Safetab outputs two-way tables of descriptive statistics.

It applies conservative small number suppression; if a cell is redacted, then the table is also redacted. Safetab creates a log file that shows what has been redacted.

Consider the following extract from a study's project.yaml:

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_safetabs:
    run: safetab:v3.0.2 output/input.csv
    needs: [generate_study_population]
    config:
      output_path: output
      redaction_limit: 5
      tables:
        two_way:
          tab_type: 2-way
          variables:
            - sex
            - age_band
    outputs:
      moderately_sensitive:
        safetab_log: output/input_tables/table_log.txt
        safetab_two_way: output/input_tables/two_way/*.md

The generate_safetabs action outputs one table: sex vs age_band. Notice the run and config properties. The run property passes a specific input table to a specific version of safetab. In this case, the specific input table is output/input.csv and the specific version of safetab is v3.0.2. The config property passes configuration to safetab; for more information, see Configuration.

output_path, which defaults to safetab_tables. Save the outputs to the given path. If the given path does not exist, then it is created.

redaction_limit, which defaults to 5. Cells (and tables) with less than or equal to this number of records are redacted.

tables

2-way: Outputs a two-way table for each pair (combination) of variables. For example, given the variables sex and age_band, it will output one table:

• sex vs age_band

Given the variables sex, age_band, and has_copd, it will output three tables:

• sex vs age_band
• sex vs has_copd
• age_band vs has_copd

target-2-way: Outputs a two-way table for each pair (combination) of variables for a target variable, which is given by the target property. For example, given the variables sex and age_band, and the target variable has_copd, it will output two tables:

• sex vs has_copd
• age_band vs has_copd

groupby-2-way: Outputs a two-way table for each pair (combination) of variables for a group-by variable, which is given by the groupby property. For example, given the variables sex and has_copd, and the group-by variable age_band, it will output one table for each unique value of age_band:

• sex vs has_copd for 16-29
• sex vs has_copd for 30-39
• ...

Please see DEVELOPERS.md.