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

Naomi output file directory

## Set dir to params$output_dir and then print tree relative to this
## fs::dir_tree uses the path arg as the text for the first node
## but this will be the path at time of generation i.e. the path
## to the dir on the server, not the path relative to output zip which
## the user will be looking at. So print relative path "." to avoid
## including confusing path as top level node
withr::with_dir(params$output_dir, fs::dir_tree("."))

The following files have been generated as part of a Naomi model fit:

fit:

• calibration_options.yml: Specifications for calibration of Naomi estimates to Spectrum totals.
• data_options.yml: Specifications for inclusion of model inputs.
• model_options.yml: Specfications for model fit parameters.
• spectrum_calibration: Tabular dataset of calibrated and an uncalibrated model outputs.

info:

• unaids_navigator_checklist: Navigator checklist.
• model_options.yml: Full model options (including advanced options).

Files containing naomi model outputs:

• indicators.csv: Naomi model outputs.
• art_attendance.csv: Tabular dataset of ART patient movement between neighbouring admin areas.
• inputs_outputs.csv: Model data inputs aligned with model estimates.
• pepfar_datapack_indicators.csv: PEPFAR district-level datapack extract

Metadata on naomi model specifications:

• boundaries.geojson: Boundary file used in model fit.
• meta_age_group.csv: Age stratification inlcuded in model fit.
• meta_area.csv: Admin areas inlcuded in model fit.
• meta_period: Time periods included in model fit.

mrc-ide/naomi documentation built on April 10, 2024, 2:13 p.m.