Update to code in replication package

.gitignore

@@ -1,95 +1,131 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# DotEnv configuration
-.env
-
-# Database
-*.db
-*.rdb
-
-# Pycharm
-.idea
-
-# VS Code
-.vscode/
-
-# Spyder
-.spyproject/
-
-# Jupyter NB Checkpoints
-.ipynb_checkpoints/
-
-# Mac OS-specific storage files
-.DS_Store
-
-# vim
-*.swp
-*.swo
-
-# Mypy cache
-.mypy_cache/
-
-# Jupyter Book
-_build/
-
-# python-dotenv
-.env
-
-# setuptools-scm/
-src/*/_version.py
+########################################################################
+#
+# Based on DIME .gitignore template version 2.0
+#
+########################################################################
+
+#######################
+# Start by ignoring everything, and below we are explicitly saying
+# what to not ignore
+*
+
+#######################
+# List of files with GitHub functionality anywhere in the repo
+# that we do not want to ignore
+
+# These files include GitHub settings
+!.gitignore
+!.gitattributes
+!.env.example
+
+!.reproducibility_report_RR_2024_WLD_175-v02.pdf
+
+# Git placeholder file (to commit empty folders)
+!/**/*.gitkeep
+
+# Keep markdown files used for documentation on GitHub
+!README.md
+!CONTRIBUTING.md
+!LICENSE*
+
+* Unignore reproot files - see https://dime-worldbank.github.io/repkit/articles/reproot-files.html
+!reproot*.yaml
+
+#######################
+# For performance reasons, if a folder is already ignored, then
+# GitHub does not check the content for that folder for matches
+# with additional rules. The line below includes folder in the
+# top folder (but not their content), so that anything matching
+# the rules below will still not be ignored.
+!*/
+
+#######################
+# The following file types are code that should always be
+# included no matter where in the repository folder they are
+# located unless you explicitly ignore that folder
+
+# Stata
+!/**/*.do
+!/**/*.ado
+!/**/*.sthlp
+!/**/*.smcl
+
+# R
+!/**/*.R
+!/**/*.Rmd
+!/**/*.Rproj
+!/**/*.qmd
+!/**/*.Rprofile
+!/**/renv/
+
+# Still ignore user file for R projects
+.Rproj.user
+
+# LaTeX
+!/**/*.tex
+!/**/*.bib
+
+# Python
+!/**/*.py
+!/**/*.ipynb
+!/**/requirements.txt
+!/**/Pipfile
+!/**/Pipfile.lock
+!/**/*.toml
+# Still ignore .ipynb files in checkpoint folders
+.ipynb_checkpoints
+
+# Matlab
+!/**/*.m
+
+# Markdown
+!/**/*.md
+
+# Julia
+!/**/*.jl
+
+#Files to create custom layout and functionality
+# in dashboards, markdown notebooks, bookdown etc.
+!/**/*.css
+!/**/*.js
+!/**/*.json
+
+#Bash scripts
+!/**/*.sh
+
+# Citations
+!/**/*.cff
+
+# .yml and .yaml files
+# These files sometimes have credentials, so only unignore these lines by removing
+# the "#" below after you checked your .yml/.yaml files for sensitive content
+!/**/*.yml
+!/**/*.yaml
+
+#######################
+# Include some additional file formats in any output folder. You might have
+# to change the name of the Output folder to whatever it is called in your
+# project, but we strongly recommend that you only include these files in
+# a subset of the folders where you are certain no private data is ever stored.
+!/**/Output/**/*.txt
+!/**/Output/**/*.csv
+!/**/Output/**/*.xml
+!/**/images/**/*.eps
+!/**/images/**/*.svg
+!/**/images/**/*.png
+!/**/images/**/*.ico
+
+#######################
+# Include all the files with passwords or tokens here. All files named
+# password or passwords are with this template ignored no matter which
+# format you are using. Additionally, all content in any folder called
+# password or passwords are also ignored. NOTE that your project might be
+# using different names and then you must edit the lines below accordingly.
+password.*
+passwords.*
+password/
+passwords/
+token.*
+tokens.*
+token/
+tokens/

01.code/R/00_MASTER.R

@@ -1,27 +1,27 @@
-#------------------------------------------------------------------------------#
-#           Population at high-risk from climate related hazards               #
-#                             R master script                                  #
-#------------------------------------------------------------------------------#
-
-# install packages using renv
-renv::restore()
-
-# set directory to root replication folder
-setwd("../../")
-
-# run from intermediate data?
-from_intermediate = TRUE
-
-# !!! Running the MASTER R script from source data is not recommended !!! #
-# !!!          (~1 TB storage required, > 14 days run time)           !!! #
-
-# run scripts   
-if (from_intermediate) {
-  source("01.code/R/10_extract_exposed_pop.R")
-  source("01.code/R/11_clean_exposed_pop.R")
-} else {
-  script_list <- list.files("01.code/R", ".R$", full.names = TRUE)
-  for (code in setdiff(script_list, "01.code/R/00_MASTER.R")) {
-    source(code)
-  }
+#------------------------------------------------------------------------------#
+#           Population at high-risk from climate related hazards               #
+#                             R master script                                  #
+#------------------------------------------------------------------------------#
+
+# install packages using renv
+# just the first time you run the package
+renv::restore()
+
+setwd("C:/Temp/08.replication package/")
+
+# run from intermediate data?
+from_intermediate = TRUE
+
+# !!! Running the MASTER R script from source data is not recommended !!! #
+# !!!          (~1 TB storage required, > 14 days run time)           !!! #
+
+# run scripts   
+if (from_intermediate) {
+  source("01.code/R/10_extract_exposed_pop.R")
+  source("01.code/R/11_clean_exposed_pop.R")
+} else {
+  script_list <- list.files("01.code/R", ".R$", full.names = TRUE)
+  for (code in setdiff(script_list, "01.code/R/00_MASTER.R")) {
+    source(code)
+  }
 }