In mrc-ide/leapfrog-hiv: Multistate Population Projection Model for Demographic and HIV Estimation

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options(tidyverse.quiet = TRUE)

leapfrog

Leapfrog is a multistate population projection model for demographic and HIV epidemic estimation.

The name leapfrog is in honor of Professor Basia Zaba.

Installation

Install the development version from GitHub via devtools:

# install.packages("devtools")
devtools::install_github("mrc-ide/leapfrog")

Example

Construct a sparse Leslie matrix:

library(tidyverse)
library(leapfrog)
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)

Simulate a cohort component population projection:

pop_proj <- ccmppR(basepop = as.numeric(burkina.faso.females$baseline.pop.counts),
                   sx = burkina.faso.females$survival.proportions,
                   fx = burkina.faso.females$fertility.rates[4:10, ],
                   gx = burkina.faso.females$migration.proportions,
                   srb = rep(1.05, ncol(burkina.faso.females$survival.proportions)),
                   age_span = 5,
                   fx_idx = 4)
pop_proj$population[ , c(1, 2, 10)]

TMB

Calculate a population projection in TMB. Carry forward 2000 values for two further periods to explore projections.

basepop_init <- as.numeric(burkina.faso.females$baseline.pop.counts)

sx_init <- burkina.faso.females$survival.proportions
sx_init <- cbind(sx_init, `2005` = sx_init[ , "2000"], `2010` = sx_init[ , "2000"])

fx_init <- burkina.faso.females$fertility.rates[4:10, ]
fx_init <- cbind(fx_init, `2005` = fx_init[ , "2000"], `2010` = fx_init[ , "2000"])

gx_init <- burkina.faso.females$migration.proportions
gx_init <- cbind(gx_init, `2005` = gx_init[ , "2000"], `2010` = gx_init[ , "2000"])

log_basepop_mean <- as.vector(log(basepop_init))
logit_sx_mean <- as.vector(qlogis(sx_init))
log_fx_mean <- as.vector(log(fx_init))
gx_mean <- as.vector(gx_init)

data <- list(log_basepop_mean = log_basepop_mean,
             logit_sx_mean = logit_sx_mean,
             log_fx_mean = log_fx_mean,
             gx_mean = gx_mean,
             srb = rep(1.05, ncol(sx_init)),
             age_span = 5,
             n_steps = ncol(sx_init),
             fx_idx = 4L,
             fx_span = 7L,
             census_log_pop = log(burkina.faso.females$census.pop.counts),
             census_year_idx = c(4L, 6L, 8L, 10L))
par <- list(log_tau2_logpop = 0,
            log_tau2_sx = 0,
            log_tau2_fx = 0,
            log_tau2_gx = 0,
            log_basepop = log_basepop_mean,
            logit_sx = logit_sx_mean,
            log_fx = log_fx_mean,
            gx = gx_mean)

obj <- make_tmb_obj(data, par)

init_sim <- obj$report()
matrix(init_sim$population, nrow = 17)[ , data$census_year_idx]

obj$fn()


input <- list(data = data, par_init = par)
fit <- fit_tmb(input)

fit[1:6]

Sample from posterior distribution and generate outputs

fit <- sample_tmb(fit)



colnames(fit$sample$population) <- 1:ncol(fit$sample$population)
colnames(fit$sample$migrations) <- 1:ncol(fit$sample$migrations)
colnames(fit$sample$fx) <- 1:ncol(fit$sample$fx)

init_pop_mat <- ccmpp_leslieR(basepop_init, sx_init, fx_init, gx_init,
                              srb = rep(1.05, ncol(sx_init)), age_span = 5, fx_idx = 4)

df <- crossing(year = seq(1960, 2015, 5),
               sex = "female",
               age_group = c(sprintf("%02d-%02d", 0:15*5, 0:15*5+4), "80+")) %>%
  mutate(init_pop = as.vector(init_pop_mat))

census_pop <- crossing(sex = "female",
                       age_group = c(sprintf("%02d-%02d", 0:15*5, 0:15*5+4), "80+")) %>%
  bind_cols(as_tibble(burkina.faso.females$census.pop.counts)) %>%
  gather(year, census_pop, `1975`:`2005`) %>%
  type_convert(cols(year = col_double()))

df <- df %>%
  left_join(census_pop) %>%
  bind_cols(as_tibble(fit$sample$population)) %>%
  gather(sample, value, `1`:last_col())

agepop <- df %>%
  group_by(year, sex, age_group) %>%
  summarise(init_pop = mean(init_pop),
            census_pop = mean(census_pop),
            mean = mean(value),
            lower = quantile(value, 0.025),
            upper = quantile(value, 0.975))

totalpop <- df %>%
  group_by(year, sample) %>%
  summarise(init_pop = sum(init_pop),
            census_pop = sum(census_pop),
            value = sum(value)) %>%
  group_by(year) %>%
  summarise(init_pop = mean(init_pop),
            census_pop = mean(census_pop),
            mean = mean(value),
            lower = quantile(value, 0.025),
            upper = quantile(value, 0.975))

ggplot(totalpop, aes(year, mean, ymin = lower, ymax = upper)) +
  geom_ribbon(alpha = 0.2) +
  geom_line() +
  geom_line(aes(y = init_pop), linetype = "dashed") +
  geom_point(aes(y = census_pop), shape = 4, color = "darkred", stroke = 2) +
  scale_y_continuous("Total population (millions)", labels = scales::number_format(scale = 1e-6)) +
  expand_limits(y = 0) +
  labs(x = NULL) +
  theme_light() +
  ggtitle("BFA females: total population")

ggplot(agepop, aes(age_group, mean, ymin = lower, ymax = upper, group = 1)) +
  geom_ribbon(alpha = 0.2) +
  geom_line() +
  geom_line(aes(y = init_pop), linetype = "dashed") +
  geom_point(aes(y = census_pop), color = "darkred") +
  facet_wrap(~year, scales = "free_y") + 
  scale_y_continuous("Total population (thousands)", labels = scales::number_format(scale = 1e-3)) +
  expand_limits(y = 0) +
  theme_light() +
  theme(axis.text.x = element_text(angle = 30, hjust = 1),
        panel.grid = element_blank()) +
  ggtitle("BFA females: population by age")

Posterior distribution for TFR:

asfr <- crossing(year = seq(1960, 2010, 5),
                 age_group = sprintf("%02d-%02d", 3:9*5, 3:9*5+4)) %>%
  mutate(init_asfr = as.vector(fx_init)) %>%
  bind_cols(as_tibble(fit$sample$fx)) %>%
  gather(sample, value, `1`:last_col()) 

tfr <- asfr %>%
  group_by(year, sample) %>%
  summarise(init_tfr = 5 * sum(init_asfr),
            value = 5 * sum(value)) %>%
  group_by(year) %>%
  summarise(init_tfr = mean(init_tfr),
         mean = mean(value),
         lower = quantile(value, 0.025),
         upper = quantile(value, 0.975))

ggplot(tfr, aes(year, mean, ymin = lower, ymax = upper)) +
  geom_ribbon(alpha = 0.2) +
  geom_line() +
  geom_line(aes(y = init_tfr), linetype = "dashed") +
  scale_y_continuous("Total fertility rate", limits = c(5, 9)) +
  labs(x = NULL) +
  theme_light() +
  theme(panel.grid = element_blank()) +
  ggtitle("BFA: total fertility rate")

migrations <- crossing(year = seq(1960, 2010, 5),
                       age_lower = 0:16*5) %>%
  mutate(init_migrations = init_sim$migrations) %>%
  bind_cols(as_tibble(fit$sample$migrations)) %>%
  gather(sample, value, `1`:last_col()) 

total_migrations <- migrations %>%
  group_by(year, sample) %>%
  summarise(init_migrations = sum(init_migrations),
            value = sum(value)) %>%
  group_by(year) %>%
  summarise(init_migrations = mean(init_migrations),
         mean = mean(value),
         lower = quantile(value, 0.025),
         upper = quantile(value, 0.975))

ggplot(total_migrations, aes(year, mean, ymin = lower, ymax = upper)) +
  geom_ribbon(alpha = 0.2) +
  geom_line() +
  geom_line(aes(y = init_migrations), linetype = "dashed") +
  scale_y_continuous("Net migration (1000s)",
                     labels = scales::number_format(scale=1e-3)) +
  labs(x = NULL) +
  theme_light() +
  theme(panel.grid = element_blank()) +
  ggtitle("BFA: total net migrations (1000s)")

Code design

Simulation model

The simulation model is implemented as templated C++ code in src/ccmpp.h. This is 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.

Statistical inference

The objective function (the negative log posterior density) is implemented in templated C++ code in the script src/TMB/ccmpp_tmb.hpp using probability functions from the Template Model Builder (TMB) R package. The TMB package provides estimates of the gradient of the objective function via automatic differentiation and Laplace approximation to integrate random effects.

The posterior density can also be sampled from using Hamiltonian Monte Carlo in Stan using the tmbstan package.

Latent Gaussian models for model components (fertiliy rates, mortality rates, migration rates) are implemented using linear algebra tools from the Eigen package. Predicted values are coerced into arrays for the CCMPP model inputs.

R functions

The file src/ccmppR.cpp contains R wrapper functions for the model simulation via Rcpp and RcppEigen.

Development notes

Simulation model

The CCMPP model is implemented as a sparse Leslie matrix formulation and using direct calculation of the projection in arrays so that interim outputs (deaths, births, migrations) are also saved. The array-based implementation appears to be faster.
Class structure for popualtion projection model needs review.
Specifying static dimensions for the state space may improve efficiency. This should be possible for common options (5x5 year, 1x1 year) through templating.
The model was implemented using Eigen containers following the initial sparse Leslie matrix specification. However, multi-dimensional arrays in the boost library may be preferable.

TMB

Further investigation is needed about the portability of AD objective function DLLs outside of the R environment.

TMB model code and testing are implemented following templates from the TMBtools package with guidance for package development with both TMB models and Rcpp code. * To add a new TMB model, save the model template in the src/TMB with extension .hpp. The model name must match the file name. The signature is slightly different -- see other .hpp files for example. * Call TMBtools::export_models() to export the new TMB model to the meta-model list. * When constructing the objective function with TMB::MakeADFun, use DLL= "leapfrog_TMBExports" and add an additional value model = "<model_name>" to the data list.