Leapfrog is a multistate population projection model for demographic and HIV epidemic estimation.
The name leapfrog is in honor of Professor Basia Zaba.
You can install the development version of frogger from GitHub with:
# install.packages("remotes")
remotes::install_github("mrc-ide/frogger")
The simulation model is implemented in a header-only C++ library located in inst/include/frogger.hpp
. This location allows the C++ code to be imported in other R packages via specifying LinkingTo: leapfrog
in the DESCRIPTION
file.
The simulation model is callable in R via a wrapper function run_model()
created with Rcpp.
You can control how the simulation model is run with the following arguments:
hiv_age_stratification
which must be “coarse” or “full”. Coarse is run with 5-year age groups and full with single year ages.run_child_model
which is FALSE
by default. Set to TRUE
to run the paediatric portion of the model.The file pjnz/bwa_aim-adult-art-no-special-elig_v6.13_2022-04-18.PJNZ
contains an example Spectrum file constructed from default country data for Botswana with Spectrum (April 2022).
Prepare model inputs.
library(frogger)
pjnz <- system.file("pjnz/bwa_aim-adult-art-no-special-elig_v6.13_2022-04-18.PJNZ",
package = "frogger", mustWork = TRUE)
demp <- prepare_leapfrog_demp(pjnz)
hivp <- prepare_leapfrog_projp(pjnz)
Simulate adult ‘full’ age group (single-year age) and ‘coarse’ age group (collapsed age groups) models from 1970 to 2030 with 10 HIV time steps per year.
lsimF <- run_model(demp, hivp, 1970:2030, 10L,
hiv_age_stratification = "full", run_child_model = FALSE)
lsimC <- run_model(demp, hivp, 1970:2030, 10L,
hiv_age_stratification = "coarse", run_child_model = FALSE)
Compare the HIV prevalence age 15-49 years and AIDS deaths 50+ years. Deaths 50+ years are to show some noticeable divergence between the "full"
and "coarse"
age group simulations.
prevF <- colSums(lsimF$p_hiv_pop[16:50,,],,2) / colSums(lsimF$p_total_pop[16:50,,],,2)
prevC <- colSums(lsimC$p_hiv_pop[16:50,,],,2) / colSums(lsimC$p_total_pop[16:50,,],,2)
deathsF <- colSums(lsimF$p_hiv_deaths[51:81,,],,2)
deathsC <- colSums(lsimC$p_hiv_deaths[51:81,,],,2)
plot(1970:2030, prevF, type = "l", main = "Prevalence 15-49")
lines(1970:2030, prevC, col = 2)
The simulation model is implemented as templated C++ code in inst/include/frogger.hpp
. This is so the simulation model may be developed as a standalone C++ library that can be called by other software without requiring R-specific code features. The code uses header-only open source libraries to maximize portability.
double
s are used in inst/include
dir. We should be using templated real_type
for TMBhiv_negative_pop
was fixed size by having dimensions specified by template, how much does this speed up the code? Is there a better way to do this?OutputState
to take a struct of state-space dimensions instead of unpacking the subset of parameters we need. See https://github.com/mrc-ide/frogger/pull/12#discussion_r1245170775