Fetch Google's global mobility report

.gitignore

@@ -67,6 +67,10 @@ Brazil/figures/*.pdf
 Brazil/figures/*.txt
 Brazil/results/*.RDS
 
+# No data files
+data/*.csv
+Brazil/data/*.csv
+Italy/data/*.csv
 
 
 # Python

Brazil/code/preprocessing-subnation-brazil.r

@@ -25,7 +25,7 @@ df=df[order(as.Date(df$DateRep, format="%Y-%m-%d")),]
 write_csv(df,"Brazil/data/df-Brazil.csv")
 
 #### Adding google mobility data
-mobility.aux = read.csv(paste0(path,"/Global-Mobility-Report.csv"))
+mobility.aux = read.csv("data/Global_Mobility_Report.csv"))
 mobility.aux2 = subset(mobility.aux,mobility.aux$country_region=="Brazil")
 mobility.aux2 = mobility.aux2[which(mobility.aux2$sub_region_1!=""),]
 
@@ -222,4 +222,4 @@ process_data <- function(countries,N2,d){
 
   return(list("stan_data" = stan_data, "dates" = dates, "reported_cases"=reported_cases, "deaths_by_country" = deaths_by_country))
 
-}
+}

Italy/code/utils/read-data-subnational.r

@@ -97,7 +97,7 @@ read_ifr_data <- function(regions){
 }
 
 read_google_mobility <- function(Country){
-  google_mobility <- read.csv('Italy/data/Global_Mobility_Report.csv', stringsAsFactors = FALSE)
+  google_mobility <- read.csv('data/Global_Mobility_Report.csv', stringsAsFactors = FALSE)
   google_mobility$date = as.Date(google_mobility$date, format = '%Y-%m-%d')
   google_mobility[, c(6,7,8,9,10,11)] <- google_mobility[, c(6,7,8,9,10,11)]/100
   google_mobility[, c(6,7,8,9,10)] <- google_mobility[, c(6,7,8,9,10)] * -1

data/fetch-ecdc.r → data/fetch-data.r

@@ -31,3 +31,19 @@ names(d)[names(d) == "deaths"] <- "Deaths"
 names(d)[names(d) == "cases"] <- "Cases"
 names(d)[names(d) == "dateRep"] <- "DateRep"
 saveRDS(d, "data/COVID-19-up-to-date.rds")
+
+# Download Google's mobility report
+url <- "https://www.gstatic.com/covid19/mobility/Global_Mobility_Report.csv"
+url_page <- "https://www.google.com/covid19/mobility/"
+tryCatch({
+  r <- RETRY("GET", url, 
+             write_disk("data/Global_Mobility_Report.csv", overwrite=TRUE))
+
+  if (http_error(r)) {
+    stop("Error downloading file")
+  }
+},
+error = function(e) {
+  stop(sprintf("Error downloading file '%s': %s, please check %s",
+               url, e$message, url_page))
+})

web-fetch-and-run.r

@@ -1,5 +1,5 @@
 # print("Fetching data from ECDC")
-# fetch_ecdc_error <- system("Rscript data/fetch-ecdc.r",intern=FALSE)
+# fetch_ecdc_error <- system("Rscript data/fetch-data.r",intern=FALSE)
 # if(fetch_ecdc_error != 0){
 #   stop(sprintf("Error while fetching data from the ECDC! Code: %d", fetch_ecdc_error))
 # }