fix merge

base.r

@@ -271,5 +271,3 @@ verify_result <- system(paste0("Rscript web-verify-output.r ", filename,'.Rdata'
 if(verify_result != 0){
   stop("Verification of web output failed!")
 }
-system("Rscript web-fix-fonts.r")
-

covariate-size-effects.r

@@ -41,7 +41,9 @@ x_lim[2] <- x_lim[2] + 0.05 * x_range
 layer_vertical_line <- if (0 > x_lim[1] && 0 < x_lim[2]) {
   vline_0(color = "gray90", size = 0.5)
 } else {
-  geom_ignore()
+  geom_blank(
+    mapping = NULL, data = NULL,
+    show.legend = FALSE, inherit.aes = FALSE)
 }
 args_outer <- list(mapping = aes_(x = ~ll, xend = ~hh, y = ~parameter, 
                                   yend = ~parameter)) #, color = bayesplot::get_color("mid"))

plot-3-panel.r

@@ -47,7 +47,11 @@ make_three_pannel_plot <- function(){
   
   all_data <- data.frame()
   intervention_data <- data.frame()
+<<<<<<< HEAD
   for(i in 1:14){
+=======
+  for(i in 1:length(countries)){
+>>>>>>> eaef0e1a56c534abf7e89b8ca7aa6c21841b9f57
     print(i)
     N <- length(dates[[i]])
     country <- countries[[i]]

plot-forecast.r

@@ -22,7 +22,7 @@ make_forecast_plot <- function(){
   
   load(paste0("results/", filename))
   
-  for(i in 1:14){
+  for(i in 1:length(countries)){
     N <- length(dates[[i]])
     N2 <- N + 7
     country <- countries[[i]]

web-fetch-and-run.r

@@ -0,0 +1,2 @@
+system("Rscript data/fetch-ecdc.r")
+system("Rscript base.r base")

web-fix-fonts.r

@@ -1,10 +0,0 @@
-filenames <- list.files("web/figures/", recursive = TRUE, full.names=TRUE)
-
-for( f in filenames ){
-  
-  x <- readLines(f)
-  y <- gsub( "Aerial", "Arial, Helvetica, sans-serif", x )
-  y <- gsub( "Arimo", "Arial, Helvetica, sans-serif", x )
-  cat(y, file=f, sep="\n")
-  
-}

web-verify-output.r

@@ -16,6 +16,14 @@ countries <- c(
   "Portugal",
   "Netherlands"
 )
+
+web_fix_fonts <- function(path){
+  x <- readLines(path)
+  y <- gsub( "Aerial", "Arial, Helvetica, sans-serif", x )
+  y <- gsub( "Arimo", "Arial, Helvetica, sans-serif", y )
+  cat(y, file=path, sep="\n")
+}
+
 verify_web_output <- function(){
   plot_names <- c("deaths", "forecast", "infections", "rt")
   plot_versions <- c("mobile", "desktop")
@@ -34,6 +42,9 @@ verify_web_output <- function(){
         if (! file.exists(path)) {
           stop(sprintf("Missing web output during verification: %s", path))
         }
+        
+        # Fix wrong fonts
+        web_fix_fonts(path)
       }
     }
     
@@ -43,7 +54,10 @@ verify_web_output <- function(){
     date_results[[country]] = latest_date
     
   }
-  
+
+  # Fix fonts for covariate change estimates
+  web_fix_fonts("web/figures/desktop/covars-alpha-reduction.svg")
+  web_fix_fonts("web/figures/mobile/covars-alpha-reduction.svg")
   
   dir.create("web/data/", showWarnings = FALSE, recursive = TRUE)
   write_json(date_results, "web/data/latest-updates.json", auto_unbox=TRUE)