hintr_run_model: Run the model and save output

In mrc-ide/naomi: Naomi Model for Subnational HIV Estimates

Run the model and save output

Description

This prepares the model inputs from data and options and saves output as a qs file.

Usage

hintr_run_model(
  data,
  options,
  model_output_path = tempfile(fileext = ".qs"),
  validate = TRUE
)

Arguments

data	List of paths to input data files.
options	List of model run options (see details).
model_output_path	Path to store model output as qs. Used in calibrating model and producing output downloads.
validate	If FALSE validation of inputs & data will be skipped.

Details

The data argument must be a list specifying paths to the following:

• pjnz

• shape

• population

• ⁠survey data⁠

• anc_testing (optional)

• art_number (optional)

Each item in list can either be a character containing the path to the file or another list of the format:

list( path = "path/to/file", hash = "file_hash", filename = "file" )

The options argument must be a list specifying minimally:

• area_scope

• area_level

• calendar_quarter_t1

• calendar_quarter_t2

• calendar_quarter_t3

• survey_prevalence

• survey_art_coverage

• survey_recently_infected

• include_art_t1

• include_art_t2

• anc_prevalence_year1

• anc_prevalence_year2

• anc_art_coverage_year1

• anc_art_coverage_year2

Value

Paths to output files

mrc-ide/naomi documentation built on Jan. 6, 2025, 10:20 a.m.