deciles-charts

deciles-charts generates a line chart for each measure table in an input directory. The line chart has time on the horizontal axis (x) and value on the vertical axis (y). Deciles are plotted as dashed lines; outer percentiles are plotted as dotted lines; the median is plotted as a solid line. For example, the following deciles chart was generated from dummy data:

Using deciles to communicate variation has several advantages when compared to the alternatives. Consequently, deciles charts are used on OpenPrescribing.net and in several OpenSAFELY publications, such as Curtis et al. (2021).

Usage

In summary:

Use cohort-extractor to extract several weekly or monthly cohorts.
Use cohort-extractor to generate one or more measure tables from these cohorts.
Use deciles-charts to generate a deciles chart for each measure table.

Let's walk through an example project.yaml.

The following cohort-extractor action extracts several monthly cohorts:

generate_cohort:
  run: >
    cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-06-30 by month"
  outputs:
    highly_sensitive:
      cohort: output/input_2021-*.csv

The following cohort-extractor action generates one or more measure tables from these cohorts:

generate_measures:
  run: >
    cohortextractor:latest generate_measures
      --study-definition study_definition
  needs: [generate_cohort]
  outputs:
    moderately_sensitive:
      measure: output/measure_*.csv

Finally, the following deciles-charts reusable action generates a deciles chart for each measure table. Remember to replace [version] with a deciles-charts version:

generate_deciles_charts:
  run: >
    deciles-charts:[version]
      --input_dir output
      --output_dir output
  needs: [generate_measures]
  outputs:
    moderately_sensitive:
      deciles_charts: output/deciles_chart_*.png

For each measure table, there will now be a corresponding deciles chart. For example, given a measure table called measure_has_sbp_event_by_stp_code.csv, there will now be a corresponding deciles chart called deciles_chart_has_sbp_event_by_stp_code.png.

Notes for developers

Please see DEVELOPERS.md.