naomi_model_frame: Construct Model Frames and Adjacency Structures
In mrc-ide/naomi: Naomi Model for Subnational HIV Estimates

naomi_model_frame

R Documentation

Construct Model Frames and Adjacency Structures

Description

Construct Model Frames and Adjacency Structures

Usage

naomi_model_frame(
  area_merged,
  population_agesex,
  spec,
  scope = area_merged$area_id[area_merged$area_level == min(area_merged$area_level)],
  level = max(area_merged$area_level),
  calendar_quarter1,
  calendar_quarter2,
  calendar_quarter3,
  calendar_quarter4 = "CY2024Q3",
  calendar_quarter5 = "CY2025Q3",
  age_groups = get_five_year_age_groups(),
  sexes = c("male", "female"),
  omega = 0.7,
  rita_param = list(OmegaT0 = 130/365, sigma_OmegaT = ((142 - 118)/365)/(2 *
    stats::qnorm(0.975)), betaT0 = 0, sigma_betaT = 1e-05, ritaT = 1),
  sigma_u_sd = 1,
  artattend = TRUE,
  artattend_t2 = FALSE,
  artattend_log_gamma_offset = -4,
  anchor_home_district = TRUE,
  rho_paed_15to49f_ratio = TRUE,
  rho_paed_x_term = FALSE,
  alpha_xst_term = FALSE,
  logit_nu_mean = 2,
  logit_nu_sd = 0.3,
  spectrum_population_calibration = "national",
  output_aware_plhiv = TRUE,
  adjust_area_growth = FALSE,
  psnu_level = NULL
)

Arguments

`area_merged`	Merged version of area hierarchy
`population_agesex`	Population by age group and sex
`spec`	Spec
`scope`	The collection of area IDs to be modelled. Defaults to all area ids.
`level`	Admin level
`calendar_quarter1`	Calendar quarter at time 1 ("CYyyyyQq")
`calendar_quarter2`	Calendar quarter at time 2 ("CYyyyyQq")
`calendar_quarter3`	Calendar quarter at time 3 ("CYyyyyQq")
`calendar_quarter4`	Calendar quarter at time 4 ("CYyyyyQq")
`calendar_quarter5`	Calendar quarter at time 5 ("CYyyyyQq")
`age_groups`	Age groups to include in model frame
`sexes`	Sexes
`omega`	Omega
`rita_param`	rita_param
`sigma_u_sd`	sigma_u_sd
`artattend`	logical; whether to estimate neighboring district ART attendance
`artattend_t2`	logical; whether to allow time-varying neighboring district ART attendance
`artattend_log_gamma_offset`	logit offset for neighboring district ART attendance
`anchor_home_district`	logical; whether to include home district random in ART attendance specification
`rho_paed_15to49f_ratio`	logical; to model paediatric prevalence as ratio of 15-49 female prevalence
`rho_paed_x_term`	logical; to include area interaction for paediatric prevalence
`alpha_xst_term`	logical; to include district-sex-time interaction for ART coverage. Default `FALSE`.
`logit_nu_mean`	mean of logit viral load suppression.
`logit_nu_sd`	standard deviation of logit viral load suppression.
`spectrum_population_calibration`	character string values "national", "subnational", "none"
`adjust_area_growth`	TRUE/FALSE: adjust PLHIV population for net change in cohort size
`psnu_level`	Level at which to output PEPFAR Data Pack outputs for planning. This doesn't have anything to do with calibration, but this is a convenient place to allow user to edit this in model workflow. Default value `NULL` indicates to read PSNU level from internal database.

Details

Argument spectrum_population_calibration determines whether to calibrate population inputs to match Spectrum population by age and sex. If the Spectrum file is a single national Spectrum file, then options "national" and "subnational" return the same results.