scripts for TB done. No issues with data imports. Excludes R4DS textbook

Author: weste

data_scripts/tuberculosis/budget.R

@@ -0,0 +1,12 @@
+library(tidyverse)
+
+
+tb_budget <- read_csv("https://extranet.who.int/tme/generateCSV.asp?ds=budget")
+
+# Data details
+dpr_document(tb_budget, extension = ".md.R", export_folder = usethis::proj_get(),
+             object_name = "tb_budget", 
+             title = "Word Health Organization (WHO) Tuberculosis budgets by country",
+             description = "See source for description of the data. tb_dictionary describes the column names.",
+             source = "https://www.who.int/tb/country/data/download/en/",
+             var_details = list(nothing = "nothing"))

data_scripts/tuberculosis/cases.R

@@ -0,0 +1,50 @@
+library(tidyverse)
+
+
+tb_cases <- read_csv("https://extranet.who.int/tme/generateCSV.asp?ds=notifications")
+
+# Wrangling
+cases_clean <- tb_cases %>%
+  select(-(new_sp:c_newinc), 
+         -contains('_fu'), -contains('_mu'), -contains('_sexunk'), 
+         -contains('gesex'), -contains('15plus'), -contains('014'),
+         -(rdx_data_available:hiv_reg_new2)) %>%
+  pivot_longer(
+    cols = new_sp_m04:newrel_f65, 
+    names_to = "key", 
+    values_to = "cases", 
+    values_drop_na = TRUE
+  ) %>% 
+  mutate(
+    key = stringr::str_replace(key, "newrel", "new_rel")
+  ) %>%
+  separate(key, c("new", "var", "sexage")) %>% 
+  select(-new, -iso2, -iso3, -iso_numeric) %>% 
+  separate(sexage, c("sex", "age"), sep = 1) %>%
+  mutate(
+    age_middle = case_when(
+      age == '04' ~ 2,
+      age == '514' ~ 9,
+      age == '1524' ~ 19,
+      age == '2534' ~ 29,
+      age == '3544' ~ 39,
+      age == '4554' ~ 49,
+      age == '5564' ~ 59,
+      age == '65' ~ 75),
+    var = case_when(
+      var == 'sp' ~ 'smear positive',
+      var == 'sn' ~ 'smear negative',
+      var == 'rel' ~ 'relapse',
+      var == 'ep' ~ 'extrapulmonary'
+    )) %>%
+  select(country, g_whoregion, year, sex, age, age_middle, var, cases)
+
+
+
+# Data details
+dpr_document(tb_cases, extension = ".md.R", export_folder = usethis::proj_get(),
+             object_name = "tb_cases", 
+             title = "Word Health Organization (WHO) Tuberculosis case notifications by country",
+             description = "See source for description of the data. tb_dictionary describes the column names.",
+             source = "https://www.who.int/tb/country/data/download/en/",
+             var_details = list(nothing = "nothing"))

data_scripts/tuberculosis/dictionary.R

@@ -0,0 +1,12 @@
+library(tidyverse)
+
+
+tb_dictionary <- read_csv("https://extranet.who.int/tme/generateCSV.asp?ds=dictionary")
+
+# Data details
+dpr_document(tb_dictionary, extension = ".md.R", export_folder = usethis::proj_get(),
+             object_name = "tb_dictionary", 
+             title = "Word Health Organization (WHO) Tuberculosis csv file column names",
+             description = "File found at https://extranet.who.int/tme/generateCSV.asp?ds=dictionary",
+             source = "https://www.who.int/tb/country/data/download/en/",
+             var_details = list(nothing = "nothing"))

data_scripts/tuberculosis/estimates.R

@@ -0,0 +1,13 @@
+library(tidyverse)
+
+
+tb_estimates <- read_csv("https://extranet.who.int/tme/generateCSV.asp?ds=estimates")
+
+# Data details
+dpr_document(tb_estimates, extension = ".md.R", export_folder = usethis::proj_get(),
+             object_name = "tb_estimates", 
+             title = "Word Health Organization (WHO) Tuberculosis csv file column names",
+             description = "File found at https://extranet.who.int/tme/generateCSV.asp?ds=dictionary",
+             source = "https://www.who.int/tb/country/data/download/en/",
+             var_details = list(nothing = "nothing"))
+

data_scripts/tuberculosis/outcomes.R

@@ -0,0 +1,13 @@
+library(tidyverse)
+
+
+tb_outcomes <- read_csv("https://extranet.who.int/tme/generateCSV.asp?ds=outcomes")
+
+# Data details
+dpr_document(tb_outcomes, extension = ".md.R", export_folder = usethis::proj_get(),
+             object_name = "tb_outcomes", 
+             title = "Word Health Organization (WHO) Tuberculosis treatment outcomes by country",
+             description = "See source for description of the data. tb_dictionary describes the column names.",
+             source = "https://www.who.int/tb/country/data/download/en/",
+             var_details = list(nothing = "nothing"))
+

data_scripts/tuberculosis/utilization.R

@@ -0,0 +1,12 @@
+library(tidyverse)
+
+
+tb_utilization <- read_csv("https://extranet.who.int/tme/generateCSV.asp?ds=expenditure_utilisation")
+
+# Data details
+dpr_document(tb_utilization, extension = ".md.R", export_folder = usethis::proj_get(),
+             object_name = "tb_utilization", 
+             title = "Word Health Organization (WHO) Tuberculosis expenditures and utilization by country",
+             description = "See source for description of the data. tb_dictionary describes the column names.",
+             source = "https://www.who.int/tb/country/data/download/en/",
+             var_details = list(nothing = "nothing"))