mirror of
https://github.com/prise6/aVirtualTwins.git
synced 2024-05-02 19:53:09 +02:00
commit
e78be83e6e
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@ -3,4 +3,5 @@
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^data-raw$
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^data-raw$
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^draft$
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^draft$
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^NEWS$
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^NEWS$
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||||||
^cran-comments.md$
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^cran-comments.md$
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^revdep$
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1
.gitignore
vendored
1
.gitignore
vendored
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@ -3,3 +3,4 @@
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.RData
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.RData
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/drafts/*
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/drafts/*
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inst/doc
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inst/doc
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/revdep/.cache.rds
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16
DESCRIPTION
16
DESCRIPTION
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@ -1,11 +1,11 @@
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Package: aVirtualTwins
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Package: aVirtualTwins
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Type: Package
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Type: Package
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||||||
Title: Adaptation of Virtual Twins Method from Jared Foster
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Title: Adaptation of Virtual Twins Method from Jared Foster
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Version: 1.0.0.9000
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Version: 1.0.1
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Date: 2016-10-09
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Date: 2018-02-03
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Authors@R: person("Francois", "Vieille", email = "vieille.francois@gmail.com",
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Authors@R: c(person("Francois", "Vieille", email = "vieille.francois@gmail.com",
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role = c("aut", "cre"))
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role = c("aut", "cre")), person("Jared", "Foster", email = "jared.foster@nih.gov", role = c("aut")))
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||||||
Description: Research of subgroups in random clinical trials with binary outcome and two treatments groups. This is an adaptation of the Jared Foster method.
|
Description: Research of subgroups in random clinical trials with binary outcome and two treatments groups. This is an adaptation of the Jared Foster method (<https://www.ncbi.nlm.nih.gov/pubmed/21815180>).
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License: GPL-3 | file LICENSE
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License: GPL-3 | file LICENSE
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||||||
URL: https://github.com/prise6/aVirtualTwins
|
URL: https://github.com/prise6/aVirtualTwins
|
||||||
BugReports: https://github.com/prise6/aVirtualTwins/issues
|
BugReports: https://github.com/prise6/aVirtualTwins/issues
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||||||
|
@ -18,7 +18,9 @@ Imports:
|
||||||
Suggests:
|
Suggests:
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||||||
caret,
|
caret,
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||||||
knitr,
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knitr,
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rpart.plot
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rpart.plot,
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rmarkdown,
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e1071
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Depends:
|
Depends:
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R (>= 3.2.0),
|
R (>= 3.2.0),
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||||||
Collate:
|
Collate:
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||||||
|
@ -42,4 +44,4 @@ Collate:
|
||||||
'tree.reg.R'
|
'tree.reg.R'
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||||||
'tree.wrapper.R'
|
'tree.wrapper.R'
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||||||
VignetteBuilder: knitr
|
VignetteBuilder: knitr
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||||||
RoxygenNote: 5.0.1
|
RoxygenNote: 6.0.1
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||||||
|
|
7
NEWS
7
NEWS
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@ -1,3 +1,10 @@
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||||||
|
aVirtualTwins 1.0.1 (2018-01-30)
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||||||
|
----------------------------------------------------------------
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||||||
|
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||||||
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* Fix CRAN warning : CRAN packages using undeclared packages in vignettes
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|
* waiting for submission approval
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||||||
|
|
||||||
|
|
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aVirtualTwins 1.0.0.9000 (2016-10-10)
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aVirtualTwins 1.0.0.9000 (2016-10-10)
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----------------------------------------------------------------
|
----------------------------------------------------------------
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||||||
|
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||||||
|
|
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@ -10,15 +10,8 @@
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#' \code{\link{vt.tree}} is users function.
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#' \code{\link{vt.tree}} is users function.
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||||||
#' }
|
#' }
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#'
|
#'
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||||||
#' @section TODO LIST:
|
|
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#' \emph{last update : 27.07.2015}
|
|
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#' \itemize{
|
|
||||||
#' \item More detailed documentation and vignettes
|
|
||||||
#' \item Write examples
|
|
||||||
#' \item ...
|
|
||||||
#' }
|
|
||||||
#'
|
#'
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||||||
#' See github.com/prise6/aVirtualTwins for last updates.
|
#' See http://github.com/prise6/aVirtualTwins for last updates.
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#'
|
#'
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#' @docType package
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#' @docType package
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#' @name aVirtualTwins
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#' @name aVirtualTwins
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|
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@ -32,23 +32,24 @@
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#' @return \code{VT.difft}
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#' @return \code{VT.difft}
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#'
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#'
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#' @examples
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#' @examples
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#' \dontrun{
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#'
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#' # data(sepsis)
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#' data(sepsis)
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#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
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#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
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#' # inside model :
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#' # inside model :
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#' vt.f <- vt.forest("one", vt.o)
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#' vt.f <- vt.forest("one", vt.o)
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#' # ...
|
#' # ...
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#' # your model :
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#' # your model :
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#' rf <- randomForest(y = vt.o$getY(),
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#' # library(randomForest)
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#' x = vt.o$getX(int = T),
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#' # rf <- randomForest(y = vt.o$getY(),
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#' mtry = 3,
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#' # x = vt.o$getX(int = T),
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#' nodesize = 15)
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#' # mtry = 3,
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#' vt.f <- vt.forest("one", vt.o, model = rf)
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#' # nodesize = 15)
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#' # ...
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#' # vt.f <- vt.forest("one", vt.o, model = rf)
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#' # Can also use ... parameters
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#' # ...
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#' vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
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#' # Can also use ... parameters
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#' # ...
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#' vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
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#' }
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#' # ...
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||||||
|
#'
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||||||
#'
|
#'
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#' @include forest.R difft.R
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#' @include forest.R difft.R
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#'
|
#'
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|
|
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@ -25,8 +25,11 @@
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#'
|
#'
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||||||
#' @examples
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#' @examples
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#' \dontrun{
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#' \dontrun{
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#' data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
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#' data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
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#' }
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#' }
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#' data(sepsis)
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#' data.format <- formatRCTDataset(sepsis, "survival", "THERAPY", T)
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#'
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||||||
#'
|
#'
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||||||
#'
|
#'
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||||||
#'
|
#'
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||||||
|
|
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@ -13,18 +13,19 @@
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#' @param ... parameters of \code{\link{VT.object}}
|
#' @param ... parameters of \code{\link{VT.object}}
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#'
|
#'
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#' @examples
|
#' @examples
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#' \dontrun{
|
#'
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#' data(sepsis)
|
#' data(sepsis)
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#' formatRCTdataset(sepsis, "survival", "THERAPY", T)
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#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
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||||||
#' }
|
|
||||||
#'
|
#'
|
||||||
#' @return \code{VT.object}
|
#' @return \code{VT.object}
|
||||||
#'
|
#'
|
||||||
#' @include object.R
|
#' @include object.R
|
||||||
#'
|
#'
|
||||||
#' @name vt.data
|
#' @name vt.data
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||||||
#'
|
#'
|
||||||
#' @export vt.data
|
#' @export vt.data
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||||||
|
#'
|
||||||
|
#' @seealso \code{\link{formatRCTDataset}}
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||||||
|
|
||||||
vt.data <- function(dataset, outcome.field, treatment.field, interactions = TRUE, ...){
|
vt.data <- function(dataset, outcome.field, treatment.field, interactions = TRUE, ...){
|
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data <- formatRCTDataset(dataset, outcome.field, treatment.field, interactions = TRUE)
|
data <- formatRCTDataset(dataset, outcome.field, treatment.field, interactions = TRUE)
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|
|
44
R/tools.R
44
R/tools.R
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@ -18,18 +18,16 @@
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#' @return data.frame of rules
|
#' @return data.frame of rules
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||||||
#'
|
#'
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||||||
#' @examples
|
#' @examples
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||||||
#' \dontrun{
|
#' data(sepsis)
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||||||
#' # data(sepsis)
|
#' vt.o <- vt.data(sepsis, "survival", "THERAPY", TRUE)
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||||||
#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
#' # inside model :
|
||||||
#' # inside model :
|
#' vt.f <- vt.forest("one", vt.o)
|
||||||
#' vt.f <- vt.forest("one", vt.o)
|
#' # use classification tree
|
||||||
#' # use classification tree
|
#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
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#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
#' # show subgroups
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#' # show subgroups
|
#' subgroups <- vt.subgroups(vt.tr)
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#' vt.subgroups(vt.tr)
|
#' # change options you'll be surprised !
|
||||||
#' # change options you'll be surprised !
|
#' subgroups <- vt.subgroups(vt.tr, verbose = TRUE, tables = TRUE)
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||||||
#' vt.subgroups(vt.tr, verbose = T, tables = T)
|
|
||||||
#' }
|
|
||||||
#'
|
#'
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||||||
#' @export vt.subgroups
|
#' @export vt.subgroups
|
||||||
#'
|
#'
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||||||
|
@ -43,7 +41,7 @@ vt.subgroups <- function(vt.trees, only.leaf = T, only.fav = T, tables = F, verb
|
||||||
unique(do.call(rbind, subgroups))
|
unique(do.call(rbind, subgroups))
|
||||||
}
|
}
|
||||||
else{
|
else{
|
||||||
subgroups <- vt.tree$getRules(only.leaf = only.leaf, only.fav = only.fav, tables = tables, verbose = verbose, compete = compete)
|
subgroups <- vt.trees$getRules(only.leaf = only.leaf, only.fav = only.fav, tables = tables, verbose = verbose, compete = compete)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -62,21 +60,27 @@ vt.getQAOriginal <- function(response, trt, ahat){
|
||||||
}
|
}
|
||||||
|
|
||||||
vt.getTable <- function(table){
|
vt.getTable <- function(table){
|
||||||
if(is.list(table)) table <- table[[1]]
|
if(is.list(table)) table <- table[[1]]
|
||||||
Incidence <- function(X) as.character(round(X[2] / X[3], digits = 3))
|
Incidence <- function(X) round(X[2] / X[3], digits = 3)
|
||||||
t <- stats::addmargins(table, margin = c(1,2), FUN = sum, quiet = T)
|
t <- stats::addmargins(table, margin = c(1,2), FUN = sum, quiet = T)
|
||||||
t <- stats::addmargins(t, FUN = Incidence, margin = 1, quiet = T)
|
t <- stats::addmargins(t, FUN = Incidence, margin = 1, quiet = T)
|
||||||
rr <- as.numeric(t["Incidence", "1"]) / as.numeric(t["Incidence", "0"])
|
rr <- NA_real_
|
||||||
|
if(nrow(t) == 4) rr <- t[4, 2] / t[4, 1]
|
||||||
return(list(table = t, rr = rr))
|
return(list(table = t, rr = rr))
|
||||||
}
|
}
|
||||||
|
|
||||||
vt.getIncidence <- function(df){
|
vt.getIncidence <- function(df){
|
||||||
if (nrow(df) == 0) table.res <- NULL
|
if (nrow(df) == 0) table.res <- NULL
|
||||||
|
if (ncol(df) != 2) table.res <- NULL
|
||||||
else{
|
else{
|
||||||
table.res <- vt.getTable(table(df[, 1],
|
table.res <- vt.getTable(
|
||||||
df[, 2],
|
table(
|
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deparse.level = 2,
|
factor(df[, 1], levels = c(0, 1)),
|
||||||
dnn = c("resp", "trt")))
|
factor(df[, 2], levels = c(0, 1)),
|
||||||
|
deparse.level = 2,
|
||||||
|
dnn = c("resp", "trt")
|
||||||
|
)
|
||||||
|
)
|
||||||
}
|
}
|
||||||
return(table.res)
|
return(table.res)
|
||||||
}
|
}
|
||||||
|
|
20
R/tree.R
20
R/tree.R
|
@ -248,17 +248,17 @@ VT.tree <- setRefClass(
|
||||||
|
|
||||||
if(isTRUE(tables)){
|
if(isTRUE(tables)){
|
||||||
cat("\n")
|
cat("\n")
|
||||||
cat(sprintf("Incidence dans la selection \n"))
|
cat(sprintf("Incidence in selection \n"))
|
||||||
print(incid$table.selected$table)
|
print(incid$table.selected$table)
|
||||||
cat("\n")
|
cat("\n")
|
||||||
cat(sprintf("Risque relatif (resub) : %0.3f \n", incid$table.selected$rr))
|
cat(sprintf("Relative risk (resub) : %0.3f \n", incid$table.selected$rr))
|
||||||
cat(sprintf("Risque relatif (snd) : %0.3f \n\n", incid$table.selected$rr.snd))
|
cat(sprintf("Relative risk (snd) : %0.3f \n\n", incid$table.selected$rr.snd))
|
||||||
|
|
||||||
cat(sprintf("Incidence dans le complementaire\n"))
|
cat(sprintf("Incidence in complement\n"))
|
||||||
print(incid$table.not.selected$table)
|
print(incid$table.not.selected$table)
|
||||||
cat("\n")
|
cat("\n")
|
||||||
cat(sprintf("Risque relatif (resub) : %0.3f \n", incid$table.not.selected$rr))
|
cat(sprintf("Relative risk (resub) : %0.3f \n", incid$table.not.selected$rr))
|
||||||
cat(sprintf("Risque relatif (snd) : %0.3f \n\n", incid$table.not.selected$rr.snd))
|
cat(sprintf("Relative risk (snd) : %0.3f \n\n", incid$table.not.selected$rr.snd))
|
||||||
}
|
}
|
||||||
|
|
||||||
cat("\n\n")
|
cat("\n\n")
|
||||||
|
@ -310,15 +310,15 @@ VT.tree <- setRefClass(
|
||||||
table.A <- table.inc$table.selected
|
table.A <- table.inc$table.selected
|
||||||
table.A.cmpl <- table.inc$table.not.selected
|
table.A.cmpl <- table.inc$table.not.selected
|
||||||
|
|
||||||
cat(sprintf("Incidence dans le sous groupe A\n"))
|
cat(sprintf("Incidence in subgroup A\n"))
|
||||||
print(table.A$table)
|
print(table.A$table)
|
||||||
cat("\n")
|
cat("\n")
|
||||||
cat(sprintf("Risque relatif : %0.3f \n\n", table.A$risque_relatif))
|
cat(sprintf("Relative risk : %0.3f \n\n", table.A$risque_relatif))
|
||||||
|
|
||||||
cat(sprintf("Incidence dans le sous groupe A complementaire\n"))
|
cat(sprintf("Incidence in complement subgroup of A\n"))
|
||||||
print(table.A.cmpl$table)
|
print(table.A.cmpl$table)
|
||||||
cat("\n")
|
cat("\n")
|
||||||
cat(sprintf("Risque relatif : %0.3f \n\n", table.A.cmpl$risque_relatif))
|
cat(sprintf("Relative risk : %0.3f \n\n", table.A.cmpl$risque_relatif))
|
||||||
}else{
|
}else{
|
||||||
return("Empty set")
|
return("Empty set")
|
||||||
}
|
}
|
||||||
|
|
|
@ -11,7 +11,7 @@
|
||||||
#' @export VT.tree.class
|
#' @export VT.tree.class
|
||||||
#'
|
#'
|
||||||
#' @import methods
|
#' @import methods
|
||||||
#' @importFrom rpart rpart
|
#'
|
||||||
VT.tree.class <- setRefClass(
|
VT.tree.class <- setRefClass(
|
||||||
Class = "VT.tree.class",
|
Class = "VT.tree.class",
|
||||||
|
|
||||||
|
|
|
@ -24,21 +24,21 @@
|
||||||
#' dimension. See examples.
|
#' dimension. See examples.
|
||||||
#'
|
#'
|
||||||
#' @examples
|
#' @examples
|
||||||
#' \dontrun{
|
#' data(sepsis)
|
||||||
#' # data(sepsis)
|
#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||||
#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
#' # inside model :
|
||||||
#' # inside model :
|
#' vt.f <- vt.forest("one", vt.o)
|
||||||
#' vt.f <- vt.forest("one", vt.o)
|
#' # use classification tree
|
||||||
#' # use classification tree
|
#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
||||||
#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
#' # return a list
|
||||||
#' # return a list
|
#' class(vt.tr)
|
||||||
#' class(vt.tr)
|
#' # access one of the tree
|
||||||
#' # access one of the tree
|
#' tree1 <- vt.tr$tree1
|
||||||
#' vt.tr$tree1
|
#' # return infos
|
||||||
#' # return infos
|
#' # vt.tr$tree1$getInfos()
|
||||||
#' vt.tr$tree1$getInfos()
|
#' # vt.tr$tree1$getRules()
|
||||||
#' # ...
|
#' # use vt.subgroups tool:
|
||||||
#' }
|
#' subgroups <- vt.subgroups(vt.tr)
|
||||||
#'
|
#'
|
||||||
#' @include tree.R
|
#' @include tree.R
|
||||||
#'
|
#'
|
||||||
|
|
|
@ -1,6 +1,6 @@
|
||||||
# aVirtualTwins
|
# aVirtualTwins
|
||||||
|
|
||||||
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/aVirtualTwins)](http://cran.r-project.org/package=aVirtualTwins)
|
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/aVirtualTwins)](https://cran.r-project.org/package=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)
|
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)
|
||||||
|
|
||||||
|
|
|
@ -1,3 +1,80 @@
|
||||||
|
submission 4
|
||||||
|
|
||||||
|
----------------------------------------------------------------
|
||||||
|
|
||||||
|
## v1.0.1 : patch to cran fix minor issues:
|
||||||
|
|
||||||
|
* make checkable examples : fix subgroups example
|
||||||
|
|
||||||
|
## Test environments
|
||||||
|
|
||||||
|
* Linux, Debian jessie, R 3.4.3
|
||||||
|
* win-builder (devel and release)
|
||||||
|
|
||||||
|
|
||||||
|
## R CMD check result
|
||||||
|
|
||||||
|
Status: OK
|
||||||
|
|
||||||
|
R CMD check results
|
||||||
|
0 errors | 0 warnings | 0 notes
|
||||||
|
|
||||||
|
|
||||||
|
This is the third submission
|
||||||
|
|
||||||
|
----------------------------------------------------------------
|
||||||
|
|
||||||
|
## v1.0.1 : patch to cran fix minor issues:
|
||||||
|
|
||||||
|
* make checkable examples
|
||||||
|
* update version date
|
||||||
|
* add reference to Jared Foster article
|
||||||
|
|
||||||
|
## Test environments
|
||||||
|
|
||||||
|
* Linux, Debian jessie, R 3.4.3
|
||||||
|
* win-builder (devel and release)
|
||||||
|
|
||||||
|
|
||||||
|
## R CMD check result
|
||||||
|
|
||||||
|
Status: OK
|
||||||
|
|
||||||
|
R CMD check results
|
||||||
|
0 errors | 0 warnings | 0 notes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
This is the second submission
|
||||||
|
|
||||||
|
----------------------------------------------------------------
|
||||||
|
|
||||||
|
## v1.0.1 : patch to cran warning:
|
||||||
|
|
||||||
|
>CRAN packages using undeclared packages in vignettes
|
||||||
|
|
||||||
|
`rmarkdown` seems to be the issue. Added `rmarkdown` to suggest field.
|
||||||
|
`e1071` was added too.
|
||||||
|
|
||||||
|
## Test environments
|
||||||
|
|
||||||
|
* Linux, Debian jessie, R 3.4.3
|
||||||
|
* win-builder (devel and release)
|
||||||
|
|
||||||
|
|
||||||
|
## R CMD check result
|
||||||
|
|
||||||
|
Status: OK
|
||||||
|
|
||||||
|
R CMD check results
|
||||||
|
0 errors | 0 warnings | 0 notes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
This is the first submission
|
This is the first submission
|
||||||
|
|
||||||
----------------------------------------------------------------
|
----------------------------------------------------------------
|
||||||
|
|
|
@ -33,13 +33,14 @@ So \emph{absolute} method is :
|
||||||
|
|
||||||
\item{\code{difft}}{vector of difference between twin1 and twin2}
|
\item{\code{difft}}{vector of difference between twin1 and twin2}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
\item{\code{computeDifft()}}{Compute difference between twin1 and twin2. See details.}
|
\item{\code{computeDifft()}}{Compute difference between twin1 and twin2. See details.}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.forest}}, \code{\link{VT.forest.one}},
|
\code{\link{VT.forest}}, \code{\link{VT.forest.one}},
|
||||||
\code{\link{VT.forest.double}}
|
\code{\link{VT.forest.double}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -14,6 +14,7 @@ An abstract reference class to compute twin via random forests
|
||||||
\describe{
|
\describe{
|
||||||
\item{\code{...}}{see fields of \code{\link{VT.difft}}}
|
\item{\code{...}}{see fields of \code{\link{VT.difft}}}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
|
@ -23,7 +24,7 @@ An abstract reference class to compute twin via random forests
|
||||||
|
|
||||||
\item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.}
|
\item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.difft}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
|
\code{\link{VT.difft}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -31,6 +31,7 @@ This is what \code{computeTwin2()} does.
|
||||||
|
|
||||||
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
|
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
|
@ -38,8 +39,8 @@ This is what \code{computeTwin2()} does.
|
||||||
|
|
||||||
\item{\code{computeTwin2()}}{Compute twin2 by the other part of data in the other forest. See details.}
|
\item{\code{computeTwin2()}}{Compute twin2 by the other part of data in the other forest. See details.}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.difft}}, \code{\link{VT.forest}},
|
\code{\link{VT.difft}}, \code{\link{VT.forest}},
|
||||||
\code{\link{VT.forest.one}}
|
\code{\link{VT.forest.one}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -28,13 +28,14 @@ interactions}
|
||||||
|
|
||||||
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
|
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
\item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.}
|
\item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.difft}}, \code{\link{VT.forest}},
|
\code{\link{VT.difft}}, \code{\link{VT.forest}},
|
||||||
\code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
|
\code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -24,6 +24,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do.
|
||||||
|
|
||||||
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
|
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
|
@ -31,7 +32,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do.
|
||||||
|
|
||||||
\item{\code{computeTwin2()}}{Compute twin2 by switching treatment and applying random forest model}
|
\item{\code{computeTwin2()}}{Compute twin2 by switching treatment and applying random forest model}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.double}}
|
\code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.double}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -33,6 +33,7 @@ treatments.}
|
||||||
\item{\code{type}}{Character : binary or continous. Only binary is currently
|
\item{\code{type}}{Character : binary or continous. Only binary is currently
|
||||||
available.}
|
available.}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
|
@ -53,6 +54,7 @@ If trt is not NULL, return predictors for T = trt}
|
||||||
|
|
||||||
\item{\code{switchTreatment()}}{Switch treatment value.}
|
\item{\code{switchTreatment()}}{Switch treatment value.}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\examples{
|
\examples{
|
||||||
\dontrun{
|
\dontrun{
|
||||||
# Default use :
|
# Default use :
|
||||||
|
@ -78,4 +80,3 @@ vt.o$getIncidences()
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.difft}}
|
\code{\link{VT.difft}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -3,10 +3,10 @@
|
||||||
\docType{methods}
|
\docType{methods}
|
||||||
\name{VT.predict}
|
\name{VT.predict}
|
||||||
\alias{VT.predict}
|
\alias{VT.predict}
|
||||||
\alias{VT.predict,RandomForest,data.frame,character-method}
|
|
||||||
\alias{VT.predict,RandomForest,missing,character-method}
|
\alias{VT.predict,RandomForest,missing,character-method}
|
||||||
\alias{VT.predict,randomForest,data.frame,character-method}
|
\alias{VT.predict,RandomForest,data.frame,character-method}
|
||||||
\alias{VT.predict,randomForest,missing,character-method}
|
\alias{VT.predict,randomForest,missing,character-method}
|
||||||
|
\alias{VT.predict,randomForest,data.frame,character-method}
|
||||||
\alias{VT.predict,train,ANY,character-method}
|
\alias{VT.predict,train,ANY,character-method}
|
||||||
\alias{VT.predict,train,missing,character-method}
|
\alias{VT.predict,train,missing,character-method}
|
||||||
\title{VT.predict generic function}
|
\title{VT.predict generic function}
|
||||||
|
|
|
@ -52,6 +52,7 @@ screening field}
|
||||||
|
|
||||||
\item{\code{Ahat}}{vector Indicator of beglonging to Ahat}
|
\item{\code{Ahat}}{vector Indicator of beglonging to Ahat}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\section{Methods}{
|
\section{Methods}{
|
||||||
|
|
||||||
\describe{
|
\describe{
|
||||||
|
@ -74,7 +75,7 @@ screening field}
|
||||||
|
|
||||||
\item{\code{run(...)}}{Compute tree with rpart parameters}
|
\item{\code{run(...)}}{Compute tree with rpart parameters}
|
||||||
}}
|
}}
|
||||||
|
|
||||||
\seealso{
|
\seealso{
|
||||||
\code{\link{VT.tree.reg}}, \code{\link{VT.tree.class}}
|
\code{\link{VT.tree.reg}}, \code{\link{VT.tree.class}}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -4,6 +4,7 @@
|
||||||
\name{aVirtualTwins}
|
\name{aVirtualTwins}
|
||||||
\alias{aVirtualTwins}
|
\alias{aVirtualTwins}
|
||||||
\alias{aVirtualTwins-package}
|
\alias{aVirtualTwins-package}
|
||||||
|
\alias{aVirtualTwins-package}
|
||||||
\title{aVirtualTwins : An adapation of VirtualTwins method created by Jared Foster.}
|
\title{aVirtualTwins : An adapation of VirtualTwins method created by Jared Foster.}
|
||||||
\description{
|
\description{
|
||||||
aVirtualTwins is written mainly with reference classes. Briefly, there is three kinds of class :
|
aVirtualTwins is written mainly with reference classes. Briefly, there is three kinds of class :
|
||||||
|
@ -15,15 +16,6 @@ aVirtualTwins is written mainly with reference classes. Briefly, there is three
|
||||||
\code{\link{vt.tree}} is users function.
|
\code{\link{vt.tree}} is users function.
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
\section{TODO LIST}{
|
\details{
|
||||||
|
See http://github.com/prise6/aVirtualTwins for last updates.
|
||||||
\emph{last update : 27.07.2015}
|
|
||||||
\itemize{
|
|
||||||
\item More detailed documentation and vignettes
|
|
||||||
\item Write examples
|
|
||||||
\item ...
|
|
||||||
}
|
}
|
||||||
|
|
||||||
See github.com/prise6/aVirtualTwins for last updates.
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
|
@ -37,10 +37,12 @@ running VirtualTwins with interaction, it creates dummy variables.
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
\dontrun{
|
\dontrun{
|
||||||
data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
|
data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
|
||||||
}
|
}
|
||||||
|
data(sepsis)
|
||||||
|
data.format <- formatRCTDataset(sepsis, "survival", "THERAPY", T)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -43,4 +43,3 @@ True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}. \emph{NOTE:} This
|
||||||
subgroup is defined with the \emph{lower} event rate (survival = 1) in
|
subgroup is defined with the \emph{lower} event rate (survival = 1) in
|
||||||
treatement arm.
|
treatement arm.
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -27,10 +27,11 @@ interactions, set to TRUE (default value)}
|
||||||
a VT.object object.
|
a VT.object object.
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
\dontrun{
|
|
||||||
data(sepsis)
|
data(sepsis)
|
||||||
formatRCTdataset(sepsis, "survival", "THERAPY", T)
|
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||||
}
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
\seealso{
|
||||||
|
\code{\link{formatRCTDataset}}
|
||||||
|
}
|
||||||
|
|
|
@ -50,23 +50,23 @@ Is only used with forest.type = "fold". Default to 5. See
|
||||||
parameter forest.type, any of these class can be used with its own parameter.
|
parameter forest.type, any of these class can be used with its own parameter.
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
\dontrun{
|
|
||||||
# data(sepsis)
|
data(sepsis)
|
||||||
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||||
# inside model :
|
# inside model :
|
||||||
vt.f <- vt.forest("one", vt.o)
|
vt.f <- vt.forest("one", vt.o)
|
||||||
# ...
|
# ...
|
||||||
# your model :
|
# your model :
|
||||||
rf <- randomForest(y = vt.o$getY(),
|
# library(randomForest)
|
||||||
x = vt.o$getX(int = T),
|
# rf <- randomForest(y = vt.o$getY(),
|
||||||
mtry = 3,
|
# x = vt.o$getX(int = T),
|
||||||
nodesize = 15)
|
# mtry = 3,
|
||||||
vt.f <- vt.forest("one", vt.o, model = rf)
|
# nodesize = 15)
|
||||||
# ...
|
# vt.f <- vt.forest("one", vt.o, model = rf)
|
||||||
# Can also use ... parameters
|
# ...
|
||||||
vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
|
# Can also use ... parameters
|
||||||
# ...
|
vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
|
||||||
}
|
# ...
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -32,18 +32,15 @@ Function which uses \code{\link{VT.tree}} intern functions. Package
|
||||||
rpart.plot must be loaded. See \code{\link{VT.tree}} for details.
|
rpart.plot must be loaded. See \code{\link{VT.tree}} for details.
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
\dontrun{
|
data(sepsis)
|
||||||
# data(sepsis)
|
vt.o <- vt.data(sepsis, "survival", "THERAPY", TRUE)
|
||||||
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
# inside model :
|
||||||
# inside model :
|
vt.f <- vt.forest("one", vt.o)
|
||||||
vt.f <- vt.forest("one", vt.o)
|
# use classification tree
|
||||||
# use classification tree
|
vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
||||||
vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
# show subgroups
|
||||||
# show subgroups
|
subgroups <- vt.subgroups(vt.tr)
|
||||||
vt.subgroups(vt.tr)
|
# change options you'll be surprised !
|
||||||
# change options you'll be surprised !
|
subgroups <- vt.subgroups(vt.tr, verbose = TRUE, tables = TRUE)
|
||||||
vt.subgroups(vt.tr, verbose = T, tables = T)
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -39,21 +39,20 @@ See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and
|
||||||
\code{\link{VT.tree.reg}} classes.
|
\code{\link{VT.tree.reg}} classes.
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
\dontrun{
|
data(sepsis)
|
||||||
# data(sepsis)
|
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||||
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
# inside model :
|
||||||
# inside model :
|
vt.f <- vt.forest("one", vt.o)
|
||||||
vt.f <- vt.forest("one", vt.o)
|
# use classification tree
|
||||||
# use classification tree
|
vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
||||||
vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
# return a list
|
||||||
# return a list
|
class(vt.tr)
|
||||||
class(vt.tr)
|
# access one of the tree
|
||||||
# access one of the tree
|
tree1 <- vt.tr$tree1
|
||||||
vt.tr$tree1
|
# return infos
|
||||||
# return infos
|
# vt.tr$tree1$getInfos()
|
||||||
vt.tr$tree1$getInfos()
|
# vt.tr$tree1$getRules()
|
||||||
# ...
|
# use vt.subgroups tool:
|
||||||
}
|
subgroups <- vt.subgroups(vt.tr)
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
5
revdep/check.R
Normal file
5
revdep/check.R
Normal file
|
@ -0,0 +1,5 @@
|
||||||
|
library("devtools")
|
||||||
|
|
||||||
|
revdep_check()
|
||||||
|
revdep_check_save_summary()
|
||||||
|
revdep_check_print_problems()
|
BIN
revdep/checks.rds
Normal file
BIN
revdep/checks.rds
Normal file
Binary file not shown.
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Reference in a new issue