Merge pull request #129 from mrc-ide/issue-91

Add separate model variant for demographic projection

.github/workflows/test-coverage.yaml

@@ -45,7 +45,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

R/generate_cpp.R

@@ -531,7 +531,9 @@ generate_state_saver_func_body <- function(output) {
 
 model_variant_to_name <- function(model_variant) {
   if (model_variant == "ModelVariant") {
-    "base"
+    "demographic"
+  } else if (model_variant == "HivSimulation") {
+    "hiv"
   } else if (model_variant == "ChildModel") {
     "children"
   } else {

R/generate_cpp_validation.R

@@ -31,8 +31,8 @@ validate_and_parse_output <- function(output, filename, row_num) {
   validate_output_dims(output)
   if (output$model_variant == "ModelVariant") {
     ## If it is included for all model variants then data is stored on
-    ## structs called "BaseModel"
-    output$struct <- "BaseModel"
+    ## structs called "DemographicProjection"
+    output$struct <- "DemographicProjection"
   } else {
     output$struct <- output$model_variant
   }

R/run_model.R

@@ -5,6 +5,7 @@
 #' @param sim_years Simulation years to run model for default 1970:2030
 #' @param hts_per_year Number of HIV time steps per year, default 10
 #' @param output_steps Which sim years to output for default same as sim_years
+#' @param run_hiv_simulation If TRUE then runs HIV simulation
 #' @param hiv_age_stratification The age stratification for HIV population,
 #'  "coarse" or "full"
 #' @param run_child_model If TRUE then run the child model
@@ -14,6 +15,7 @@
 run_model <- function(data, parameters, sim_years,
                       hts_per_year,
                       output_steps = NULL,
+                      run_hiv_simulation = TRUE,
                       hiv_age_stratification = "full",
                       run_child_model = TRUE) {
   if (is.null(sim_years)) {
@@ -36,23 +38,27 @@ run_model <- function(data, parameters, sim_years,
     output_steps <- which(sim_years %in% output_steps)
   }
 
-  assert_enum(hiv_age_stratification, c("full", "coarse"))
-  if (hiv_age_stratification == "full" && !run_child_model) {
-    model_variant <- "BaseModelFullAgeStratification"
+  assert_enum(hiv_age_stratification, c("full", "coarse", "none"))
+  if (!run_hiv_simulation) {
+    model_variant <- "DemographicProjection"
+  } else if (hiv_age_stratification == "full" && !run_child_model) {
+    model_variant <- "HivFullAgeStratification"
   } else if (hiv_age_stratification == "coarse" && !run_child_model) {
-    model_variant <- "BaseModelCoarseAgeStratification"
+    model_variant <- "HivCoarseAgeStratification"
   } else if (hiv_age_stratification == "full" && run_child_model) {
     model_variant <- "ChildModel"
   } else if (hiv_age_stratification == "coarse" && run_child_model) {
     stop("Cannot run child model with coarse age stratification")
+  } else if (hiv_age_stratification == "none" && run_hiv_simulation) {
+    stop("Cannot run HIV simulation with unspecified age stratification")
   }
   if (hiv_age_stratification == "full") {
     parameters$hAG_SPAN <- parameters[["hAG_SPAN_full"]]
     parameters$cd4_initdist <- parameters[["cd4_initdist_full"]]
     parameters$cd4_prog <- parameters[["cd4_prog_full"]]
     parameters$cd4_mort <- parameters[["cd4_mort_full"]]
     parameters$art_mort <- parameters[["art_mort_full"]]
-  } else {
+  } else if (hiv_age_stratification == "coarse") {
     parameters$hAG_SPAN <- parameters[["hAG_SPAN_coarse"]]
     parameters$cd4_initdist <- parameters[["cd4_initdist_coarse"]]
     parameters$cd4_prog <- parameters[["cd4_prog_coarse"]]

README.Rmd

@@ -9,6 +9,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   fig.path = "man/figures/README-",
+  fig.cap = "",
   out.width = "100%"
 )
 ```
@@ -42,8 +43,9 @@ The simulation model is callable in R via a wrapper function `run_model()` creat
 
 You can control how the simulation model is run with the following arguments:
 
+* `run_hiv_simulation` which is `TRUE` by default. Set to `FALSE` to turn off the HIV simulation and run only the demographic projection.
 * `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.
+* `run_child_model` which is `FALSE` by default. Set to `TRUE` to run the child portion of the model.
 
 ## Example
 
@@ -55,7 +57,7 @@ Prepare model inputs.
 ```{r example}
 library(frogger)
 
-pjnz <- system.file("pjnz/bwa_aim-adult-art-no-special-elig_v6.13_2022-04-18.PJNZ", 
+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)
@@ -66,14 +68,14 @@ Simulate adult 'full' age group (single-year age) and 'coarse' age group (collap
 age groups) models from 1970 to 2030 with 10 HIV time steps per year.
 
 ```{r simulate_leapfrog}
-lsimF <- run_model(demp, hivp, 1970:2030, 10L, 
+lsimF <- run_model(demp, hivp, 1970:2030, 10L,
                    hiv_age_stratification = "full", run_child_model = FALSE)
-lsimC <- run_model(demp, hivp, 1970:2030, 10L, 
+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"` 
+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.
 
 ```{r sim_prev}
@@ -88,7 +90,7 @@ lines(1970:2030, prevC, col = 2)
 
 plot(1970:2030, deathsF, type = "l", main = "AIDS Deaths 50+ years")
 lines(1970:2030, deathsC, col = 2)
-``` 
+```
 
 ## Benchmarking
 
@@ -119,8 +121,8 @@ The code uses header-only open source libraries to maximize portability.
 
 ### R functions
 
-The file `src/frogger.cpp` contains R wrapper functions for the model simulation 
-via [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html) and 
+The file `src/frogger.cpp` contains R wrapper functions for the model simulation
+via [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html) and
 [RcppEigen](http://dirk.eddelbuettel.com/code/rcpp.eigen.html).
 
 

README.md

@@ -44,10 +44,12 @@ The simulation model is callable in R via a wrapper function
 You can control how the simulation model is run with the following
 arguments:
 
+- `run_hiv_simulation` which is `TRUE` by default. Set to `FALSE` to
+  turn off the HIV simulation and run only the demographic projection.
 - `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 child portion of the model.
 
 ## Example
 
@@ -60,7 +62,7 @@ Prepare model inputs.
 ``` r
 library(frogger)
 
-pjnz <- system.file("pjnz/bwa_aim-adult-art-no-special-elig_v6.13_2022-04-18.PJNZ", 
+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)
@@ -72,9 +74,9 @@ Simulate adult ‘full’ age group (single-year age) and ‘coarse’ age group
 per year.
 
 ``` r
-lsimF <- run_model(demp, hivp, 1970:2030, 10L, 
+lsimF <- run_model(demp, hivp, 1970:2030, 10L,
                    hiv_age_stratification = "full", run_child_model = FALSE)
-lsimC <- run_model(demp, hivp, 1970:2030, 10L, 
+lsimC <- run_model(demp, hivp, 1970:2030, 10L,
                    hiv_age_stratification = "coarse", run_child_model = FALSE)
 ```
 

configure

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-$R_HOME/bin/Rscript inst/cpp_generation/generate.R
+##$R_HOME/bin/Rscript inst/cpp_generation/generate.R

frogger.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: f4ca7c6e-22e0-47c2-85b1-781bf7e5f806
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

inst/cpp_generation/model_input.csv

@@ -4,22 +4,22 @@ Sx,Demography.survival_probability,real_type,,,FALSE,3,base.pAG + 1,base.NS,proj
 netmigr_adj,Demography.net_migration,real_type,,,FALSE,3,base.pAG,base.NS,proj_years,
 asfr,Demography.age_specific_fertility_rate,real_type,,,FALSE,2,options.p_fertility_age_groups,proj_years,,
 births_sex_prop,Demography.births_sex_prop,real_type,,,FALSE,2,base.NS,proj_years,,
-incidinput,Incidence.total_rate,real_type,,,FALSE,1,proj_years,,,
-incrr_age,Incidence.relative_risk_age,real_type,,,FALSE,3,base.pAG - options.p_idx_hiv_first_adult,base.NS,proj_years,
-incrr_sex,Incidence.relative_risk_sex,real_type,,,FALSE,1,proj_years,,,
-cd4_mort,NaturalHistory.cd4_mortality,real_type,,,FALSE,3,base.hDS,base.hAG,base.NS,
-cd4_prog,NaturalHistory.cd4_progression,real_type,,,FALSE,3,base.hDS - 1,base.hAG,base.NS,
-artcd4elig_idx,Art.idx_hm_elig,int,,,TRUE,1,proj_years,,,
-cd4_initdist,NaturalHistory.cd4_initial_distribution,real_type,,,FALSE,3,base.hDS,base.hAG,base.NS,
-art_mort,Art.mortality,real_type,,,FALSE,4,base.hTS,base.hDS,base.hAG,base.NS
-artmx_timerr,Art.mortaility_time_rate_ratio,real_type,,,FALSE,2,base.hTS,proj_years,,
-art_dropout_recover_cd4,Art.dropout_recover_cd4,int,,,FALSE,1,1,,,
-art_dropout_rate,Art.dropout_rate,real_type,,,FALSE,1,proj_years,,,
-art15plus_num,Art.adults_on_art,real_type,,,FALSE,2,base.NS,proj_years,,
-art15plus_isperc,Art.adults_on_art_is_percent,int,,,FALSE,2,base.NS,proj_years,,
-,Art.h_art_stage_dur,real_type,,0.5,FALSE,1,base.hTS - 1,,,
-scale_cd4_mort,NaturalHistory.scale_cd4_mortality,int,,,FALSE,1,1,,,
-art_alloc_mxweight,Art.initiation_mortality_weight,real_type,,,FALSE,1,1,,,
+incidinput,Incidence.total_rate,real_type,ModelVariant::run_hiv_simulation,,FALSE,1,proj_years,,,
+incrr_age,Incidence.relative_risk_age,real_type,ModelVariant::run_hiv_simulation,,FALSE,3,base.pAG - options.p_idx_hiv_first_adult,base.NS,proj_years,
+incrr_sex,Incidence.relative_risk_sex,real_type,ModelVariant::run_hiv_simulation,,FALSE,1,proj_years,,,
+cd4_mort,NaturalHistory.cd4_mortality,real_type,ModelVariant::run_hiv_simulation,,FALSE,3,base.hDS,base.hAG,base.NS,
+cd4_prog,NaturalHistory.cd4_progression,real_type,ModelVariant::run_hiv_simulation,,FALSE,3,base.hDS - 1,base.hAG,base.NS,
+artcd4elig_idx,Art.idx_hm_elig,int,ModelVariant::run_hiv_simulation,,TRUE,1,proj_years,,,
+cd4_initdist,NaturalHistory.cd4_initial_distribution,real_type,ModelVariant::run_hiv_simulation,,FALSE,3,base.hDS,base.hAG,base.NS,
+art_mort,Art.mortality,real_type,ModelVariant::run_hiv_simulation,,FALSE,4,base.hTS,base.hDS,base.hAG,base.NS
+artmx_timerr,Art.mortaility_time_rate_ratio,real_type,ModelVariant::run_hiv_simulation,,FALSE,2,base.hTS,proj_years,,
+art_dropout_recover_cd4,Art.dropout_recover_cd4,int,ModelVariant::run_hiv_simulation,,FALSE,1,1,,,
+art_dropout_rate,Art.dropout_rate,real_type,ModelVariant::run_hiv_simulation,,FALSE,1,proj_years,,,
+art15plus_num,Art.adults_on_art,real_type,ModelVariant::run_hiv_simulation,,FALSE,2,base.NS,proj_years,,
+art15plus_isperc,Art.adults_on_art_is_percent,int,ModelVariant::run_hiv_simulation,,FALSE,2,base.NS,proj_years,,
+,Art.h_art_stage_dur,real_type,ModelVariant::run_hiv_simulation,0.5,FALSE,1,base.hTS - 1,,,
+scale_cd4_mort,NaturalHistory.scale_cd4_mortality,int,ModelVariant::run_hiv_simulation,,FALSE,1,1,,,
+art_alloc_mxweight,Art.initiation_mortality_weight,real_type,ModelVariant::run_hiv_simulation,,FALSE,1,1,,,
 paed_incid_input,Children.hc_nosocomial,real_type,ModelVariant::run_child_model,,FALSE,1,proj_years,,,
 paed_cd4_dist,Children.hc1_cd4_dist,real_type,ModelVariant::run_child_model,,FALSE,1,children.hc2DS,,,
 paed_cd4_transition,Children.hc_cd4_transition,real_type,ModelVariant::run_child_model,,FALSE,2,children.hc2DS,children.hc1DS,,

inst/cpp_generation/model_output.csv

@@ -2,15 +2,15 @@ r_name,cpp_name,r_type,model_variant,output_when,dims,dim1,dim2,dim3,dim4,dim5
 p_total_pop,p_total_pop,REAL,ModelVariant,,3,base.pAG,base.NS,output_years,,
 births,births,REAL,ModelVariant,,1,output_years,,,,
 p_total_pop_natural_deaths,p_total_pop_natural_deaths,REAL,ModelVariant,,3,base.pAG,base.NS,output_years,,
-p_hiv_pop,p_hiv_pop,REAL,ModelVariant,,3,base.pAG,base.NS,output_years,,
-p_hiv_pop_natural_deaths,p_hiv_pop_natural_deaths,REAL,ModelVariant,,3,base.pAG,base.NS,output_years,,
-h_hiv_adult,h_hiv_adult,REAL,ModelVariant,,4,base.hDS,base.hAG,base.NS,output_years,
-h_art_adult,h_art_adult,REAL,ModelVariant,,5,base.hTS,base.hDS,base.hAG,base.NS,output_years
-h_hiv_deaths_no_art,h_hiv_deaths_no_art,REAL,ModelVariant,,4,base.hDS,base.hAG,base.NS,output_years,
-p_infections,p_infections,REAL,ModelVariant,,3,base.pAG,base.NS,output_years,,
-h_hiv_deaths_art,h_hiv_deaths_art,REAL,ModelVariant,,5,base.hTS,base.hDS,base.hAG,base.NS,output_years
-h_art_initiation,h_art_initiation,REAL,ModelVariant,,4,base.hDS,base.hAG,base.NS,output_years,
-p_hiv_deaths,p_hiv_deaths,REAL,ModelVariant,,3,base.pAG,base.NS,output_years,,
+p_hiv_pop,p_hiv_pop,REAL,HivSimulation,ModelVariant::run_hiv_simulation,3,base.pAG,base.NS,output_years,,
+p_hiv_pop_natural_deaths,p_hiv_pop_natural_deaths,REAL,HivSimulation,ModelVariant::run_hiv_simulation,3,base.pAG,base.NS,output_years,,
+h_hiv_adult,h_hiv_adult,REAL,HivSimulation,ModelVariant::run_hiv_simulation,4,base.hDS,base.hAG,base.NS,output_years,
+h_art_adult,h_art_adult,REAL,HivSimulation,ModelVariant::run_hiv_simulation,5,base.hTS,base.hDS,base.hAG,base.NS,output_years
+h_hiv_deaths_no_art,h_hiv_deaths_no_art,REAL,HivSimulation,ModelVariant::run_hiv_simulation,4,base.hDS,base.hAG,base.NS,output_years,
+p_infections,p_infections,REAL,HivSimulation,ModelVariant::run_hiv_simulation,3,base.pAG,base.NS,output_years,,
+h_hiv_deaths_art,h_hiv_deaths_art,REAL,HivSimulation,ModelVariant::run_hiv_simulation,5,base.hTS,base.hDS,base.hAG,base.NS,output_years
+h_art_initiation,h_art_initiation,REAL,HivSimulation,ModelVariant::run_hiv_simulation,4,base.hDS,base.hAG,base.NS,output_years,
+p_hiv_deaths,p_hiv_deaths,REAL,HivSimulation,ModelVariant::run_hiv_simulation,3,base.pAG,base.NS,output_years,,
 hc1_hiv_pop,hc1_hiv_pop,REAL,ChildModel,ModelVariant::run_child_model,5,children.hc1DS,children.hcTT,children.hc1AG,base.NS,output_years
 hc2_hiv_pop,hc2_hiv_pop,REAL,ChildModel,ModelVariant::run_child_model,5,children.hc2DS,children.hcTT,children.hc2AG,base.NS,output_years
 hc1_art_pop,hc1_art_pop,REAL,ChildModel,ModelVariant::run_child_model,5,base.hTS,children.hc1DS,children.hc1AG,base.NS,output_years