Package index • cd4backcalc

Simulation

Simulate HIV diagnosis data for model fitting

simulate_diagnoses(): Simulate HIV Epidemic Data
sim_remodel(): Remodel the simulated diagnosis data for fitting a different model type.

Model fitting

Fit and configure CD4-staged back-calculation models

run_backcalc(): Run CD4 back-calculation model
create_stan_inits(): Create initial values for Stan from a fitted model

Visualisation

Plot model estimates, diagnostics, and goodness of fit

plot_estimates(): Plot estimated model quantities
plot_simulations(): Plot simulated quantities
plot_diagnostics(): Plot diagnostics for fitted model
bias_plot(): Box plots of bias.
mse_plot(): Box plots of mean squared error (MSE).

Data extraction

Extract model estimates and data for custom analysis

get_estimates(): Get estimates from HIV model results for plotting.
extract_simulated_quantity(): Extract simulated quantities based on the provided configuration.
extract_real_data(): Extract real data for plotting