removed tabulzer dependent functions

thiyangt · Apr 22, 2023 · 98586c5 · 98586c5
1 parent 82eaa0a
commit 98586c5
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diff --git a/.DS_Store b/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: denguedatahub
 Title: A Tidy Format Datasets of Dengue by Country 
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: 
     person("Thiyanga S.", "Talagala", , "ttalagala@sjp.ac.lk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0656-9789"))
@@ -12,19 +12,10 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.1
 Imports: 
-    magrittr,
-    rvest,
-    stringr,
-    xml2,
     dplyr,
-    tabulizer,
-    purrr,
-    tibble,
-    tidyr,
     rlang (>= 0.4.11)
 Depends: 
     R (>= 3.5.0)
-SystemRequirements: Java (>= 7.0)
 LazyData: true
 Suggests: 
     roxygen2
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,20 +4,12 @@ export(":=")
 export(.data)
 export(as_label)
 export(as_name)
-export(convert_srilanka_wer_to_tidy)
 export(enquo)
 export(enquos)
-export(filter_year_wer)
-export(get_addresses)
 export(min_max)
-importFrom(dplyr,bind_rows)
-importFrom(dplyr,filter)
-importFrom(dplyr,select)
-importFrom(magrittr,"%>%")
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,as_label)
 importFrom(rlang,as_name)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
-importFrom(tabulizer,extract_tables)
diff --git a/R/convert_srilanka_wer_to_tidy.R b/R/convert_srilanka_wer_to_tidy.R
diff --git a/R/filter_year_wer_link.R b/R/filter_year_wer_link.R
diff --git a/R/get_address.R b/R/get_address.R
diff --git a/R/min_max.R b/R/min_max.R
@@ -11,7 +11,7 @@ min_max <- function(data, variable.to.minmax, local=FALSE, group.var){
 
     cases = as.name(variable.to.minmax)
 
-    data.tbl <- data %>% 
+    data.tbl <- data |> 
       dplyr::mutate(
         min.cases = min(!!enquo(cases)),
         max.cases = max(!!enquo(cases)),
@@ -23,7 +23,7 @@ min_max <- function(data, variable.to.minmax, local=FALSE, group.var){
     group_var <- as.name(group.var)
     cases = as.name(variable.to.minmax)
 
-    data.tbl <- data %>% dplyr::group_by(!!enquo(group_var)) %>% 
+    data.tbl <- data |> dplyr::group_by(!!enquo(group_var)) |>
       dplyr::mutate(
         min.group = min(!!enquo(cases)),
         max.group = max(!!enquo(cases)),

diff --git a/README.Rmd b/README.Rmd
@@ -44,20 +44,11 @@ head(level_of_risk)
 ## Sri Lanka Weekly Dengue Cases
 
 ```{r}
-head(srilanka_weekly_data)
+srilanka_weekly_data
 ```
 
-## Obtain dengue data from weekly epidemiological reports published by [Epidemiology Unit, Ministry of Health, Sri Lanka](https://www.epid.gov.lk/web/index.php?option=com_content&view=article&id=148&Itemid=449&lang=en)
-
-```{r, warning=FALSE, message=FALSE}
-ad.list <- get_addresses("http://www.epid.gov.lk/web/index.php?option=com_content&view=article&id=148&Itemid=449&lang=en")
-wer2023url <- filter_year_wer(2023, ad.list[1:9])
-data2023 <- convert_srilanka_wer_to_tidy(year=2023, url.part2=wer2023url, 
-start.date.first = "2022-12-31",
-end.date.first = "2023-01-06",
-start.date.last = "2023-01-28", 
-end.date.last = "2023-02-03",
-week.no=c(52, 1:4))
-data2023
-```
+## World
 
+```{r}
+world_annual
+```
diff --git a/README.md b/README.md
@@ -45,42 +45,39 @@ head(level_of_risk)
 ## Sri Lanka Weekly Dengue Cases
 
 ``` r
-head(srilanka_weekly_data)
-#> # A tibble: 6 × 6
-#>    year  week start.date end.date   district    cases
-#>   <dbl> <dbl> <date>     <date>     <chr>       <dbl>
-#> 1  2006    52 2006-12-23 2006-12-29 Colombo        71
-#> 2  2006    52 2006-12-23 2006-12-29 Gampaha        12
-#> 3  2006    52 2006-12-23 2006-12-29 Kalutara       12
-#> 4  2006    52 2006-12-23 2006-12-29 Kandy          20
-#> 5  2006    52 2006-12-23 2006-12-29 Matale          4
-#> 6  2006    52 2006-12-23 2006-12-29 NuwaraEliya     1
+srilanka_weekly_data
+#> # A tibble: 21,960 × 6
+#>     year  week start.date end.date   district    cases
+#>    <dbl> <dbl> <date>     <date>     <chr>       <dbl>
+#>  1  2006    52 2006-12-23 2006-12-29 Colombo        71
+#>  2  2006    52 2006-12-23 2006-12-29 Gampaha        12
+#>  3  2006    52 2006-12-23 2006-12-29 Kalutara       12
+#>  4  2006    52 2006-12-23 2006-12-29 Kandy          20
+#>  5  2006    52 2006-12-23 2006-12-29 Matale          4
+#>  6  2006    52 2006-12-23 2006-12-29 NuwaraEliya     1
+#>  7  2006    52 2006-12-23 2006-12-29 Galle           1
+#>  8  2006    52 2006-12-23 2006-12-29 Hambanthota     1
+#>  9  2006    52 2006-12-23 2006-12-29 Matara         11
+#> 10  2006    52 2006-12-23 2006-12-29 Jaffna          0
+#> # ℹ 21,950 more rows
 ```
 
-## Obtain dengue data from weekly epidemiological reports published by [Epidemiology Unit, Ministry of Health, Sri Lanka](https://www.epid.gov.lk/web/index.php?option=com_content&view=article&id=148&Itemid=449&lang=en)
+## World
 
 ``` r
-ad.list <- get_addresses("http://www.epid.gov.lk/web/index.php?option=com_content&view=article&id=148&Itemid=449&lang=en")
-wer2023url <- filter_year_wer(2023, ad.list[1:9])
-data2023 <- convert_srilanka_wer_to_tidy(year=2023, url.part2=wer2023url, 
-start.date.first = "2022-12-31",
-end.date.first = "2023-01-06",
-start.date.last = "2023-01-28", 
-end.date.last = "2023-02-03",
-week.no=c(52, 1:4))
-data2023
-#> # A tibble: 130 × 6
-#>     year  week start.date end.date   district    cases
-#>    <dbl> <dbl> <date>     <date>     <chr>       <dbl>
-#>  1  2023    52 2022-12-31 2023-01-06 Colombo        25
-#>  2  2023    52 2022-12-31 2023-01-06 Gampaha        23
-#>  3  2023    52 2022-12-31 2023-01-06 Kalutara       74
-#>  4  2023    52 2022-12-31 2023-01-06 Kandy          50
-#>  5  2023    52 2022-12-31 2023-01-06 Matale         25
-#>  6  2023    52 2022-12-31 2023-01-06 NuwaraEliya     3
-#>  7  2023    52 2022-12-31 2023-01-06 Galle          28
-#>  8  2023    52 2022-12-31 2023-01-06 Hambantota     13
-#>  9  2023    52 2022-12-31 2023-01-06 Matara         22
-#> 10  2023    52 2022-12-31 2023-01-06 Jaffna         12
-#> # ℹ 120 more rows
+world_annual
+#> # A tibble: 6,750 × 4
+#>    entity      code   year incidence
+#>    <chr>       <chr> <dbl>     <dbl>
+#>  1 Afghanistan AFG    1990     23371
+#>  2 Afghanistan AFG    1991     25794
+#>  3 Afghanistan AFG    1992     29766
+#>  4 Afghanistan AFG    1993     32711
+#>  5 Afghanistan AFG    1994     34268
+#>  6 Afghanistan AFG    1995     35823
+#>  7 Afghanistan AFG    1996     37397
+#>  8 Afghanistan AFG    1997     38862
+#>  9 Afghanistan AFG    1998     39660
+#> 10 Afghanistan AFG    1999     39987
+#> # ℹ 6,740 more rows
 ```
diff --git a/data-raw/.DS_Store b/data-raw/.DS_Store
diff --git a/man/convert_srilanka_wer_to_tidy.Rd b/man/convert_srilanka_wer_to_tidy.Rd
diff --git a/man/filter_year_wer.Rd b/man/filter_year_wer.Rd