Updated Dockerfile to R 4.4 and fixed Makevars and .stan files to run on arm64

Dockerfile

@@ -1,36 +1,43 @@
 # This runs an R script belonging to a local library and saves its plotly graphs as image files
 
-FROM rocker/r-ver:4.0.3
+FROM rocker/r-ver:4.4
 
 RUN apt-get update \
-   && apt-get install -y --no-install-recommends \
-   apt-utils \
-   ed \
-   libnlopt-dev \
+  && apt-get install -y --no-install-recommends \
+  apt-utils \
+  ed \
+  libnlopt-dev \
   && apt-get clean \
   && rm -rf /var/lib/apt/lists/
 
 RUN apt-get update && apt-get install -y  --no-install-recommends \
-   software-properties-common \
-   dirmngr \
-   git-core \
-   libcurl4-openssl-dev \
-   libgit2-dev \
-   libssh2-1-dev \
-   libicu-dev \
-   libpng-dev \
-   libudunits2-dev \
-   zlib1g-dev \
-   libgdal-dev \
-   libproj-dev \
-   xml2 \
-   openssl \
-   python3
-# `python` needed for `save_image()`
+  software-properties-common \
+  dirmngr \
+  git-core \
+  libcurl4-openssl-dev \
+  libgit2-dev \
+  libssh2-1-dev \
+  libicu-dev \
+  libpng-dev \
+  libudunits2-dev \
+  zlib1g-dev \
+  libgdal-dev \
+  libproj-dev \
+  xml2 \
+  openssl \
+  python3  # needed for `save_image()`
 
-RUN add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0"
-RUN add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
-RUN apt install -y r-cran-rcpparmadillo
+# needed to install devtools
+RUN apt-get update && apt-get install -y  --no-install-recommends \
+  libssl-dev \
+  libfontconfig1-dev \
+  libxml2-dev \
+  libharfbuzz-dev \
+  libfribidi-dev \
+  libfreetype6-dev \
+  libpng-dev \
+  libtiff5-dev \
+  libjpeg-dev
 
 RUN mkdir /epiline/
 
@@ -56,7 +63,7 @@ RUN Rscript -e "install.packages('moments', repos='http://cran.rstudio.com/')"
 # needed for `save_image()`
 RUN Rscript -e "install.packages('reticulate', repos='http://cran.rstudio.com/')"
 
-# needed to use local library
+# # needed to use local library
 RUN Rscript -e "install.packages('devtools', repos='http://cran.rstudio.com/')"
 RUN Rscript -e "devtools::load_all()"
 RUN Rscript -e "devtools::install()"

src/Makevars

@@ -1,5 +1,5 @@
-STANHEADERS_SRC = `"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`
-PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=ignore_error -std=c++14
+PKG_LIBS =  '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb
+PKG_CPPFLAGS =   -I"/usr/local/lib/R/site-library/Rcpp/include/"  -I"/usr/local/lib/R/site-library/RcppEigen/include/"  -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported"  -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/"  -I"/usr/local/lib/R/site-library/StanHeaders/include/"  -I"/usr/local/lib/R/site-library/RcppParallel/include/"  -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1
 SOURCES = stan_files/symptom_report_model.stan stan_files/symptom_report_model_gamma.stan 
 OBJECTS = $(SOURCES:.stan=.o) init.o
 

src/stan_files/symptom_report_model.stan

@@ -91,9 +91,10 @@ transformed data {
   line_list = rep_matrix( 0, t_rep_symptoms, t_max );
   for( idx in 1:n_ll ) {
     tau  = ll_report[ idx ] - ll_symptoms[ idx];
-    ddxx = tau + t_symptom_post + 1;
-    ddxx = max( min( ddxx, t_rep_symptoms ), 1 );
-    sdxx = max( min( ll_symptoms[idx] + t_symptom_pre, t_max ), 1 );
+    int ddxx_left = min( ddxx, t_rep_symptoms );
+    ddxx = max( ddxx_left, 1 );
+    int sdxx_left = min( ll_symptoms[idx] + t_symptom_pre, t_max );
+    sdxx = max( sdxx_left, 1 );
     line_list[ ddxx, sdxx ] = ll_N[ idx ];
   }
 

src/stan_files/symptom_report_model_gamma.stan

@@ -79,9 +79,10 @@ transformed data {
   line_list = rep_matrix( 0, t_rep_symptoms, t_max );
   for( idx in 1:n_ll ) {
     tau  = ll_report[ idx ] - ll_symptoms[ idx];
-    ddxx = tau + 1;
-    ddxx = max( min( ddxx, t_rep_symptoms ), 1 );
-    sdxx = max( min( ll_symptoms[idx] + t_symptom_pre, t_max ), 1 );
+    int ddxx_left = min( ddxx, t_rep_symptoms );
+    ddxx = max( ddxx_left, 1 );
+    int sdxx_left = min( ll_symptoms[idx] + t_symptom_pre, t_max );
+    sdxx = max( sdxx_left, 1 );
     line_list[ ddxx, sdxx ] = ll_N[ idx ];
   }