Update JPN

R/ds_github.lisphilar.covid19sir.R

@@ -0,0 +1,83 @@
+#' Hirokazu Takaya
+#'
+#' Data source for: Japan
+#'
+#' @param level 1, 2
+#'
+#' @section Level 1:
+#' - confirmed cases
+#' - deaths
+#' - recovered
+#' - tests
+#' - total vaccine doses administered
+#' - people with at least one vaccine dose
+#' - people fully vaccinated
+#' - hospitalizations
+#' - intensive care
+#'
+#' @section Level 2:
+#' - confirmed cases
+#' - deaths
+#' - recovered
+#' - tests
+#' - hospitalizations
+#' - intensive care
+#'
+#' @source https://github.com/lisphilar/covid19-sir
+#'
+#' @keywords internal
+#'
+github.lisphilar.covid19sir <- function(level) {
+  if(!level %in% 1:2) return(NULL)
+
+  if(level==1){  
+
+    url <- "https://raw.githubusercontent.com/lisphilar/covid19-sir/main/data/japan/covid_jpn_total.csv"
+    x <- read.csv(url, na.strings = c("0", "NA"))
+
+    x <- x[x$Location=="Domestic",]
+    x <- map_data(x, c(
+      "Date" = "date",
+      "Positive" = "confirmed",
+      "Tested" = "tests",
+      "Discharged" = "recovered",
+      "Hosp_require" = "hosp",
+      "Hosp_severe" = "icu",
+      "Fatal" = "deaths",
+      "Vaccinated_1st" = "people_vaccinated",
+      "Vaccinated_2nd" = "people_fully_vaccinated",
+      "Vaccinated_3rd" = "vaccines_3",
+      "Vaccinated_4th" = "vaccines_4",
+      "Vaccinated_5th" = "vaccines_5"
+    ))
+
+    x$vaccines <- x$people_vaccinated + 
+      tidyr::replace_na(x$people_fully_vaccinated, 0) + 
+      tidyr::replace_na(x$vaccines_3, 0) + 
+      tidyr::replace_na(x$vaccines_4, 0) + 
+      tidyr::replace_na(x$vaccines_5, 0)
+
+  }
+
+  if(level==2){
+
+    url <- "https://raw.githubusercontent.com/lisphilar/covid19-sir/main/data/japan/covid_jpn_prefecture.csv"
+    x <- read.csv(url, na.strings = c("0", "NA"))
+
+    x <- map_data(x, c(
+      "Date" = "date",
+      "Prefecture" = "prefecture",
+      "Positive" = "confirmed",
+      "Tested" = "tests",
+      "Discharged" = "recovered",
+      "Hosp_require" = "hosp",
+      "Hosp_severe" = "icu",
+      "Fatal" = "deaths"
+    ))
+
+  }
+
+  x$date <- as.Date(x$date)
+
+  return(x)
+}

R/iso_JPN.R

@@ -13,26 +13,18 @@ JPN <- function(level){
   #' 
   if(level==1){
 
-    #' - \href{`r repo("toyokeizai.net")`}{Toyo Keizai}:
+    #' - \href{`r repo("github.lisphilar.covid19sir")`}{Hirokazu Takaya}:
     #' confirmed cases,
     #' deaths,
     #' recovered,
     #' tests,
-    #' hospitalizations,
-    #' intensive care.
-    #'
-    x1 <- toyokeizai.net(level = level)
-
-    #' - \href{`r repo("ourworldindata.org")`}{Our World in Data}:
     #' total vaccine doses administered,
     #' people with at least one vaccine dose,
-    #' people fully vaccinated.
+    #' people fully vaccinated,
+    #' hospitalizations,
+    #' intensive care.
     #'
-    x2 <- ourworldindata.org(id = "JPN") %>%
-      select(-c("tests", "hosp", "icu"))
-
-    # merge
-    x <- full_join(x1, x2, by = "date")
+    x <- github.lisphilar.covid19sir(level = level)
 
   }
 
@@ -44,16 +36,16 @@ JPN <- function(level){
   #' 
   if(level==2){
 
-    #' - \href{`r repo("toyokeizai.net")`}{Toyo Keizai}:
+    #' - \href{`r repo("github.lisphilar.covid19sir")`}{Hirokazu Takaya}:
     #' confirmed cases,
     #' deaths,
     #' recovered,
     #' tests,
     #' hospitalizations,
     #' intensive care.
     #'
-    x <- toyokeizai.net(level = level)
-    x$id <- id(x$prefecture, iso = "JPN", ds = "toyokeizai.net", level = level)
+    x <- github.lisphilar.covid19sir(level = level)
+    x$id <- id(x$prefecture, iso = "JPN", ds = "github.lisphilar.covid19sir", level = level)
 
   }