Import project

Author: ghurault

.Rprofile

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+source("renv/activate.R")

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# Custom
+models/*.rds
+results/*
+results*
+docs/*
+*.html

Dockerfile

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+# Take inspiration from
+# https://github.com/jrnold/docker-stan/blob/master/rstan/Dockerfile
+
+FROM rocker/tidyverse:4.1.3
+
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends apt-utils ed libnlopt-dev \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/
+
+# Global site-wide config -- neeeded for building packages
+RUN mkdir -p $HOME/.R/ \
+    && echo "CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -ffat-lto-objects  -Wno-unused-local-typedefs \n" >> $HOME/.R/Makevars \
+    && echo "CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -ffat-lto-objects  -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations\n" >> $HOME/.R/Makevars
+
+# Install rstan
+# Instead, we can install rstan by restoring package library with renv (remove dependency on EczemaPredPOEM first)
+RUN install2.r --error --deps TRUE \
+    rstan \
+    rstantools \
+    && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+# Create a user variable
+ENV USER=rstudio
+
+# Create project directory and set it as working directory
+WORKDIR /home/$USER/EczemaTreat
+
+# Install R packages to local library using renv
+COPY [".Rprofile", "renv.lock", "./"]
+COPY renv/activate.R ./renv/
+RUN chown -R rstudio . \
+ && sudo -u rstudio R -e 'renv::restore(confirm = FALSE, exclude = "TanakaData")'

EczemaTreat.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX