Malawi runs if you remove islands (roll-eyes)

src/2_cv/script.R

@@ -42,6 +42,6 @@ run_ic <- function(survey, type, inf_function) {
 }
 
 ic_pars <- expand.grid("survey" = surveys, "inf_function" = fs)
-ic <- purrr::pmap(ic_pars, safely(run_ic))
+ic <- purrr::pmap(ic_pars, run_ic)
 
 saveRDS(ic, file = "ic.rds")

src/2_plot_ladder/orderly.yml

@@ -5,6 +5,7 @@ artefacts:
       description: Prevalence ladder plots
       filenames:
         - ladder-civ2017phia.png
+        - ladder-mwi2016phia.png
         - ladder-tza2017phia.png
         - ladder-zwe2016phia.png
 

src/2_plot_ladder/script.R

@@ -6,14 +6,14 @@ ic <- readRDS("depends/ic_iid.rds")
 
 lapply(ic, function(x) {
 
-  if(is.null(x$result)) return(NULL)
+  if(is.null(x)) return(NULL)
 
-  ggplot(x$result, aes(x = forcats::fct_reorder(area_name, mean), y = mean, ymin = lower, ymax = upper)) +
+  ggplot(x, aes(x = forcats::fct_reorder(area_name, mean), y = mean, ymin = lower, ymax = upper)) +
     geom_pointrange(position = position_dodge(width = 0.6), alpha = 0.8) +
     coord_flip() +
     theme_minimal() +
     scale_y_continuous(labels = scales::percent) +
     labs(x = "Area name", y = "Prevalence estimate")
 
-  ggsave(paste0("ladder-", tolower(x$result$survey_id[1]), ".png"), h = 8, w = 6.25, bg = "white")
+  ggsave(paste0("ladder-", tolower(x$survey_id[1]), ".png"), h = 8, w = 6.25, bg = "white")
 })

src/2_process_surveys/script.R

@@ -44,6 +44,9 @@ surveys <- lapply(iso3, function(x) {
     st_as_sf() %>%
     st_transform(4326)
 
+  #' Remove the islands from Malawi
+  if(x == "mwi") sf <- filter(sf, !(area_name %in% c("Likoma", "Chizumulu")))
+
   st_write(sf, paste0(tolower(survey_name[toupper(x)]), ".geojson"))
 
   return(sf)