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UMR-ASTRE
Covid19-Mortality-Visualisation
Commits
c8650448
Commit
c8650448
authored
Jul 01, 2020
by
Renaud Lancelot
🌍
Browse files
Changes in plan to updtate the West and Central Africa analysis
parent
792fff62
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#14858
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src/plan.R
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c8650448
...
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@@ -40,152 +40,174 @@ plan <- drake_plan(
"Georgia"
,
"Israel"
,
"Jordan"
,
"Lebanon"
,
"Libya"
,
"Moldova"
,
"Morocco"
,
"Syria"
,
"Tunisia"
,
"Ukraine"
),
wcAfrica
=
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"
),
## Total population counts and densities by Country, Year and Sex.
## Source: United Nations'[World Population Prospects
## 2019](https://population.un.org/wpp/)
## https://population.un.org/wpp/Download/Standard/CSV/
world_population
=
read.table
(
file_in
(
"https://population.un.org/wpp/Download/Files/1_Indicators%20(Standard)/CSV_FILES/WPP2019_TotalPopulationBySex.csv"
),
header
=
T
,
sep
=
","
,
as.is
=
T
,
check.names
=
F
,
quote
=
"\""
),
## ECDC Covid19 geographic distribution data
last_day
=
Sys.Date
()
-
1
,
## string for today
sdt
=
format
(
Sys.Date
(),
"%d %b %Y"
),
covid
=
ecdc_covid19
(
Sys.Date
()
-
1
),
## ## String notice for data update
## data_update_date = format(Sys.Date() - 1,
## "%d %b %Y"),
## Lock-down dates
lockdown_dates
=
read_excel
(
file_in
(
"data/lockdown.xlsx"
))
%>%
transmute
(
name
=
standardise_country_names
(
raster
::
trim
(
name
)),
lockdown
=
as.Date
(
lockdown
)
file_in
(
"https://population.un.org/wpp/Download/Files/1_Indicators%20(Standard)/CSV_FILES/WPP2019_TotalPopulationBySex.csv"
),
header
=
T
,
sep
=
","
,
as.is
=
T
,
check.names
=
F
,
quote
=
"\""
),
## 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"
),
## 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"
),
## geo_europe = readOGR(dsn = file_in("data/geo_europe.gpkg"),
## layer = "geo_europe"),
## GIS vector layer for the region of interest covering European
## countries described above
## roi_europe = readOGR(dsn = file_in("data/roi_europe.gpkg"),
## layer = "roi_europe"),
## DERIVED DATA ----------------------------------------
## ## Deaths by country and date
## deaths_by_ctry_dt =
## covid %>%
## group_by(date, name) %>%
## summarise(deaths = sum(deaths)) %>%
## ungroup() %>%
## mutate(date = as.Date(date)),
## Population counts in thousands of people
pop_countries_2019
=
pop_countries
(
world_population
,
year
=
2019
),
## ## today (ANSI)
## tod = format(Sys.Date(), "%Y%m%d"),
## Coordinate Reference Systems
wgs84
=
CRS
(
"+proj=longlat +ellps=WGS84"
,
doCheckCRSArgs
=
FALSE
),
merc
=
CRS
(
"+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs"
,
doCheckCRSArgs
=
FALSE
),
eust
=
"MOOD has received funding from the EU Horizon 2020 Research and Innovation programme under grant agreement No 874850."
,
report_euro_html
=
rmarkdown
::
render
(
knitr_in
(
"src/Covid19MortalityEurope.Rmd"
),
# knit_root_dir = "../public", # Is this necessary or convenient?
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_format
=
rmdformats
::
readthedown
(
dev
=
"png"
,
toc_depth
=
3
,
lightbox
=
T
,
gallery
=
T
,
use_bookdown
=
T
,
number_sections
=
T
),
output_file
=
file_out
(
"public/covid19MortalityEurope.html"
),
quiet
=
FALSE
),
report_euro_pdf
=
rmarkdown
::
render
(
knitr_in
(
"src/Covid19MortalityEurope.Rmd"
),
## ECDC Covid19 geographic distribution data
last_day
=
Sys.Date
()
-
1
,
## string for today
sdt
=
format
(
Sys.Date
(),
"%d %b %Y"
),
covid
=
ecdc_covid19
(
Sys.Date
()
-
1
),
## ## String notice for data update
## data_update_date = format(Sys.Date() - 1,
## "%d %b %Y"),
## Lock-down dates
lockdown_dates
=
read_excel
(
file_in
(
"data/lockdown.xlsx"
))
%>%
transmute
(
name
=
standardise_country_names
(
raster
::
trim
(
name
)),
lockdown
=
as.Date
(
lockdown
)
),
## 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"
),
## 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"
),
## GIS vector layer for West and Central African countries
geoWCAfrica
=
readOGR
(
dsn
=
"data/geoWCAfricaLight.gpkg"
,
layer
=
"geoWCAfricaLight"
),
roiWCAfrica
=
readOGR
(
dsn
=
"data/roiWCAfricaLight.gpkg"
,
layer
=
"roiWCAfricaLight"
),
## DERIVED DATA ----------------------------------------
## ## Deaths by country and date
## deaths_by_ctry_dt =
## covid %>%
## group_by(date, name) %>%
## summarise(deaths = sum(deaths)) %>%
## ungroup() %>%
## mutate(date = as.Date(date)),
## Population counts in thousands of people
pop_countries_2019
=
pop_countries
(
world_population
,
year
=
2019
),
## ## today (ANSI)
## tod = format(Sys.Date(), "%Y%m%d"),
## Coordinate Reference Systems
wgs84
=
CRS
(
"+proj=longlat +ellps=WGS84"
,
doCheckCRSArgs
=
FALSE
),
merc
=
CRS
(
"+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs"
,
doCheckCRSArgs
=
FALSE
),
eust
=
"MOOD has received funding from the EU Horizon 2020 Research and Innovation programme under grant agreement No 874850."
,
report_euro_html
=
rmarkdown
::
render
(
knitr_in
(
"src/Covid19MortalityEurope.Rmd"
),
# knit_root_dir = "../public", # Is this necessary or convenient?
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_format
=
bookdown
::
pdf_document2
(
dev
=
"pdf"
,
includes
=
list
(
in_header
=
"preamble.tex"
,
before_body
=
"before_body.tex"
),
toc
=
T
,
toc_depth
=
3
,
number_sections
=
T
,
latex_engine
=
"xelatex"
),
output_file
=
file_out
(
"public/covid19MortalityEurope.pdf"
),
quiet
=
FALSE
),
## report_wcafrica_html =
## rmarkdown::render(
## knitr_in("src/Covid19MortalityWCAfrica.Rmd"),
## ## knit_root_dir = "../public", # Is this necessary or convenient?
## output_dir = "public", # https://github.com/ropensci/drake/issues/742
## output_format =
## rmdformats::readthedown(
## toc_depth = 3,
## lightbox = T,
## gallery = T,
## use_bookdown = T,
## number_sections = T),
## output_file = file_out("public/covid19MortalityWCAfrica.html"),
## quiet = FALSE
## ),
# WEBSITE AND README ------------------------------------------------------
readme_md
=
rmarkdown
::
render
(
knitr_in
(
"README.Rmd"
),
output_file
=
file_out
(
"README.md"
),
quiet
=
FALSE
),
index_html
=
## Render to html within public
rmarkdown
::
render
(
knitr_in
(
"README.Rmd"
),
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_file
=
file_out
(
"public/index.html"
),
quiet
=
FALSE
),
)
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_format
=
rmdformats
::
readthedown
(
dev
=
"png"
,
toc_depth
=
3
,
lightbox
=
T
,
gallery
=
T
,
use_bookdown
=
T
,
number_sections
=
T
),
output_file
=
file_out
(
"public/covid19MortalityEurope.html"
),
quiet
=
FALSE
),
report_euro_pdf
=
rmarkdown
::
render
(
knitr_in
(
"src/Covid19MortalityEurope.Rmd"
),
# knit_root_dir = "../public", # Is this necessary or convenient?
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_format
=
bookdown
::
pdf_document2
(
dev
=
"pdf"
,
includes
=
list
(
in_header
=
"preamble.tex"
,
before_body
=
"before_body.tex"
),
toc
=
T
,
toc_depth
=
3
,
number_sections
=
T
,
latex_engine
=
"xelatex"
),
output_file
=
file_out
(
"public/covid19MortalityEurope.pdf"
),
quiet
=
FALSE
),
report_euro_docx
=
rmarkdown
::
render
(
knitr_in
(
"src/Covid19MortalityEurope.Rmd"
),
# knit_root_dir = "../public", # Is this necessary or convenient?
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_format
=
bookdown
::
word_document2
(
dev
=
"png"
,
toc
=
T
,
toc_depth
=
3
,
number_sections
=
T
),
output_file
=
file_out
(
"public/covid19MortalityEurope.docx"
),
quiet
=
FALSE
),
## report_wcafrica_html =
## rmarkdown::render(
## knitr_in("src/Covid19MortalityWCAfrica.Rmd"),
## ## knit_root_dir = "../public", # Is this necessary or convenient?
## output_dir = "public", # https://github.com/ropensci/drake/issues/742
## output_format =
## rmdformats::readthedown(
## toc_depth = 3,
## lightbox = T,
## gallery = T,
## use_bookdown = T,
## number_sections = T),
## output_file = file_out("public/covid19MortalityWCAfrica.html"),
## quiet = FALSE
## ),
# WEBSITE AND README ------------------------------------------------------
readme_md
=
rmarkdown
::
render
(
knitr_in
(
"README.Rmd"
),
output_file
=
file_out
(
"README.md"
),
quiet
=
FALSE
),
index_html
=
## Render to html within public
rmarkdown
::
render
(
knitr_in
(
"README.Rmd"
),
output_dir
=
"public"
,
# https://github.com/ropensci/drake/issues/742
output_file
=
file_out
(
"public/index.html"
),
quiet
=
FALSE
),
)
future
::
plan
(
future.callr
::
callr
)
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