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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# multimcm: Multilevel mixture cure modelling in Stan <img src='man/figures/hexbadge.png' align="right" height="139" />
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://github.com/StatisticsHealthEconomics/rstanbmcm/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
The goal of multimcm is to jointly model two event time distributions (e.g. time to disease progression (PFS) and time to death (OS)) within a Bayesian relative survival mixture cure model framework, using the Stan engine called from R.
## Installation
You can install the development version from [GitHub](https://github.com/) with:
``` r
# install.packages("remotes")
remotes::install_github("StatisticsHealthEconomics/multimcm")
```
## Motivation
Mixture cure models are increasingly popular in health problems and in particular in oncology.
A Bayesian paradigm allows the explicitly incorporation of uncertainties and principled synthesis of prior knowledge such as via expert elicitation or previous trials.
By extending current methods to account for the dependence between event times we leverage additional information to make better inferences and decisions.
## Workflow
The Stan engine can be called either with the compile C code or with the Stan script without precompiling.
* The precompiled Stan code is in `inst/stan` and the compiled code in `src/`
* The non-compiled Stan code is in `scripts/`
There are two runner scripts:
* `scripts/stan_checkmate.R`: Run Stan mixture cure model with _separate_ model for PFS and OS data.
* `scripts/stan_checkmate_joint.R`: Run Stan mixture cure model with _joint_ model for PFS and OS data.
## Output
Because the Stan output files are large, we do not save a single list of all model outputs as a single objects.
Instead `stan_filenames.RData` is a list of file names of the model outputs and each output is saved in a separate file.
The file name formats are:
* For the separate OS, PFS models: `stan_<distn>_<event type>_<treatment name>.Rds`
* For the joint OS, PFS models: `stan_<distn>_<distn>_<treatment name>.Rds`
### Code of Conduct
Please note that this project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.