BRA

R/ds_covid19br_git.R

@@ -0,0 +1,61 @@
+covid19br_git <- function(cache, level){
+
+  if(level<=2){
+
+    # download
+    url <- "https://raw.githubusercontent.com/wcota/covid19br/master/cases-brazil-states.csv"
+    x <- read.csv(url, cache = cache)
+
+    # formatting
+    x <- map_data(x, c(
+      "date" = "date",
+      "state" = "state",
+      "deaths" = "deaths",
+      "totalCases" = "confirmed",
+      "recovered" = "recovered",
+      "tests" = "tests",
+      "vaccinated" = "vaccines_1",
+      "vaccinated_second" = "vaccines_2"
+    ))
+
+    # total number of doses
+    x$vaccines <- x$vaccines_1 + x$vaccines_2
+
+    # filter
+    idx <- which(x$state=="TOTAL")
+    if(level==1)
+      x <- x[idx,]
+    else
+      x <- x[-idx,]
+
+  }
+  else {
+
+    # url
+    url <- "https://raw.githubusercontent.com/wcota/covid19br/master/cases-brazil-cities-time.csv.gz"
+
+    # download  
+    tmp <- tempfile()
+    download.file(url, destfile=tmp, mode="wb", quiet = TRUE)
+    x <- read.csv(tmp, cache = cache)
+
+    # formatting
+    x <- map_data(x, c(
+      "date" = "date",
+      "ibgeID" = "code",
+      "state" = "state",
+      "deaths" = "deaths",
+      "totalCases" = "confirmed"
+    ))
+
+    # filter cities
+    x <- x[nchar(x$code)==7,]
+
+  }
+
+  # date
+  x$date <- as.Date(x$date)
+
+  # return
+  return(x)
+}

R/ds_gov_br.R

@@ -0,0 +1,36 @@
+gov_br <- function(cache, level){
+
+  if(level!=3)
+    return(NULL)
+
+  # url
+  url <- "https://s3-sa-east-1.amazonaws.com/ckan.saude.gov.br/PNI/vacina/2021/part-00000-090405dc-80c4-4889-84c3-a9a390d06947-c000.csv"
+
+  # download
+  tmp <- tempfile()
+  download.file(url, tmp)
+
+  # read
+  colClasses <- rep("NULL", 32)
+  colClasses[8] <- "character"
+  colClasses[28] <- "Date"
+  x <- read.csv(tmp, colClasses = colClasses)
+
+  # clean 
+  file.remove(tmp)
+
+  # formatting
+  colnames(x) <- c("city", "date")
+
+  # cumulate
+  x <- x %>%
+    dplyr::filter(date > "2020-12-01") %>%
+    dplyr::group_by(city, date) %>%
+    dplyr::summarise(vaccines = dplyr::n()) %>%
+    dplyr::group_by(city) %>%
+    dplyr::arrange(date) %>%
+    dplyr::mutate(vaccines = cumsum(vaccines))
+
+  # return
+  return(x)
+}

R/iso_BRA.R

@@ -1,18 +1,29 @@
 BRA <- function(level, cache) {
 
-  # fallback
-  if(level < 2)
-    return(NULL)
+  x <- covid19br_git(level = level, cache = cache)
 
-  # download (Espirito Santo)
-  x <- gov_br_es(level = level, cache = cache)
+  if(level==2)
+    x$id <- id(x$state, iso = "BRA", ds = "covid19br_git", level = level)
 
-  # id
-  if(level == 2)
-    x$id <- id(x$State, iso = "BRA", ds = "gov_br_es", level = level)
-  if(level == 3)
-    x$id <- id(x$Municipio, iso = "BRA", ds = "gov_br_es", level = level)
+  if(level==3){  
 
+    # download Espirito Santo
+    y <- gov_br_es(level = level, cache = cache)
+    y$id <- id(y$Municipio, iso = "BRA", ds = "gov_br_es", level = level)
+
+    # vaccines
+    v <- gov_br(level = level, cache = cache)
+    v$id <- id(v$city, iso = "BRA", ds = "gov_br", level = level)
+
+    # merge
+    x$id <- id(x$code, iso = "BRA", ds = "covid19br_git", level = level)
+    x <- x %>%
+      dplyr::filter(state != "ES") %>%
+      dplyr::bind_rows(y) %>%
+      dplyr::left_join(v, by = c("id", "date"))
+
+  }
+
   # return
   return(x)