Commit 4577542d authored by Renaud Lancelot's avatar Renaud Lancelot 🌍
Browse files

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

parent f85acb8e
Pipeline #15360 failed with stage
in 1 minute and 57 seconds
...@@ -7,8 +7,7 @@ library(drake) ...@@ -7,8 +7,7 @@ library(drake)
## ## loadd() ## ## loadd()
# The workflow plan data frame outlines what you are going to do. # The workflow plan data frame outlines what you are going to do.
plan <- drake_plan( plan <- drake_plan(## raw_data = read_excel(
## raw_data = read_excel(
## file_in(here("data/...")) ## file_in(here("data/..."))
## ), ## ),
## clean_data = raw_data %>% cleanup(), ## clean_data = raw_data %>% cleanup(),
...@@ -40,13 +39,15 @@ plan <- drake_plan( ...@@ -40,13 +39,15 @@ plan <- drake_plan(
"Georgia", "Israel", "Jordan", "Lebanon", "Libya", "Georgia", "Israel", "Jordan", "Lebanon", "Libya",
"Moldova", "Morocco", "Syria", "Tunisia", "Ukraine"), "Moldova", "Morocco", "Syria", "Tunisia", "Ukraine"),
europe = c(eu28, efta, candi, noneu),
wca = c("Cameroon", "Central African Republic", "Chad", wca = c("Cameroon", "Central African Republic", "Chad",
"Congo DR", "Congo", "Equatorial Guinea", "Gabon", "Congo DR", "Congo", "Equatorial Guinea", "Gabon",
"Sao Tome and Principe", "Benin", "Burkina Faso", "Sao Tome and Principe", "Benin", "Burkina Faso",
"Cape Verde", "The Gambia", "Ghana", "Guinea", "Cape Verde", "The Gambia", "Ghana", "Guinea",
"Guinea Bissau", "Cote d'Ivoire", "Liberia", "Mali", "Guinea Bissau", "Côte d'Ivoire", "Liberia", "Mali",
"Mauritania", "Niger", "Nigeria", "Senegal", "Mauritania", "Niger", "Nigeria", "Senegal",
"Sierra Leone", "Togo"), "Sierra Leone", "Togo"),
## Total population counts and densities by Country, Year and Sex. ## Total population counts and densities by Country, Year and Sex.
## Source: United Nations'[World Population Prospects ## Source: United Nations'[World Population Prospects
...@@ -80,28 +81,33 @@ plan <- drake_plan( ...@@ -80,28 +81,33 @@ plan <- drake_plan(
lockdown = as.Date(lockdown) 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 + ## GIS vector layer for European countries (EU 27 + UK + EFTA +
## candidate countries + non-EU countries). Source GADM.org ## candidate countries + non-EU countries). Source GADM.org
## version 3.6 ## version 3.6
geo_europe_light = readOGR(dsn = "data/geo_europe_light.gpkg", geo_europe_light = geosimplify(
layer = "geo_europe_light"), world_map[world_map$name %in%
standardise_country_names(europe), ]),
## GIS vector layer for the region of interest covering European roi_europe_light = region_of_interest(
## countries described above geo_europe_light, world_map),
roi_europe_light = readOGR(dsn = "data/roi_europe_light.gpkg",
layer = "roi_europe_light"),
## GIS vector layer for West and Central African countries ## GIS vector layer for West and Central African countries
geoWCAfrica = world_map[world_map$ISO %in% get_iso3(wca),] %>% geowca = geosimplify(world_map[world_map$name %in%
geosimplify(), standardise_country_names(wca),]),
roiWCAfrica = region_of_interest(geoWCAfrica, world_map) %>% roiwca = region_of_interest(geowca, world_map),
geosimplify(),
## DERIVED DATA ---------------------------------------- ## DERIVED DATA ----------------------------------------
...@@ -136,7 +142,6 @@ plan <- drake_plan( ...@@ -136,7 +142,6 @@ plan <- drake_plan(
output_format = output_format =
rmdformats::readthedown( rmdformats::readthedown(
dev = "png", dev = "png",
toc_depth = 3,
lightbox = T, lightbox = T,
gallery = T, gallery = T,
use_bookdown = T, use_bookdown = T,
...@@ -157,8 +162,7 @@ plan <- drake_plan( ...@@ -157,8 +162,7 @@ plan <- drake_plan(
includes = list( includes = list(
in_header = "preamble.tex", in_header = "preamble.tex",
before_body = "before_body.tex"), before_body = "before_body.tex"),
toc = T, classoption = "a4paper",
toc_depth = 3,
number_sections = T, number_sections = T,
latex_engine = "xelatex" latex_engine = "xelatex"
), ),
...@@ -174,8 +178,6 @@ plan <- drake_plan( ...@@ -174,8 +178,6 @@ plan <- drake_plan(
output_format = output_format =
bookdown::word_document2( bookdown::word_document2(
dev = "png", dev = "png",
toc = T,
toc_depth = 3,
number_sections = T number_sections = T
), ),
output_file = file_out("public/covid19MortalityEurope.docx"), output_file = file_out("public/covid19MortalityEurope.docx"),
......
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