starsimhub/hiv_kenya

Model of HIV transmission and PrEP delivery in Kenya # HIV Kenya Agent-based model of HIV transmission and intervention delivery in Kenya, built on HIVsim/STIsim and Starsim. The model includes structured sexual networks with risk groups, HIV testing (FSW-targeted, general population, and opportunistic), ART, and PrEP. Both Python and R interfaces are provided. The R interface uses rstarsim, which calls the Python engine via reticulate. ## Prerequisites ### Python environment If you are a Python user, do this step. If you are an R user, do this step if you want to use the same Python environment with R. Alternatively, you do not need to install the Python packages directly if you are letting R manage your Python environment (see next section). To install: ```bash pip install -e . ``` or equivalently, `bash install_python.sh`. This will install Starsim and STIsim into your current Python environment. ### R environment (for R users only) To install everything for R, including using an R-managed Python environment, run `bash install_R.sh`, or follow the steps below: ```r # Install core dependencies; takes some time install.packages(c("reticulate", "pak")) pak::pak("starsimhub/rstarsim") # Install Starsim (also creates a Python environment; also takes time) library(starsim) init_starsim() # Install STIsim (does not take much time) library(reticulate) reticulate::py_install("stisim", pip = TRUE) ``` On first use, `rstarsim` will set up a conda environment automatically if needed. To use an existing environment instead (e.g., the one you used `pip install` with above): ```r # Optional custom environment library(starsim) load_starsim("my_env_name") ``` where `"my_env_name"` is the name of your Python environment. ## Quick start (R) Set your working directory to the repo root, then: ```r library(starsim) load_starsim() source("hiv_model.R") # Create and run a single simulation sim <- make_sim() sim$run() # View results df <- sim$to_df(resample = "year", use_years = TRUE, sep = ".") head(df) ``` ### O …