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avirtualtwins

Adaptation of Virtual Twins method from Jared Foster

https://github.com/prise6/avirtualtwins

Science Score: 23.0%

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    Found 1 DOI reference(s) in README
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    Links to: wiley.com
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Keywords

r rpackage subgroup-identification trials
Last synced: 6 months ago · JSON representation

Repository

Adaptation of Virtual Twins method from Jared Foster

Basic Info
  • Host: GitHub
  • Owner: prise6
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 689 KB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 3
  • Open Issues: 1
  • Releases: 0
Topics
r rpackage subgroup-identification trials
Created over 10 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

aVirtualTwins

CRAN_Status_Badge

An adaptation of VirtualTwins method from Foster, J. C., Taylor, J. M.G. and Ruberg, S. J. (2011)

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

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

```r

Load data

data(sepsis)

Format data

vt.obj <- vt.data(dataset = sepsis, outcome.field = "survival", treatment.field = "THERAPY", interactions = TRUE)

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(forest.type = "one", vt.data = vt.obj, interactions = TRUE, ntree = 500)

Second step : find rules in data

vt.trees <- vt.tree(tree.type = "class", vt.difft = 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.

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

Of course, subgroup identification in general with two treatment and severals group can be possible.

Help & Documentation

See wiki tab.

Or:

r vignette("full-example", package = "aVirtualTwins")

Or:

Here's a link to my intern dissertation (french version) La recherche de sous-groupes par Virtual Twins (parts V & VI).

Install

``` r

use devtools library

library(devtools)

install from github

devtools::installgithub("prise6/aVirtualTwins", buildvignettes = TRUE)

load library

library(aVirtualTwins) ```

To-do list

  • 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

Owner

  • Name: François Vieille
  • Login: prise6
  • Kind: user
  • Location: France

:)

GitHub Events

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  • Watch event: 1
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Last Year
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  • Fork event: 2

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 85
  • Total Committers: 2
  • Avg Commits per committer: 42.5
  • Development Distribution Score (DDS): 0.012
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
prise6 v****s@g****m 84
prise6 f****6@h****r 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 1
  • Average time to close issues: 4 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 1.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • prise6 (1)
  • LuxiCao (1)
  • davidechicco (1)
Pull Request Authors
  • prise6 (1)
Top Labels
Issue Labels
question (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 271 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: aVirtualTwins

Adaptation of Virtual Twins Method from Jared Foster

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 271 Last month
Rankings
Forks count: 21.9%
Stargazers count: 28.5%
Dependent packages count: 29.8%
Average: 33.6%
Dependent repos count: 35.5%
Downloads: 52.3%
Maintainers (1)
vieille.francois@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • methods * imports
  • party * imports
  • randomForest * imports
  • rpart * imports
  • stats * imports
  • caret * suggests
  • e1071 * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • rpart.plot * suggests