Merge pull request #77 from NSAPH-Software/JOSS

Joss updates

_pkgdown.yml

@@ -31,7 +31,9 @@ reference:
 articles:
   - title: Introduction
     navbar: Introduction
-    contents: [Standard-Gaussian-Processes, Nearest-neighbor-Gaussian-Processes]
+    contents: [Standard-Gaussian-Processes,
+               Nearest-neighbor-Gaussian-Processes,
+               A-Note-on-Choosing-Hyperparameters]
 
   - title: Collabration
     navbar: Collabration

docker_singularity/Dockerfile

@@ -1,30 +1,38 @@
-FROM rocker/verse:4.1.0
+FROM rocker/verse:4.2.3
 
 LABEL org.opencontainers.image.authors="nkhoshnevis@g.harvard.edu"
 
-RUN install2.r --error --repo https://mran.microsoft.com/snapshot/2022-05-26 \ 
-	data.table \
-	xgboost \
-	stats \
-	MASS \
-    spatstat.geom \
-	logger \
-	Rcpp \
-    RcppArmadillo \
-	ggplot2 \
-	rlang \
-	covr 
+# Linux internal commands
+RUN apt-get update
+RUN apt-get install -y --no-install-recommends vim
+RUN apt-get install -y --no-install-recommends zsh
+RUN apt-get install -y --no-install-recommends libgsl-dev
+RUN apt-get clean
+
+# R package installation from CRAN
+RUN R -e "install.packages(c( \
+    'covr', \
+    'roxygen2', \
+    'devtools'), repos='https://cloud.r-project.org')"
+
+# R package installation from CRAN
+RUN R -e "install.packages(c( \
+    'parallel', \
+    'xgboost', \
+    'stats', \
+    'MASS', \
+    'spatstat.geom', \
+    'logger', \
+    'Rcpp', \
+    'RcppArmadillo', \
+    'ggplot2', \
+    'cowplot', \
+    'rlang', \
+    'Rfast', \
+    'SuperLearner', \
+    'wCorr'), repos='https://cloud.r-project.org')"
 
 ENV RENV_VERSION 0.15.1
 RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
 RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
 
-
-# Linux internal commands
-RUN apt-get update \
-	&& apt-get install -y --no-install-recommends \
-		vim \
-		zsh \
-		&& apt-get clean
-
-#