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: cohort-report:v2.1.0 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
generate_report action generates a report that contains a table and a chart for each variable in the input file.
The table contains unsafe statistics and should be checked thoroughly before it is released.
The chart contains statistics that have been made safe.
Cells in the underlying frequency table have been redacted, if:
- They contain less than 10 units
- They contain greater than 90% of the total number of units
run property passes a specific input file 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.
config property passes configuration to cohortreport; for more information, see Configuration.
Notice that the HTML document is called
descriptives_[the name of the specific input file, without the extension].html.
It is saved to the
output_path (see below).
output_path, which defaults to
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.