doctor’s visits with CLI (COVID-like illness) computed from medical insurance claims} +\item{case_rate_7d_av}{7-day average signal of number of new confirmed deaths due to COVID-19 per 100,000 population, daily} } } \source{ @@ -21,9 +21,11 @@ by Johns Hopkins University on behalf of its Center for Systems Science in Engin Copyright Johns Hopkins University 2020. Modifications: -* \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html}{From the COVIDcast Doctor Visits API}: The signal `percent_cli` is taken directly from the API without changes. -* \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: `case_rate_7d_av` signal was computed by Delphi from the original JHU-CSSE data by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive. -* Furthermore, the data is a subset of the full dataset, the signal names slightly altered, and formatted into a tibble. +\itemize{ +\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html}{From the COVIDcast Doctor Visits API}: The signal \code{percent_cli} is taken directly from the API without changes. +\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: \code{case_rate_7d_av} signal was computed by Delphi from the original JHU-CSSE data by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive. +\item Furthermore, the data is a subset of the full dataset, the signal names slightly altered, and formatted into a tibble. +} } \usage{ archive_cases_dv_subset_dt diff --git a/man/can_prov_cases.Rd b/man/can_prov_cases.Rd index c3e5cd7..7385654 100644 --- a/man/can_prov_cases.Rd +++ b/man/can_prov_cases.Rd @@ -31,6 +31,6 @@ which also reports vaccine-related signals. } \details{ This dataset contains versioned data covering the period from April 2020 to -December 2021 and is used in the [epipredict] slide vignette. +December 2021 and is used in the epipredict slide vignette. } \keyword{datasets} diff --git a/man/cases_deaths_subset.Rd b/man/cases_deaths_subset.Rd index b272891..c29fe64 100644 --- a/man/cases_deaths_subset.Rd +++ b/man/cases_deaths_subset.Rd @@ -7,37 +7,39 @@ \format{ A tibble with 4026 rows and 6 variables: \describe{ - \item{geo_value}{the geographic value associated with each row - of measurements.} - \item{time_value}{the time value associated with each row of measurements.} - \item{case_rate_7d_av}{7-day average signal of number of new - confirmed COVID-19 cases per 100,000 population, daily} - \item{death_rate_7d_av}{7-day average signal of number of new confirmed - deaths due to COVID-19 per 100,000 population, daily} - \item{cases}{Number of new confirmed COVID-19 cases, daily} - \item{cases_7d_av}{7-day average signal of number of new confirmed - COVID-19 cases, daily} +\item{geo_value}{the geographic value associated with each row +of measurements.} +\item{time_value}{the time value associated with each row of measurements.} +\item{case_rate_7d_av}{7-day average signal of number of new +confirmed COVID-19 cases per 100,000 population, daily} +\item{death_rate_7d_av}{7-day average signal of number of new confirmed +deaths due to COVID-19 per 100,000 population, daily} +\item{cases}{Number of new confirmed COVID-19 cases, daily} +\item{cases_7d_av}{7-day average signal of number of new confirmed +COVID-19 cases, daily} } } \source{ This object contains a modified part of the - \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} - as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. - This data set is licensed under the terms of the - \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} - by the Johns Hopkins University on behalf of its Center for Systems Science - in Engineering. Copyright Johns Hopkins University 2020. +\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} +as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. +This data set is licensed under the terms of the +\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} +by the Johns Hopkins University on behalf of its Center for Systems Science +in Engineering. Copyright Johns Hopkins University 2020. Modifications: -* \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: - These signals are taken directly from the JHU CSSE - \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} - without changes. The 7-day average signals are computed by Delphi by - calculating moving averages of the preceding 7 days, so the signal for - June 7 is the average of the underlying data for June 1 through 7, - inclusive. -* Furthermore, the data has been limited to a very small number of rows, - the signal names slightly altered, and formatted into a tibble. +\itemize{ +\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: +These signals are taken directly from the JHU CSSE +\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} +without changes. The 7-day average signals are computed by Delphi by +calculating moving averages of the preceding 7 days, so the signal for +June 7 is the average of the underlying data for June 1 through 7, +inclusive. +\item Furthermore, the data has been limited to a very small number of rows, +the signal names slightly altered, and formatted into a tibble. +} } \usage{ cases_deaths_subset diff --git a/man/counts_subset.Rd b/man/counts_subset.Rd index bff6bca..c2e2b1d 100644 --- a/man/counts_subset.Rd +++ b/man/counts_subset.Rd @@ -21,6 +21,6 @@ Data set for 5 states containing COVID-19 Incident Cases and Deaths as reported by JHU-CSSE and downloaded from the CMU Delphi COVIDcast Epidata API. This data set covers the period from June 2021 to December 2021, and is -used in the [epipredict] Vignette on ... . +used in the epipredict Vignette on ... . } \keyword{datasets} diff --git a/man/covid_case_death_rates.Rd b/man/covid_case_death_rates.Rd index 3a2a90f..dd5b9dd 100644 --- a/man/covid_case_death_rates.Rd +++ b/man/covid_case_death_rates.Rd @@ -7,32 +7,34 @@ \format{ A tibble with 20,496 rows and 4 variables: \describe{ - \item{geo_value}{the geographic value associated with each row - of measurements.} - \item{time_value}{the time value associated with each row of measurements.} - \item{case_rate}{7-day average signal of number of new - confirmed COVID-19 cases per 100,000 population, daily} - \item{death_rate}{7-day average signal of number of new confirmed - deaths due to COVID-19 per 100,000 population, daily} +\item{geo_value}{the geographic value associated with each row +of measurements.} +\item{time_value}{the time value associated with each row of measurements.} +\item{case_rate}{7-day average signal of number of new +confirmed COVID-19 cases per 100,000 population, daily} +\item{death_rate}{7-day average signal of number of new confirmed +deaths due to COVID-19 per 100,000 population, daily} } } \source{ This object contains a modified part of the - \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} - as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. - This data set is licensed under the terms of the - \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} - by the Johns Hopkins University on behalf of its Center for Systems Science - in Engineering. Copyright Johns Hopkins University 2020. +\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} +as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. +This data set is licensed under the terms of the +\href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} +by the Johns Hopkins University on behalf of its Center for Systems Science +in Engineering. Copyright Johns Hopkins University 2020. Modifications: -* \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: - These signals are taken directly from the JHU CSSE - \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} - without changes. The 7-day average signals are computed by Delphi by - calculating moving averages of the preceding 7 days, so the signal for - June 7 is the average of the underlying data for June 1 through 7, - inclusive. +\itemize{ +\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: +These signals are taken directly from the JHU CSSE +\href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} +without changes. The 7-day average signals are computed by Delphi by +calculating moving averages of the preceding 7 days, so the signal for +June 7 is the average of the underlying data for June 1 through 7, +inclusive. +} } \usage{ covid_case_death_rates diff --git a/man/covid_incidence_county_subset.Rd b/man/covid_incidence_county_subset.Rd index 0f5786e..b0d328c 100644 --- a/man/covid_incidence_county_subset.Rd +++ b/man/covid_incidence_county_subset.Rd @@ -7,11 +7,11 @@ \format{ A tibble with 16,212 rows and 5 variables: \describe{ - \item{geo_value}{the geographic value associated with each row of measurements.} - \item{time_value}{the time value associated with each row of measurements.} - \item{cases}{Number of new confirmed COVID-19 cases, daily} - \item{county_name}{the name of the county} - \item{state_name}{the full name of the state} +\item{geo_value}{the geographic value associated with each row of measurements.} +\item{time_value}{the time value associated with each row of measurements.} +\item{cases}{Number of new confirmed COVID-19 cases, daily} +\item{county_name}{the name of the county} +\item{state_name}{the full name of the state} } } \source{ @@ -21,8 +21,10 @@ by the Johns Hopkins University on behalf of its Center for Systems Science in E Copyright Johns Hopkins University 2020. Modifications: -* \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: These signals are taken directly from the JHU CSSE \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} without changes. The 7-day average signals are computed by Delphi by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive. -* Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble. +\itemize{ +\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: These signals are taken directly from the JHU CSSE \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} without changes. The 7-day average signals are computed by Delphi by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive. +\item Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble. +} } \usage{ covid_incidence_county_subset diff --git a/man/covid_incidence_outliers.Rd b/man/covid_incidence_outliers.Rd index 180434a..42394cb 100644 --- a/man/covid_incidence_outliers.Rd +++ b/man/covid_incidence_outliers.Rd @@ -7,9 +7,9 @@ \format{ A tibble with 730 rows and 3 variables: \describe{ - \item{geo_value}{the geographic value associated with each row of measurements.} - \item{time_value}{the time value associated with each row of measurements.} - \item{cases}{Number of new confirmed COVID-19 cases, daily} +\item{geo_value}{the geographic value associated with each row of measurements.} +\item{time_value}{the time value associated with each row of measurements.} +\item{cases}{Number of new confirmed COVID-19 cases, daily} } An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 730 rows and 3 columns. @@ -21,9 +21,11 @@ by the Johns Hopkins University on behalf of its Center for Systems Science in E Copyright Johns Hopkins University 2020. Modifications: -* \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: +\itemize{ +\item \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: These signals are taken directly from the JHU CSSE \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} without changes. -* Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble. +\item Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble. +} This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} @@ -46,6 +48,6 @@ and is limited to California and Florida. Data set for 2 states containing COVID-19 Incident Cases as reported by JHU-CSSE and Downloaded from the CMU Delphi COVIDcast Epidata API. This data set covers the period from June 2020 to May 2021, and is -used in the [epiprocess] Vignette on Outliers. +used in the epiprocess Vignette on Outliers. } \keyword{datasets} diff --git a/man/jhu_confirmed_cumulative_num.Rd b/man/jhu_confirmed_cumulative_num.Rd index d7b08c6..7375331 100644 --- a/man/jhu_confirmed_cumulative_num.Rd +++ b/man/jhu_confirmed_cumulative_num.Rd @@ -20,6 +20,6 @@ jhu_confirmed_cumulative_num Data set for 4 states containing COVID-19 Cumulative Cases as reported by JHU-CSSE and downloaded from the CMU Delphi COVIDcast Epidata API. This data set covers the period from March 2020 to January 2022, and is -used in the [epiprocess] Vignette on ... . +used in the epiprocess Vignette on ... . } \keyword{datasets} diff --git a/man/state_census.Rd b/man/state_census.Rd index 1a773bb..fa840fb 100644 --- a/man/state_census.Rd +++ b/man/state_census.Rd @@ -6,23 +6,23 @@ \title{State population data} \format{ Data frame with 57 rows (including one for the United States as a - whole, plus the District of Columbia, Puerto Rico Commonwealth, - American Samoa, Guam, the U.S. Virgin Islands, and the Northern Mariana, - Islands). +whole, plus the District of Columbia, Puerto Rico Commonwealth, +American Samoa, Guam, the U.S. Virgin Islands, and the Northern Mariana, +Islands). \describe{ - \item{fips}{FIPS code} - \item{name}{Full name of the state or territory} - \item{pop}{Estimate of the location's resident population in - 2019.} - \item{abbr}{Postal abbreviation for the location} +\item{fips}{FIPS code} +\item{name}{Full name of the state or territory} +\item{pop}{Estimate of the location's resident population in +2019.} +\item{abbr}{Postal abbreviation for the location} } } \source{ United States Census Bureau, at - \url{https://www2.census.gov/programs-surveys/popest/datasets/2010-2019/counties/totals/co-est2019-alldata.pdf}, - \url{https://www.census.gov/data/tables/time-series/demo/popest/2010s-total-puerto-rico-municipios.html}, - and \url{https://www.census.gov/data/tables/2010/dec/2010-island-areas.html} +\url{https://www2.census.gov/programs-surveys/popest/datasets/2010-2019/counties/totals/co-est2019-alldata.pdf}, +\url{https://www.census.gov/data/tables/time-series/demo/popest/2010s-total-puerto-rico-municipios.html}, +and \url{https://www.census.gov/data/tables/2010/dec/2010-island-areas.html} } \usage{ state_census