Changes in the plan to account for changes in the datasets used in the analysis.

src/plan.R

@@ -7,8 +7,7 @@ library(drake)
 ## ## loadd()
 
 # The workflow plan data frame outlines what you are going to do.
-plan <- drake_plan(
-    ## raw_data = read_excel(
+plan <- drake_plan(## raw_data = read_excel(
     ##   file_in(here("data/..."))
     ## ),
     ## clean_data = raw_data %>% cleanup(),
@@ -40,13 +39,15 @@ plan <- drake_plan(
             "Georgia", "Israel", "Jordan", "Lebanon", "Libya",
             "Moldova", "Morocco",  "Syria", "Tunisia", "Ukraine"),
 
+    europe = c(eu28, efta, candi, noneu),
+
     wca = c("Cameroon", "Central African Republic", "Chad",
-                 "Congo DR", "Congo", "Equatorial Guinea", "Gabon",
-                 "Sao Tome and Principe", "Benin", "Burkina Faso",
-                 "Cape Verde", "The Gambia", "Ghana", "Guinea",
-                 "Guinea Bissau", "Cote d'Ivoire", "Liberia", "Mali",
-                 "Mauritania", "Niger", "Nigeria", "Senegal",
-                 "Sierra Leone", "Togo"),
+            "Congo DR", "Congo", "Equatorial Guinea", "Gabon",
+            "Sao Tome and Principe", "Benin", "Burkina Faso",
+            "Cape Verde", "The Gambia", "Ghana", "Guinea",
+            "Guinea Bissau", "Côte d'Ivoire", "Liberia", "Mali",
+            "Mauritania", "Niger", "Nigeria", "Senegal",
+            "Sierra Leone", "Togo"),
 
     ## Total population counts and densities by Country, Year and Sex.
     ## Source: United Nations'[World Population Prospects
@@ -80,28 +81,33 @@ plan <- drake_plan(
             lockdown = as.Date(lockdown)
         ),
 
+    ## Coronavirus Government Response Tracker
+
+    ## Governments are taking a wide range of measures in response to
+    ## the COVID-19 outbreak.
+    ## This tool aims to track and compare
+    ## policy responses around the world, rigorously and consistently.
 
-    # CARTOGRAPHY ---------------------------------------------------
+    lock = stringency(),
+    ## CARTOGRAPHY ---------------------------------------------------
 
-    world_map = getData("countries"),
+    world_map = get_world_map(),
 
     ## GIS vector layer for European countries (EU 27 + UK + EFTA +
     ## candidate countries + non-EU countries). Source GADM.org
     ## version 3.6
-    geo_europe_light = readOGR(dsn = "data/geo_europe_light.gpkg",
-                               layer = "geo_europe_light"),
+    geo_europe_light = geosimplify(
+        world_map[world_map$name %in%
+                  standardise_country_names(europe), ]),
 
-    ## GIS vector layer for the region of interest covering European
-    ## countries described above
-    roi_europe_light = readOGR(dsn = "data/roi_europe_light.gpkg",
-                               layer = "roi_europe_light"),
+    roi_europe_light = region_of_interest(
+        geo_europe_light, world_map),
 
     ## GIS vector layer for West and Central African countries
-    geoWCAfrica = world_map[world_map$ISO %in% get_iso3(wca),] %>%
-      geosimplify(),
+    geowca = geosimplify(world_map[world_map$name %in%
+                       standardise_country_names(wca),]),
 
-    roiWCAfrica = region_of_interest(geoWCAfrica, world_map) %>%
-      geosimplify(),
+    roiwca = region_of_interest(geowca, world_map),
 
     ## DERIVED DATA ----------------------------------------
 
@@ -136,7 +142,6 @@ plan <- drake_plan(
                        output_format =
                            rmdformats::readthedown(
                                            dev = "png",
-                                           toc_depth = 3,
                                            lightbox = T,
                                            gallery = T,
                                            use_bookdown = T,
@@ -157,8 +162,7 @@ plan <- drake_plan(
                                          includes = list(
                                              in_header = "preamble.tex",
                                              before_body = "before_body.tex"),
-                                         toc = T,
-                                         toc_depth = 3,
+                                         classoption = "a4paper",
                                          number_sections = T,
                                          latex_engine = "xelatex"
                                      ),
@@ -174,8 +178,6 @@ plan <- drake_plan(
                        output_format =
                            bookdown::word_document2(
                                          dev = "png",
-                                         toc = T,
-                                         toc_depth = 3,
                                          number_sections = T
                                      ),
                        output_file = file_out("public/covid19MortalityEurope.docx"),