rStuff.sh

R_BASEDIR=$HOME/Library/R/3.3

# Create 3 dirs in $R_BASEDIR library, library.github, library.cran
mkdir -p  R_LIBS=$R_BASEDIR/library $R_BASEDIR/library.github $R_BASEDIR/library.cran

# Directory to log all output
mkdir -p $HOME/Library/Logs/R

export R_LIBS=$R_BASEDIR/library:$R_BASEDIR/library.github:$R_BASEDIR/library.cran

# Bash functions to install R packages with ease.
# TODO color messages with crayon

mkdir -p $HOME/Library/Logs/R

# setup default options when starting r/R/Rscript
alias R='/usr/local/bin/R --quiet --no-save --no-restore'
alias r='/usr/local/bin/R --quiet --no-save --no-restore'
alias Rscript='/usr/local/bin/RScript --quiet --no-save --no-restore'


# Checks if a package is installed.
# Also reports the path where the package is installed.
rIsPkgInstalled() {
  pkg=${1:-JUNK_PACKAGE}

  ret=1
  dirs=($(Rscript -e 'cat(paste(.libPaths(),collapse=" "))'))
  for dir in ${dirs[@]}; do
    if [ -d "${dir}/${pkg}" ]; then
      echo "$pkg Installed in dir: $dir"
      ret=0
    fi
  done

  return $ret
}

# Install R packages from CRAN.
# Skip the ones that are already installed.
# Log output under $HOME/Library/Logs/R
# e.g. rInstPackages dplyr purrr tidyr
rInstPackages() {
  packages=$(echo "$@" | sed -e 's/^/"/;s/ /", "/g;s/$/"/')
  code='
    packages <- c('$packages');
    packages.all <- installed.packages();
    packages.i <- intersect(packages, packages.all);
    packages.ni <- setdiff(packages, packages.all);
    if(length(packages.i) > 0) {
      print("------------------------------------------------------------")
      print(sprintf("%s : Already Installed. Skipping.",
        paste(packages.i, collapse=", ")));
      print("------------------------------------------------------------")
    };
    if (length(packages.ni) > 0) {
      print(sprintf("Installing : %s",paste(packages.ni, collapse=", ")));
      install.packages(packages.ni, lib="'$R_BASEDIR/library.cran'")
    } 
  '
  (
    echo "Installing ${@}"
    R --slave <<-EOT
    ${code}
EOT
    echo
  ) 2>&1 | tee -a $HOME/Library/Logs/R/${1}-$(date +'%F_%H%M').txt
}

# Build R source packages from CRAN.
# Skip the ones that are already installed.
# Log output under $HOME/Library/Logs/R
# e.g. rInstSrcPackages dplyr purrr tidyr
rInstSrcPackages() {
  packages=$(echo "$@" | sed -e 's/^/"/;s/ /", "/g;s/$/"/')
  code='
    packages <- c('$packages');
    packages.all <- installed.packages();
    packages.i <- intersect(packages, packages.all);
    packages.ni <- setdiff(packages, packages.all);
    if(length(packages.i) > 0) {
      print("------------------------------------------------------------")
      print(sprintf("%s : Already Installed. Skipping.",paste(packages.i, collapse=", ")));
      print("------------------------------------------------------------")
    };
    if (length(packages.ni) > 0) {
      print(sprintf("Installing : %s",paste(packages.ni, collapse=", ")));
      install.packages(packages.ni, type="source", lib="'$R_BASEDIR/library.cran'")
    } 
  '
  (
    echo "Installing ${@}"
    R --slave <<-EOT
    $code
EOT
    echo
  ) 2>&1 | tee -a $HOME/Library/Logs/R/${1}-$(date +'%F_%H%M').txt
}

# Install R packages from CRAN.
# The ones that are already installed are reinstalled.
# Log output under $HOME/Library/Logs/R
# e.g. rInstPackagesForce dplyr purrr tidyr
rInstPackagesForce() {
  packages=$(echo "$@" | sed -e "s/^/'/;s/ /', '/g;s/$/'/")
  (
    echo "Installing ${1}"
    Rscript --slave -e "install.packages(c($packages), lib='$R_BASEDIR/library.cran')"
  ) 2>&1 | tee -a $HOME/Library/Logs/R/${1}-$(date +'%F_%H%M').txt
}

# Build R source packages from CRAN.
# The ones that are already installed are reinstalled.
# Log output under $HOME/Library/Logs/R
# e.g. rInstSrcPackagesForce dplyr purrr tidyr
rInstSrcPackagesForce() {
  packages=$(echo "$@" | sed -e "s/^/'/;s/ /', '/g;s/$/'/")
  (
    echo "Installing ${1}"
    Rscript --slave -e "install.packages(c($packages), type='source', lib='$R_BASEDIR/library.cran')"
  ) 2>&1 | tee -a $HOME/Library/Logs/R/${1}-$(date +'%F_%H%M').txt
}

# Install R packages from Github using devtools.
# The ones that are already installed are reinstalled.
# Log output under $HOME/Library/Logs/R
# e.g. rInstGithub dplyr purrr tidyr
rInstGithub() {
  (
    echo "Installing $1 from github"
    Rscript --slave -e "devtools::install_github('$1', lib='$R_BASEDIR/library.github')"
  ) 2>&1 | tee -a $HOME/Library/Logs/R/${1/\//_}-$(date +'%F_%H%M').txt
}

# Helper functions for some famous github repo authors
rInstBob() {
  rInstGithub "hrbrmstr/$1"
}
rInstKent() {
  rInstGithub "timelyportfolio/$1"
}
rInstHadley() {
  rInstGithub "hadley/$1"
}
rInstRstudio() {
  rInstGithub "rstudio/$1"
}
rInstRopenGov() {
  rInstGithub "ropengov/$1"
}
rInstOliver() {
  rInstGithub "ironholds/$1"
}
rInstRopenSci() {
  rInstGithub "ropensci/$1"
}
rInstRopenScilabs() {
  rInstGithub "ropenscilabs/$1"
}

# Update R packages from CRAN.
# Log output under $HOME/Library/Logs/R
# e.g. rUpdatePackages
rUpdatePackages() {
  (
    echo "Updating R Packages from CRAN"
    Rscript --slave -e "update.packages(ask=FALSE, lib.loc='$R_BASEDIR/library.cran', instlib='$R_BASEDIR/library.cran')"
  ) 2>&1 | tee -a $HOME/Library/Logs/R/cran_update-$(date +'%F_%H%M').txt
}

# Update R packages from Github.
# Log output under $HOME/Library/Logs/R
# e.g. rUpdateGithubPackages
rUpdateGithubPackages() {
  (
    echo "Updating R Packages from Github"
    Rscript --slave -e "dtupdate::github_update(ask=FALSE, auto.install=TRUE)"
  ) 2>&1 | tee -a $HOME/Library/Logs/R/github_update-$(date +'%F_%H%M').txt
}

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