threemc_aggregate: Produce Population Weighted Aggregated Samples for All Area...

In mrc-ide/threemc: (Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa

Produce Population Weighted Aggregated Samples for All Area Levels

Description

Aggregate by area, year, age and type (weighted by population), and convert to a percentage/probability.

Usage

threemc_aggregate(
  .data,
  fit,
  areas,
  populations,
  age_var = c("age", "age_group"),
  type = c("probability", "incidence", "prevalence"),
  area_lev,
  N = 100,
  prev_year = 2008,
  probs = c(0.025, 0.5, 0.975),
  ...
)

Arguments

.data	data.frame of unaggregated modelling results.
fit	TMB list containing model parameters, nested list of samples for the (cumulative) incidence and hazard rate of circumcision for the region(s) in question.
areas	sf shapefiles for specific country/region.
populations	data.frame containing populations for each region in tmb fits.
age_var	Determines whether you wish to aggregate by discrete ages or age groups (0-4, 5-9, 10-14, and so on).
type	Determines which aspect of MC in the regions in question you wish to aggregate for. Can be one of "probability", "incidence" or "prevalence".
area_lev	PSNU area level for specific country.
N	Number of samples to be generated, Default: 100
prev_year	If type == "prevalence", choose year to compare prevalence with.
probs	Percentiles to provide quantiles at. Set to NULL to skip computing quantiles.
...	Further arguments to internal functions.

Value

data.frame with samples aggregated by aggr_cols and weighted by population.

mrc-ide/threemc documentation built on Feb. 9, 2024, 5:16 p.m.