tests/testthat/helper-model-frame.R

In mrc-ide/naomi.extensions: Core Naomi model for Subnational HIV Estimates

a_area_merged <- sf::read_sf(system.file("extdata/areas/area_merged.geojson",
                                         package = "naomi"))
a_spec <- naomi::extract_pjnz_naomi(system.file("extdata/mwi2019.PJNZ",
                                                package = "naomi"))


a_naomi_mf <- naomi::naomi_model_frame(
  a_area_merged,
  mwi_population_agesex,
  a_spec,
  scope = "MWI_1_1",
  level = 4,
  calendar_quarter1 = "CY2016Q1",
  calendar_quarter2 = "CY2018Q3",
  calendar_quarter3 = "CY2019Q2",
  artattend = FALSE,
  spectrum_population_calibration = "none")

a_naomi_data <- naomi::select_naomi_data(
  a_naomi_mf,
  mwi_survey_hiv_indicators,
  mwi_anc_testing,
  mwi_art_number,
  prev_survey_ids = c("MWI2016PHIA", "MWI2015DHS"),
  artcov_survey_ids = "MWI2016PHIA",
  recent_survey_ids = "MWI2016PHIA")


a_tmb_inputs <- naomi::prepare_tmb_inputs(a_naomi_data)