Use [start,end) notation for age groups

Fix #15
Bisaloo · Nov 2, 2024 · 6b440f6 · 6b440f6
1 parent ab1cae6
commit 6b440f6
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Showing 24 changed files with 12 additions and 11 deletions.
diff --git a/data-raw/contact_matrices_2017.R b/data-raw/contact_matrices_2017.R
@@ -1,4 +1,6 @@
-owd <- setwd(tempdir())
+owd <- getwd()
+
+setwd(tempdir())
 
 fix_names <- function(name) {
 
@@ -49,7 +51,7 @@ for (l in locations) {
       skip = 1,
       .name_repair = "minimal"
     ))
-    rownames(df) <- colnames(df) <- sprintf("%02i_%02i", seq(0, 75, 5), seq(5, 80, 5))
+    rownames(df) <- colnames(df) <- sprintf("[%02i,%02i)", seq(0, 75, 5), seq(5, 80, 5))
     c <- fix_names(c)
     res[[c]] <- df
   }
@@ -60,7 +62,7 @@ for (l in locations) {
       sheet = c,
       .name_repair = "minimal"
     ))
-    rownames(df) <- colnames(df) <- sprintf("%02i_%02i", seq(0, 75, 5), seq(5, 80, 5))
+    rownames(df) <- colnames(df) <- sprintf("[%02i,%02i)", seq(0, 75, 5), seq(5, 80, 5))
     c <- fix_names(c)
     res[[c]] <- df
   }

diff --git a/data-raw/contact_matrices_2020.R b/data-raw/contact_matrices_2020.R
@@ -1,6 +1,5 @@
-owd <- setwd(tempdir())
-
-system("svn export https://github.com/kieshaprem/synthetic-contact-matrices/trunk/output/syntheticmatrices")
+# Download https://github.com/kieshaprem/synthetic-contact-matrices/tree/master/output/syntheticmatrices
+files <- unzip("syntheticmatrices.zip", exdir = "syntheticmatrices", unzip = "internal")
 
 library(fs)
 
@@ -28,13 +27,13 @@ for (i in seq_along(fichiers)) {
 
   res <- lapply(eval(parse(text = dataset)), function(df) {
 
-    rownames(df) <- colnames(df) <- sprintf("%02i_%02i", seq(0, 75, 5), seq(5, 80, 5))
+    rownames(df) <- colnames(df) <- sprintf("[%02i,%02i)", seq(0, 75, 5), seq(5, 80, 5))
     return(df)
 
   })
 
   names(res) <- countrycode::countrycode(names(res), origin = "iso3c", destination = "cldr.short.en")
 
-  saveRDS(res, paste0(owd, "/inst/extdata/", new_names_all[[i]]))
+  saveRDS(res, paste0("inst/extdata/", new_names_all[[i]]))
 
 }
diff --git a/data-raw/population.R b/data-raw/population.R
@@ -26,10 +26,10 @@ population_byage <- vroom::vroom(file.path("data-raw", "idb5yr.all")) %>%
   # we need to sum
   group_by(country) %>%
   summarise(across(everything(), sum)) %>%
-  rowwise() %>%
-  mutate("75+" = sum(`75_79`, `80_84`, `85_89`, `90_94`, `95_99`), .keep = "unused") %>%
   tidyr::pivot_longer(-country, names_to = "age", values_to = "population") %>%
-  mutate(age = gsub("^(\\d)_(\\d)$", "0\\1_0\\2", age)) %>%
+  tidyr::separate(age, into = c("age_start", "age_end"), sep = "_") %>%
+  dplyr::mutate(across(c(age_start, age_end), as.integer)) %>%
+  mutate(age = sprintf("[%02i,%02i)", age_start, age_end+1)) %>%
   arrange(country, age) %>%
   as.data.frame()
 

diff --git a/inst/extdata/contact_2017_all_all.rds b/inst/extdata/contact_2017_all_all.rds
diff --git a/inst/extdata/contact_2017_home_all.rds b/inst/extdata/contact_2017_home_all.rds
diff --git a/inst/extdata/contact_2017_other_all.rds b/inst/extdata/contact_2017_other_all.rds
diff --git a/inst/extdata/contact_2017_school_all.rds b/inst/extdata/contact_2017_school_all.rds
diff --git a/inst/extdata/contact_2017_work_all.rds b/inst/extdata/contact_2017_work_all.rds
diff --git a/inst/extdata/contact_2020_all_all.rds b/inst/extdata/contact_2020_all_all.rds
diff --git a/inst/extdata/contact_2020_all_rural.rds b/inst/extdata/contact_2020_all_rural.rds
diff --git a/inst/extdata/contact_2020_all_urban.rds b/inst/extdata/contact_2020_all_urban.rds
diff --git a/inst/extdata/contact_2020_home_all.rds b/inst/extdata/contact_2020_home_all.rds
diff --git a/inst/extdata/contact_2020_home_rural.rds b/inst/extdata/contact_2020_home_rural.rds
diff --git a/inst/extdata/contact_2020_home_urban.rds b/inst/extdata/contact_2020_home_urban.rds
diff --git a/inst/extdata/contact_2020_other_all.rds b/inst/extdata/contact_2020_other_all.rds
diff --git a/inst/extdata/contact_2020_other_rural.rds b/inst/extdata/contact_2020_other_rural.rds
diff --git a/inst/extdata/contact_2020_other_urban.rds b/inst/extdata/contact_2020_other_urban.rds
diff --git a/inst/extdata/contact_2020_school_all.rds b/inst/extdata/contact_2020_school_all.rds
diff --git a/inst/extdata/contact_2020_school_rural.rds b/inst/extdata/contact_2020_school_rural.rds
diff --git a/inst/extdata/contact_2020_school_urban.rds b/inst/extdata/contact_2020_school_urban.rds
diff --git a/inst/extdata/contact_2020_work_all.rds b/inst/extdata/contact_2020_work_all.rds
diff --git a/inst/extdata/contact_2020_work_rural.rds b/inst/extdata/contact_2020_work_rural.rds
diff --git a/inst/extdata/contact_2020_work_urban.rds b/inst/extdata/contact_2020_work_urban.rds
diff --git a/inst/extdata/population_byage.rds b/inst/extdata/population_byage.rds