simulate Command Reference

The simulate command runs a model's optional simulate entry point to generate disease data for the locations and periods in a covariate CSV.

Synopsis

chap simulate <MODEL_NAME> <DATASET_CSV> <OUT_FILE> [OPTIONS]

Description

chap simulate:

1. Loads the model template from a local MLProject directory or a GitHub URL.
2. Loads covariates from a CSV file (auto-discovering the matching .geojson if present). The CSV does not need a disease_cases column; rows that have one are kept as observed history.
3. Invokes the MLProject's simulate entry point.
4. Checks that the output covers the same locations and periods, has the target for every row, and keeps the observed values unchanged.
5. Writes the result to out_file, plus a .geojson next to it if the input had polygons.

Each parameter can also be passed as a keyword flag (--model-name, --dataset-csv, --out-file). The output is a regular Chap dataset and can be used with chap eval. See Additional Configuration → Simulate Entry Point for how to define the entry point.

Options

Parameter	Description	Default
--model-configuration-yaml	YAML file with user_option_values, e.g. simulation parameters or a seed	None
--run-config.ignore-environment	Skip automatic environment setup	false
--run-config.debug	Enable verbose debug logging	false

Example

chap simulate \
    --model-name tests/fixture_models/climate_simulation_model \
    --dataset-csv ./covariates.csv \
    --out-file ./simulated.csv

To continue a simulation, append the new periods' covariates to the previous output (leaving disease_cases empty for them) and run the command again on that file. Only the new periods are simulated.