R/RcppExports.R

In mrc-ide/ccmpp.tmb: Cohort Component Population Projection and Reconstruction in TMB

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' Construct a sparse Leslie matrix
#'
#' @param sx a vector of survivorship probabilities.
#' @param fx a vector of fertility rates, only amongst fertile ages.
#' @param srb sex ratio at birth.
#' @param age_span the interval for age and projection time step.
#' @param fx_idx first in
#'
#' @return A sparse matrix representation of a Leslie matrix.
#'
#' @details
#' The first index of fertility `fx_idx` must be greater than 1, that is, it is
#' assumed there is no fertility in the youngest age group. The reason for this
#' restriction is that fertility among the youngest age group would require 
#' calculation of offspring among births during the second half of the
#' projection interval.
#'
#' @examples
#'
#' library(popReconstruct)
#' data(burkina_faso_females)
#' make_leslie_matrixR(sx = burkina.faso.females$survival.proportions[,1],
#'                     fx = burkina.faso.females$fertility.rates[4:10, 1],
#'                     srb = 1.05,
#'                     age_span = 5,
#'                     fx_idx = 4)
#'
#' @importClassesFrom Matrix dgCMatrix
#' @export
make_leslie_matrixR <- function(sx, fx, srb, age_span, fx_idx) {
    .Call(`_ccmpp_tmb_make_leslie_matrixR`, sx, fx, srb, age_span, fx_idx)
}

#' Simulate cohort component population projection
#'
#' @param basepop vector of baseline population size.
#' @param sx a matrix of survivorship probabilities.
#' @param fx a matrix of fertility rates, only amongst fertile ages.
#' @param gx a matrix of proportion of migrants during projection period.
#' @param srb a vector of sex ratio at birth.
#' @param age_span the interval for age and projection time step.
#' @param fx_idx first in
#'
#' @return
#' `ccmppR()` returns a list with matrices for population, (cohort)
#' deaths, births by age, number of infants, and migrations.
#'
#' `ccmpp_leslieR()` simulates the same population projection using a 
#' Leslie matrix formulation and returns a matrix of population. This
#' is exactly equal to `population` returned by `ccmppR()` (see examples).
#'
#' @details
#' Arguments `sx`, `fx`, and `gx` are matrices with one column for each
#' projection period, and `srb` is a vector of length number of projection 
#' periods.
#'
#' The number of age groups in the deaths array are one greater than then number
#' of age groups because deaths are counted separately for those ageing into
#' the open ended age group and survivors in the open ended age group.
#'
#' @examples
#'
#' library(popReconstruct)
#' data(burkina_faso_females)
#'
#' bf_basepop <- as.numeric(burkina.faso.females$baseline.pop.counts)
#' bf_sx <- burkina.faso.females$survival.proportions
#' bf_fx <- burkina.faso.females$fertility.rates[4:10, 1]
#' bf_gx <- burkina.faso.females$migration.proportions
#' bf_srb <- rep(1.05, ncol(burkina.faso.females$survival.proportions))
#'
#' pop_leslie <- ccmpp_leslieR(basepop = bf_basepop, sx = bf_sx, fx = bf_fx,
#'                             gx = bf_gx, srb = bf_srb, 
#'                             age_span = 5, fx_idx = 4)
#' pop_proj <- ccmppR(basepop = bf_basepop, sx = bf_sx, fx = bf_fx,
#'                    gx = bf_gx, srb = bf_srb, 
#'                    age_span = 5, fx_idx = 4)
#' 
#' all(pop_leslie == pop_proj$population)
#'
#' @export
ccmppR <- function(basepop, sx, fx, gx, srb, age_span, fx_idx) {
    .Call(`_ccmpp_tmb_ccmppR`, basepop, sx, fx, gx, srb, age_span, fx_idx)
}

#' @rdname ccmppR
#' @export
ccmpp_leslieR <- function(basepop, sx, fx, gx, srb, age_span, fx_idx) {
    .Call(`_ccmpp_tmb_ccmpp_leslieR`, basepop, sx, fx, gx, srb, age_span, fx_idx)
}