From f8d21ac3a848912f603723c118654b139016aaaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Vieille?= Date: Sun, 9 Oct 2016 02:44:33 +0200 Subject: [PATCH] Update README --- README.md | 48 +++++++++++++++++++++++++++++------------------- 1 file changed, 29 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 7d62cfe..0e7d3a5 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ An adaptation of VirtualTwins method from [Foster, J. C., Taylor, J. M.G. and Ru 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. +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. ## (Very) Quick Preview @@ -12,7 +12,10 @@ As an intern in a french pharmaceutical group, i worked on this method and devel # Load data data(sepsis) # Format data -vt.obj <- vt.data(sepsis, "survival", "THERAPY", T) +vt.obj <- vt.data(dataset = sepsis, + outcome.field = "survival", + treatment.field = "THERAPY", + interactions = TRUE) # Print Incidences of sepsis data vt.obj$getIncidences() # $table @@ -27,12 +30,15 @@ vt.obj$getIncidences() # [1] 1.197059 # # First step : create random forest model -vt.for <- vt.forest("one", vt.obj, T, ntree = 500) +vt.for <- vt.forest(forest.type = "one", + vt.data = vt.obj, + interactions = TRUE, + ntree = 500) # Second step : find rules in data -vt.trees <- vt.tree("class", - vt.for, +vt.trees <- vt.tree(tree.type = "class", + vt.difft = vt.for, threshold = quantile(vt.for$difft, seq(.5,.8,.1)), - maxdepth = 2) + maxdepth = 2) # Print results vt.sbgrps <- vt.subgroups(vt.trees) knitr::kable(vt.sbgrps) @@ -48,31 +54,26 @@ knitr::kable(vt.sbgrps) 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. - +Of course, subgroup identification in general with two treatment and severals group can be possible. ## Help & Documentation -_Vignette is not finished ..._ - -See full-example - -or when installed : ``` r vignette("full-example", package = "aVirtualTwins") ``` +Here's a link to my intern dissertation (french version) [La recher de sous-groupes par Virtual Twins](http://upload.timfaitsoncinema.fr/p/2016-09/57e6a8ff.pdf) (parts V & VI). + + ## Install ``` r # use devtools library library(devtools) # install from github -devtools::install_github("prise6/aVirtualTwins@dev") +devtools::install_github("prise6/aVirtualTwins", build_vignettes = TRUE) # load library library(aVirtualTwins) ``` @@ -80,10 +81,19 @@ library(aVirtualTwins) ## To-do list -* More description -* Finish full-example vignette * Link to my simulation -* ... +* Submit to CRAN +* Use R6 for perfs issues +* Vignette on-line +## News + +See NEWS file + + +## Contact + +vieille.francois _at_ gmail.com +