safetab

This is an action that can be called into the project.yaml. It requires data in a support data file format (.csv, csv.gz, .dta, feather), and outputs a folder of markdown files. This action takes in a dataset and a configuration and outputs different types of 2 way tables for descriptive statistics.

Small numbers suppression is applied. A conservative approach is adopted where any indiviudal cell that needs to be redacted, results in the whole table being redacted. A log file is created that shows what has been redacted.

The following example blocks should be included in the project.yaml file.

inputs: 
  input: tests/test_data/input.feather

The --config should contain a key called tables containing the tables requested. See test1_config. The available tables are:

• 2-way - simple 2-way table. For example, sex by copd. It creates all combinations of available variables if given a list. For example if provided with age, sex and copd. It will produce 3 tables - age vs sex, age vs copd, and sex vs copd.
• target-2-way - 2 way tables by one specified variable. For example if target variable is death and the other variables provided are sex and copd, it will produce 2 tables: sex vs death and copd vs death.
• groupby-2-way - simple 2 way table that is stratifed by a third variable. If variable to group by is 2 age groups (under 50, over 50), and the variables provided are copd and heart disease, it will produce 2 tables: copd vs heart disease for under 50s, and copd vs heart disease for over 50s.

If you require the safetab markdown files to be saved in a particular folder, you can specify this in the --config with output_path. If no output path is provided, the default place is safetab_tables. The action will make this folder if it does not exist.

If you want to change the limit at which redaction occurs, specify this in the --config with redaction_limit. The default is 5 or below.

actions: 
  safetab_data:
    run: safetab:latest input.csv
config:
  tables:
    simple_2_way_tabs:
      tab_type: 2-way
      variables:
      - sex
      - ageband
      - copd
    death_2_way_tab:
      tab_type: target-2-way
      variables:
      - sex
      - ageband
      - copd
      target: death
    grouped_by_sex:
      tab_type: groupby-2-way
      variables:
      - ageband
      - copd
      - death
      groupby: sex
  output_path: safetab_outputs
  redaction_limit: 5