Basic Install

At the command line:

$ pip install clarite

Running R code from CLARITE

In order to use the “r_survey” “regression_kind” in the ewas function, R must be installed.

  • The version of R must be compatible with the installed version of rpy2 (usually the latest version).

  • The R installation must have the ‘survey’ package installed: Rscript -e ‘install.packages(“survey”)’

  • The R_HOME environment variable may need to be set, and R must be on the PATH. This can be done in each script:

import os
os.environ["R_HOME"] = r"C:\Program Files\R\R-4.0.2"
os.environ["PATH"]   = r"C:\Program Files\R\R-4.0.2\bin\x64" + ";" + os.environ["PATH"]

Troubleshooting rpy2

From the command line:

python -m rpy2.situation

Or within a jupyter notebook environment:

import rpy2.situation
for row in rpy2.situation.iter_info():