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)
# Print Incidences of sepsis data
vt.obj$getIncidences()
# $table
#            trt
# resp        0    1     sum  
#   0         101  188   289  
#   1         52   129   181  
#   sum       153  317   470  
#   Incidence 0.34 0.407 0.385
#
# $rr
# [1] 1.197059
#
# First step : create random forest model
vt.for <- vt.forest("one", vt.obj, T, ntree = 500)
# Second step : find rules in data 
vt.trees <- vt.tree("class",
                    vt.for, 
                    threshold = quantile(vt.for$difft, seq(.5,.8,.1)),
                    maxdepth = 2)
# Print results
vt.sbgrps <- vt.subgroups(vt.trees)
knitr::kable(vt.sbgrps)
```
|      |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|    1.856|
|tree3 |PRAPACHE>=26.5 & AGE>=51.74 |120           |0.897                 |0.31               |78                    |42                  |      2.894|    1.991|



## 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.


## Help & Documentation

_Vignette is not finished ..._

See <a href="http://htmlpreview.github.io/?https://github.com/prise6/aVirtualTwins/blob/dev/inst/doc/full-example.html" target="_blank">full-example</a>

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

## Install

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


## To-do list

* More description
* Finish full-example vignette
* Link to my simulation
* ...