diff --git a/R/forest.wrapper.R b/R/forest.wrapper.R index e5c5d14..1500c82 100644 --- a/R/forest.wrapper.R +++ b/R/forest.wrapper.R @@ -32,23 +32,24 @@ #' @return \code{VT.difft} #' #' @examples -#' \dontrun{ -#' # data(sepsis) -#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T) -#' # inside model : -#' vt.f <- vt.forest("one", vt.o) -#' # ... -#' # your model : -#' rf <- randomForest(y = vt.o$getY(), -#' x = vt.o$getX(int = T), -#' mtry = 3, -#' 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) -#' # ... -#' } +#' +#' data(sepsis) +#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T) +#' # inside model : +#' vt.f <- vt.forest("one", vt.o) +#' # ... +#' # your model : +#' # library(randomForest) +#' # rf <- randomForest(y = vt.o$getY(), +#' # x = vt.o$getX(int = T), +#' # mtry = 3, +#' # 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) +#' # ... +#' #' #' @include forest.R difft.R #' diff --git a/R/formatRCTDataset.R b/R/formatRCTDataset.R index d37c099..a4fbfa9 100644 --- a/R/formatRCTDataset.R +++ b/R/formatRCTDataset.R @@ -25,8 +25,11 @@ #' #' @examples #' \dontrun{ -#' data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE) -#' } +#' data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE) +#' } +#' data(sepsis) +#' data.format <- formatRCTDataset(sepsis, "survival", "THERAPY", T) +#' #' #' #' diff --git a/R/object.wrapper.R b/R/object.wrapper.R index c09d1c0..bf69b5c 100644 --- a/R/object.wrapper.R +++ b/R/object.wrapper.R @@ -13,18 +13,19 @@ #' @param ... parameters of \code{\link{VT.object}} #' #' @examples -#' \dontrun{ -#' data(sepsis) -#' formatRCTdataset(sepsis, "survival", "THERAPY", T) -#' } +#' +#' data(sepsis) +#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T) #' #' @return \code{VT.object} #' -#' @include object.R +#' @include object.R #' #' @name vt.data #' #' @export vt.data +#' +#' @seealso \code{\link{formatRCTDataset}} vt.data <- function(dataset, outcome.field, treatment.field, interactions = TRUE, ...){ data <- formatRCTDataset(dataset, outcome.field, treatment.field, interactions = TRUE) diff --git a/R/tools.R b/R/tools.R index 4deb750..94974aa 100644 --- a/R/tools.R +++ b/R/tools.R @@ -18,18 +18,16 @@ #' @return data.frame of rules #' #' @examples -#' \dontrun{ -#' # data(sepsis) -#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T) -#' # inside model : -#' vt.f <- vt.forest("one", vt.o) -#' # use classification tree -#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) -#' # show subgroups -#' vt.subgroups(vt.tr) -#' # change options you'll be surprised ! -#' vt.subgroups(vt.tr, verbose = T, tables = T) -#' } +#' data(sepsis) +#' vt.o <- vt.data(sepsis, "survival", "THERAPY", TRUE) +#' # inside model : +#' vt.f <- vt.forest("one", vt.o) +#' # use classification tree +#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) +#' # show subgroups +#' subgroups <- vt.subgroups(vt.tr) +#' # change options you'll be surprised ! +#' subgroups <- vt.subgroups(vt.tr, verbose = TRUE, tables = TRUE) #' #' @export vt.subgroups #' diff --git a/R/tree.class.R b/R/tree.class.R index a2d6e9a..147eed3 100644 --- a/R/tree.class.R +++ b/R/tree.class.R @@ -11,7 +11,7 @@ #' @export VT.tree.class #' #' @import methods -#' @importFrom rpart rpart +#' VT.tree.class <- setRefClass( Class = "VT.tree.class", diff --git a/R/tree.wrapper.R b/R/tree.wrapper.R index 2a1cfec..43a5358 100644 --- a/R/tree.wrapper.R +++ b/R/tree.wrapper.R @@ -24,21 +24,21 @@ #' dimension. See examples. #' #' @examples -#' \dontrun{ -#' # data(sepsis) -#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T) -#' # inside model : -#' vt.f <- vt.forest("one", vt.o) -#' # use classification tree -#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) -#' # return a list -#' class(vt.tr) -#' # access one of the tree -#' vt.tr$tree1 -#' # return infos -#' vt.tr$tree1$getInfos() -#' # ... -#' } +#' data(sepsis) +#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T) +#' # inside model : +#' vt.f <- vt.forest("one", vt.o) +#' # use classification tree +#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) +#' # return a list +#' class(vt.tr) +#' # access one of the tree +#' tree1 <- vt.tr$tree1 +#' # return infos +#' # vt.tr$tree1$getInfos() +#' # vt.tr$tree1$getRules() +#' # use vt.subgroups tool: +#' subgroups <- vt.subgroups(vt.tr) #' #' @include tree.R #' diff --git a/man/aVirtualTwins.Rd b/man/aVirtualTwins.Rd index 8f91663..b4e8383 100644 --- a/man/aVirtualTwins.Rd +++ b/man/aVirtualTwins.Rd @@ -16,15 +16,6 @@ aVirtualTwins is written mainly with reference classes. Briefly, there is three \code{\link{vt.tree}} is users function. } } -\section{TODO LIST}{ - -\emph{last update : 27.07.2015} -\itemize{ - \item More detailed documentation and vignettes - \item Write examples - \item ... +\details{ +See http://github.com/prise6/aVirtualTwins for last updates. } - -See github.com/prise6/aVirtualTwins for last updates. -} - diff --git a/man/formatRCTDataset.Rd b/man/formatRCTDataset.Rd index 0844031..db8ccf9 100644 --- a/man/formatRCTDataset.Rd +++ b/man/formatRCTDataset.Rd @@ -37,8 +37,11 @@ running VirtualTwins with interaction, it creates dummy variables. } \examples{ \dontrun{ -data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE) -} + data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE) +} +data(sepsis) +data.format <- formatRCTDataset(sepsis, "survival", "THERAPY", T) + diff --git a/man/vt.data.Rd b/man/vt.data.Rd index 1b4ddb2..050b80b 100644 --- a/man/vt.data.Rd +++ b/man/vt.data.Rd @@ -27,9 +27,11 @@ interactions, set to TRUE (default value)} a VT.object object. } \examples{ -\dontrun{ - data(sepsis) - formatRCTdataset(sepsis, "survival", "THERAPY", T) -} + +data(sepsis) +vt.o <- vt.data(sepsis, "survival", "THERAPY", T) } +\seealso{ +\code{\link{formatRCTDataset}} +} diff --git a/man/vt.forest.Rd b/man/vt.forest.Rd index ffbf0e1..71abbb3 100644 --- a/man/vt.forest.Rd +++ b/man/vt.forest.Rd @@ -50,22 +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. } \examples{ -\dontrun{ - # data(sepsis) - vt.o <- vt.data(sepsis, "survival", "THERAPY", T) - # inside model : - vt.f <- vt.forest("one", vt.o) - # ... - # your model : - rf <- randomForest(y = vt.o$getY(), - x = vt.o$getX(int = T), - mtry = 3, - 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) - # ... -} + +data(sepsis) +vt.o <- vt.data(sepsis, "survival", "THERAPY", T) +# inside model : +vt.f <- vt.forest("one", vt.o) +# ... +# your model : +# library(randomForest) +# rf <- randomForest(y = vt.o$getY(), +# x = vt.o$getX(int = T), +# mtry = 3, +# 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) +# ... + } diff --git a/man/vt.subgroups.Rd b/man/vt.subgroups.Rd index 5eb2f65..935bb1e 100644 --- a/man/vt.subgroups.Rd +++ b/man/vt.subgroups.Rd @@ -32,17 +32,15 @@ Function which uses \code{\link{VT.tree}} intern functions. Package rpart.plot must be loaded. See \code{\link{VT.tree}} for details. } \examples{ -\dontrun{ - # data(sepsis) - vt.o <- vt.data(sepsis, "survival", "THERAPY", T) - # inside model : - vt.f <- vt.forest("one", vt.o) - # use classification tree - vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) - # show subgroups - vt.subgroups(vt.tr) - # change options you'll be surprised ! - vt.subgroups(vt.tr, verbose = T, tables = T) -} +data(sepsis) +vt.o <- vt.data(sepsis, "survival", "THERAPY", TRUE) +# inside model : +vt.f <- vt.forest("one", vt.o) +# use classification tree +vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) +# show subgroups +subgroups <- vt.subgroups(vt.tr) +# change options you'll be surprised ! +subgroups <- vt.subgroups(vt.tr, verbose = TRUE, tables = TRUE) } diff --git a/man/vt.tree.Rd b/man/vt.tree.Rd index f2e6241..414853f 100644 --- a/man/vt.tree.Rd +++ b/man/vt.tree.Rd @@ -39,20 +39,20 @@ See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and \code{\link{VT.tree.reg}} classes. } \examples{ -\dontrun{ - # data(sepsis) - vt.o <- vt.data(sepsis, "survival", "THERAPY", T) - # inside model : - vt.f <- vt.forest("one", vt.o) - # use classification tree - vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) - # return a list - class(vt.tr) - # access one of the tree - vt.tr$tree1 - # return infos - vt.tr$tree1$getInfos() - # ... -} +data(sepsis) +vt.o <- vt.data(sepsis, "survival", "THERAPY", T) +# inside model : +vt.f <- vt.forest("one", vt.o) +# use classification tree +vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05)) +# return a list +class(vt.tr) +# access one of the tree +tree1 <- vt.tr$tree1 +# return infos +# vt.tr$tree1$getInfos() +# vt.tr$tree1$getRules() +# use vt.subgroups tool: +subgroups <- vt.subgroups(vt.tr) }