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108 lines
3.1 KiB
Markdown
108 lines
3.1 KiB
Markdown
# aVirtualTwins
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[](https://cran.r-project.org/package=aVirtualTwins)
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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)
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VirtualTwins is a method of subgroup identification from randomized clinical trial data.
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In 2015, as an intern in a french pharmaceutical group, i worked on this method and develop a package based on Jared Foster and al method.
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## (Very) Quick Preview
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```r
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# Load data
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data(sepsis)
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# Format data
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vt.obj <- vt.data(dataset = sepsis,
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outcome.field = "survival",
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treatment.field = "THERAPY",
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interactions = TRUE)
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# Print Incidences of sepsis data
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vt.obj$getIncidences()
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# $table
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# trt
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# resp 0 1 sum
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# 0 101 188 289
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# 1 52 129 181
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# sum 153 317 470
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# Incidence 0.34 0.407 0.385
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#
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# $rr
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# [1] 1.197059
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#
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# First step : create random forest model
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vt.for <- vt.forest(forest.type = "one",
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vt.data = vt.obj,
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interactions = TRUE,
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ntree = 500)
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# Second step : find rules in data
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vt.trees <- vt.tree(tree.type = "class",
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vt.difft = vt.for,
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threshold = quantile(vt.for$difft, seq(.5,.8,.1)),
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maxdepth = 2)
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# Print results
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vt.sbgrps <- vt.subgroups(vt.trees)
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knitr::kable(vt.sbgrps)
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```
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| |Subgroup |Subgroup size |Treatement event rate |Control event rate |Treatment sample size |Control sample size | RR (resub)| RR (snd)|
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|:-----|:---------------------------|:-------------|:---------------------|:------------------|:---------------------|:-------------------|----------:|--------:|
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|tree1 |PRAPACHE>=26.5 |157 |0.752 |0.327 |105 |52 | 2.300| 1.856|
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|tree3 |PRAPACHE>=26.5 & AGE>=51.74 |120 |0.897 |0.31 |78 |42 | 2.894| 1.991|
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## Infos
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Currently this package works for RCT with two treatments groups and binary outcome.
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Most of the package use Reference Class programing (in R). Feel free to create your own classes.
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Of course, subgroup identification in general with two treatment and severals group can be possible.
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## Help & Documentation
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See wiki tab.
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Or:
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``` r
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vignette("full-example", package = "aVirtualTwins")
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```
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Or:
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Here's a link to my intern dissertation (french version) [La recherche de sous-groupes par Virtual Twins](http://upload.timfaitsoncinema.fr/p/2016-09/57e6a8ff.pdf) (parts V & VI).
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## Install
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``` r
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# use devtools library
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library(devtools)
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# install from github
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devtools::install_github("prise6/aVirtualTwins", build_vignettes = TRUE)
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# load library
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library(aVirtualTwins)
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```
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## To-do list
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* Link to my simulation
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* ~~Submit to CRAN~~
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* Use R6 for perfs issues
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* ~~Vignette on-line~~
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## News
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See NEWS file
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## Contact
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vieille.francois _at_ gmail.com
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