Cohort Report outputs graphs of variables in a study input file.

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_report:
    run: cohortreport:v1.0.0 output/input.csv
    needs: [generate_study_population]
    config:
      variable_types:
          age: int
          sex: categorical
          ethnicity: categorical
          bmi: float
          diabetes: binary
          chronic_liver_disease: binary
          imd: categorical
          region: categorical
          stp: categorical
          rural_urban: categorical
          prior_covid_date: date
      output_path: output/cohort_reports_outputs
    outputs:
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input.html

The generate_report action outputs one HTML document with a graph for each variable specified. Where graphs have a category of 5 or less, small number suppression is applied and the whole graph is redacted.

Notice the run and config properties.

The run property passes a specific input table to a specific version of cohortreport. In this case, the specific input file is output/input.csv and the specific version of cohortreport is v1.0.0. The config property passes configuration to cohortreport; for more information, see Configuration.

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

variable_types - this is an optional argument that should be used if the input files contain data without a type, for example, a CSV. cohortreport can take in other files such as '.feather' and '.dta' which contain the type of the data in each column. In these cases, a variable_types config if not needed.

Please see DEVELOPERS.md.