Merge pull request #15 from IDEELResearch/feature/covars

Feature/covars

analysis/02_covariate_maps.R

@@ -1,15 +1,13 @@
 # Load pkgs ---------------------------------------------------------------
 
 library(sf)
-library(raster)
 library(tidyverse)
 
 # Read data ---------------------------------------------------------------
 
-covars <- readRDS("analysis/data_raw/final_covariates.rds")
+covars <- readRDS(url("https://github.com/IDEELResearch/scrape/raw/refs/heads/main/analysis/data-derived/final_covariates.rds"))
 sf_adm0 <- readRDS("analysis/data_derived/sf_admin0_africa.rds") # adm0 map data
 
-
 # Unlist and combine dfs in long format with map --------------------------
 
 # Use the custom (but very specific) get_map_covar_data() fxn

analysis/03_get_data_for_grff.R

@@ -0,0 +1,38 @@
+library(sf)
+
+# variables needed for dataframe: lat, lon, time, num, denom, covar1
+
+# find lat lon from stave -> merge with shp -> convert to df (remove geometries)
+
+covars <- readRDS(url("https://github.com/IDEELResearch/scrape/raw/refs/heads/main/analysis/data-derived/final_covariates.rds"))
+stave <- readRDS(url("https://github.com/IDEELResearch/stitch/raw/refs/heads/main/analysis/data_derived/mock_stave_prevalence.rds"))
+
+map_data <- get_map_covar_data(covars)
+
+stave %>% st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%  # EPSG:4326 for WGS84
+  ggplot() +
+    geom_sf() +
+    coord_sf()
+
+get_grff_input <- function(stave_obj, covar_obj){
+
+  covar_processed <- get_map_covar_data(covar_obj)
+  covar_names <- covar_processed %>% select(-c(iso3c:year)) %>% st_drop_geometry() %>% names()
+
+  sf_use_s2(FALSE)
+
+  stave_obj %>%
+    st_as_sf(coords = c("lon", "lat"), crs = 4326, remove = F) %>% # EPSG:4326 for WGS84 same as MAP shp files
+    st_join(covar_processed, left = TRUE) %>%
+    as.data.frame() %>%
+    select(lat, lon, collection_day, numerator, denominator, year, all_of(covar_names)) %>%
+    mutate(collection_year = year(as.Date(collection_day))) %>%
+    filter(collection_year == year) %>%
+    relocate(collection_year, .after = collection_day) %>%
+    select(-year)
+
+}
+
+input_df <- get_grff_input(stave, covars)
+
+saveRDS(input_df, "analysis/data_derived/input_for_grff.rds")