sickSickerMicrosimPack

sickSickerMicrosimPack provides a set of functions to build and run a microsimulation model with four health states: Healthy (H), Sick (S1), Sicker (S2) and Dead (D). The model is vectorised to efficiently simulate large cohorts of individuals. Transition probabilities can depend on the time spent in a state and on individual characteristics, and both costs and utilities can be modified by covariates.

Structure of GitHub repository

#> .
#> ├── DESCRIPTION
#> ├── LICENSE
#> ├── LICENSE.md
#> ├── Meta
#> │   └── vignette.rds
#> ├── NAMESPACE
#> ├── R
#> │   ├── calc_costsV.R
#> │   ├── calc_discount_wts.R
#> │   ├── calc_effsV.R
#> │   ├── data.R
#> │   ├── run_microSimV.R
#> │   ├── sampleV.R
#> │   └── update_probsV.R
#> ├── README.Rmd
#> ├── README.md
#> ├── _pkgdown.yml
#> ├── codecov.yml
#> ├── data
#> │   ├── cycle_length.rda
#> │   ├── discount_rate_QALYs.rda
#> │   ├── discount_rate_costs.rda
#> │   ├── l_trans_probs.rda
#> │   ├── m_indi_features.rda
#> │   ├── num_cycles.rda
#> │   ├── num_i.rda
#> │   ├── seed.rda
#> │   ├── v_cost_coeffs.rda
#> │   ├── v_starting_states.rda
#> │   ├── v_states_costs.rda
#> │   ├── v_states_costs1.rda
#> │   ├── v_states_costs2.rda
#> │   ├── v_states_names.rda
#> │   ├── v_states_utilities.rda
#> │   ├── v_states_utilities1.rda
#> │   ├── v_states_utilities2.rda
#> │   ├── v_util_coeffs.rda
#> │   ├── v_util_t_decs.rda
#> │   └── wtp.rda
#> ├── data-raw
#> │   └── model_inputs.R
#> ├── doc
#> │   ├── sickSickerMicrosimPack.R
#> │   ├── sickSickerMicrosimPack.Rmd
#> │   └── sickSickerMicrosimPack.html
#> ├── inst
#> │   └── bibliography
#> │       └── references.bib
#> ├── man
#> │   ├── calc_costsV.Rd
#> │   ├── calc_discount_wts.Rd
#> │   ├── calc_effsV.Rd
#> │   ├── cycle_length.Rd
#> │   ├── discount_rate_QALYs.Rd
#> │   ├── discount_rate_costs.Rd
#> │   ├── l_trans_probs.Rd
#> │   ├── m_indi_features.Rd
#> │   ├── num_cycles.Rd
#> │   ├── num_i.Rd
#> │   ├── run_microSimV.Rd
#> │   ├── sampleV.Rd
#> │   ├── seed.Rd
#> │   ├── update_probsV.Rd
#> │   ├── v_cost_coeffs.Rd
#> │   ├── v_starting_states.Rd
#> │   ├── v_states_costs.Rd
#> │   ├── v_states_costs1.Rd
#> │   ├── v_states_costs2.Rd
#> │   ├── v_states_names.Rd
#> │   ├── v_states_utilities.Rd
#> │   ├── v_states_utilities1.Rd
#> │   ├── v_states_utilities2.Rd
#> │   ├── v_util_coeffs.Rd
#> │   ├── v_util_t_decs.Rd
#> │   └── wtp.Rd
#> ├── sickSickerMicrosimPack.Rproj
#> ├── tests
#> │   ├── testthat
#> │   │   ├── test_calc_costsV.R
#> │   │   ├── test_calc_discount_wts.R
#> │   │   ├── test_calc_effsV.R
#> │   │   ├── test_run_microSimV.R
#> │   │   ├── test_sampleV.R
#> │   │   ├── test_update_probsV.R
#> │   │   └── testdata
#> │   │       ├── data_run_microSimV.rds
#> │   │       └── data_update_probsV.rds
#> │   └── testthat.R
#> └── vignettes
#>     └── sickSickerMicrosimPack.Rmd

Installation

You can install the development version of sickSickerMicrosimPack from GitHub with:

# install.packages("pak")
pak::pak("W-Mohammed/sickSickerMicrosimPack")

Alternatively, you can clone the repository and build/install it manually.

Quick example

The following example simulates a small cohort of 10 individuals for five cycles. Individual ages and sexes are sampled, and transition probabilities are provided along with cost and utility parameters. The example returns average costs and QALYs per individual.

# load the package
library(sickSickerMicrosimPack)
# define model inputs
num_i <- 10
num_cycles <- 5
v_start <- rep("H", num_i)
m_feats <- cbind(
  age = rnorm(num_i, 50, 3), 
  sex = sample(c(0,1), num_i, replace = TRUE)
)
v_states_names <- c("H", "S1", "S2", "D")
v_states_costs <- c(H = 2000, S1 = 4000, S2 = 15000, D = 0)
v_cost_coeffs  <- c(age = 11.5, sex = 300)
v_states_utilities <- c(H = 1, S1 = 0.75, S2 = 0.5, D = 0)
v_util_coeffs <- c(age = -0.0018, sex = -0.015)
v_util_t_decs <- c(S1 = -0.0015, S2 = -0.0020)
l_trans_probs <- list(
  p_HD = 0.005, 
  p_HS1 = 0.15, 
  p_S1H = 0.5,
  p_S1S2 = 0.105,
  p_S1D = 0.01488751,
  p_S2D = 0.04877166,
  rp_S1 = 0.2,
  rp_S2 = 0.29
)

res <- run_microSimV(
  v_starting_states = v_start,
  num_i = num_i,
  num_cycles = num_cycles,
  m_indi_features = m_feats,
  v_states_names = v_states_names,
  v_states_costs = v_states_costs,
  v_cost_coeffs = v_cost_coeffs,
  v_states_utilities = v_states_utilities,
  v_util_coeffs = v_util_coeffs,
  v_util_t_decs = v_util_t_decs,
  l_trans_probs = l_trans_probs,
  discount_rate_costs = 0.03,
  discount_rate_QALYs = 0.015,
  cycle_length = 1,
  starting_seed = 1
)

res$mean_costs
#> [1] 14552.97
res$mean_qalys
#> [1] 5.143042

Refer to the documentation of individual functions for further details on parameters and usage.