# dpasurv

R-package for Dynamic Path Analysis of survival data.

## Overview

The *dpasurv* package is designed to perform dynamic path
analysis via calls to the following principal functions:

`dpa()`

fits the dynamic path models corresponding to a
given dynamic path diagram; returns an object of class dpa
`effect()`

estimates the cumulative direct and indirect
effects from the fitted dpa-object; returns an object of class
effect

The effect-objects can be summed together to obtain the total effect
(i.e. direct effect + indirect effect) as well as plotted with bootstrap
confidence intervals.

## Installation

```
# To install the most recent stable version on CRAN:
install.packages("dpasurv")
# To get bug fixes or new features, install the development version:
devtools::install_github("Novartis/dpasurv")
```

## Usage

A vignette on how to use the *dpasurv* package can be found here,
and basic usage is summarized below:

```
library(dpasurv)
# Perform dynamic path analysis
s <- dpa(Surv(start, stop, event) ~ M + x, list(M ~ x), id = "subject", data = simdata, boot.n = 500)
# Extract direct, indirect and total effect
direct <- effect(x ~ outcome, s, alpha=0.05)
indirect <- effect(x ~ M ~ outcome, s, alpha=0.05)
total <- sum(direct, indirect)
# Plot the results
par(mfrow=c(1,3))
plot(direct); abline(h=0, lty=2, col=2)
plot(indirect); abline(h=0, lty=2, col=2)
plot(total); abline(h=0, lty=2, col=2)
# Plot the results with ggplot2 graphics:
ggplot.effect(list(direct, indirect, total))
```

## Citation

The dpasurv package was created as supplementary code for the
following manuscript:

```
@article{dpasurv,
title={Dynamic path analysis for exploring treatment effect mediation processes in clinical trials with time-to-event endpoints},
author={Kormaksson, M. and Lange, M. R. and Demanse, D. and Strohmaier, S. and Duan, J. and Xie, Q. and Carbini, M. and Bossen, C. and Guettner, A. and Maniero, A.},
journal={Statistics in Medicine (Accepted)},
volume={},
number={},
pages={},
year={2024},
}
```

If you publish results obtained from the dpasurv package, please cite
the above paper.

## Code authors

- Matthias Kormaksson, matthias-1.kormaksson_ext@novartis.com
(maintainer)
- Susanne Strohmaier, susanne.strohmaier@meduniwien.ac.at
- Markus Lange, markus.lange@novartis.com
- David Demanse, david.demanse@novartis.com