aVirtualTwins/README.md

# aVirtualTwins

An adaptation of VirtualTwins method from [Foster, J. C., Taylor, J. M.G. and Ruberg, S. J. (2011)](http://onlinelibrary.wiley.com/doi/10.1002/sim.4322/abstract)

VirtualTwins is a method of subgroup identification from randomized clinical trial data.

As an intern in a french pharmaceutical group, i worked on this method and develop a package based on Jared Foster and al method.

## (Very) Quick Preview

```r
# Load data
data(sepsis)
# Format data
vt.obj <- vt.data(sepsis, "survival", "THERAPY", T)
# First step : create random forest model
vt.for <- vt.forest("one", vt.obj, T, ntree = 500)
# Second step : find rules in data 
vt.trees <- vt.tree("class", vt.for, threshold = quantile(vt.for$difft, seq(.5,.8,.1)), maxdepth = 2)
# Print results
(vt.subgroups <- lapply(vt.trees, function(x)x$getRules(only.fav = T, verbose = F)))
```
|        |Subgroup                    |Subgroup size |Treatement event rate |Control event rate |Treatment sample size |Control sample size | RR (resub)| RR (snd)|
|:-------|:---------------------------|:-------------|:---------------------|:------------------|:---------------------|:-------------------|----------:|--------:|
|tree1   |PRAPACHE>=26.5              |157           |0.752                 |0.327              |105                   |52                  |      2.300|    1.873|
|tree2   |PRAPACHE>=26.5              |157           |0.752                 |0.327              |105                   |52                  |      2.300|    1.873|
|tree3.3 |PRAPACHE>=26.5              |157           |0.752                 |0.327              |105                   |52                  |      2.300|    1.873|
|tree3.7 |PRAPACHE>=26.5 & AGE>=54.88 |111           |0.887                 |0.325              |71                    |40                  |      2.729|    2.026|
|tree4.3 |PRAPACHE>=26.5              |157           |0.752                 |0.327              |105                   |52                  |      2.300|    1.873|
|tree4.7 |PRAPACHE>=26.5 & AGE>=54.88 |111           |0.887                 |0.325              |71                    |40                  |      2.729|    2.026|



## Infos 

Currently this package works for RCT with two treatments groups and binary outcome.

This is the *dev version 0.0.0.2* and often updated.

Most of the package use Reference Class programing (in R). Feel free to create your own classes.

I got a *WARNING* when Checking package for "cheking PDF version of manual" because of my version of LaTeX. Need to fix it.

## To-do list

* Description and help
* Vignette example
* ...

## Install

``` r
# use devtools library
library(devtools)
# install from github
devtools::install_github("prise6/aVirtualTwins@dev")
# load library
library(aVirtualTwins)
```

## Help

* _Vignette is really not finished ..._

See [full-example](http://htmlpreview.github.io/?https://github.com/prise6/aVirtualTwins/blob/dev/inst/doc/full-example.html)

or when installed : 
``` r
vignette("full-example", package = "aVirtualTwins")
```

## Few Examples

* _Coming..._