R notes
Installing and updating
On Debian
To install R:
sudo apt-get install r-base r-base-dev
On MacOS
brew install r
Package management
Install packages using install.packages()
. Whenever R has a new update in the distribution (3.4 to 3.5, for example), packages will generally need to be reinstalled also. The location they are installed to can vary and R may ask.
Often R complains about missing Debian packages (curl, ssl) and may fail if miniconda/anaconda is already installed (may want to change dir name).
On Debian
Packages are installed from a CRAN repository to a local library
directory. The default users library must be created at
~/R/x86_64-pc-linux-gnu-library/{version#}
, but packages can also
be installed to /usr/local/lib/R/site-library
if permissions allow.
On MacOS
Packages are installed to /Library/Frameworks/R.framework/Versions/3.6/Resources/library
Package list
My usual list of packages to update is:
install.packages(c('tidyverse', 'xts', 'rgdal', 'data.table', 'automap', 'forecast', 'ggmap', 'cowplot', 'raster', 'SPEI', 'lubridate'))
Sometimes the core R packages on Debian go out of date and need to be updated. Start R with sudo and run:
update.packages()
Jupyter R notebooks
To run R in Jupyter notebooks install IRKernel using the linux source method (libzmq3-dev first).