cli.rst

CLI Reference

Once CLARITE is installed, the command line interface can be run using the clarte-cli command.

The command line interface has command groups that are the same as the modules in the package (except for survey).

The --help option will show documentation when run with any command or command group:

$ clarite-cli --help
Usage: clarite-cli [OPTIONS] COMMAND [ARGS]...

Options:
--help  Show this message and exit.

Commands:
  analyze
  describe
  load
  modify
  plot

--skip and --only

Many commands in the CLI have the skip and only options. These will limit the command to specific variables. If skip is specified, all variables except the specified ones will be processed. If only is specified, only the specified variables will be processed.

Only one or the other option may be used in a single command. They may be passed in any combination of two ways:

1. As the name of a file containing one variable name per line
2. As the variable name specfied directly in the terminal

For example:

clarite-cli modify rowfilter-incomplete-obs 1_nhanes_w_sddsrvyr test -o covars.txt -o BMXBMI

results in:

-------------------------------------------------------------------------------------------------------------------------
--only: 1 variable(s) specified directly
        8 variable(s) loaded from 'covars.txt'
=========================================================================================================================
Running rowfilter_incomplete_obs
-------------------------------------------------------------------------------------------------------------------------
Removed 3,687 of 22,624 observations (16.30%) due to NA values in any of 9 variables
=========================================================================================================================

Commands

clarite.cli:analyze_cli

clarite.cli:describe_cli

clarite.cli:load_cli

clarite.cli:modify_cli

clarite.cli:plot_cli