Make example checkable + delete import rpart function

R/forest.wrapper.R

@@ -32,23 +32,24 @@
 #' @return \code{VT.difft}
 #'  
 #' @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)
-#' }   
+#' # ...
+#'    
 #' 
 #' @include forest.R difft.R
 #'   

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)
+#'  
 #'
 #'  
 #'   

R/object.wrapper.R

@@ -13,18 +13,19 @@
 #' @param ... parameters of \code{\link{VT.object}}
 #'   
 #' @examples
-#' \dontrun{
+#' 
-#'  data(sepsis)
+#' data(sepsis)
-#'  formatRCTdataset(sepsis, "survival", "THERAPY", T)
+#' 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)

R/tools.R

@@ -18,18 +18,16 @@
 #' @return data.frame of rules
 #'   
 #' @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) 
-#' }
 #' 
 #' @export vt.subgroups
 #'   

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",
   

R/tree.wrapper.R

@@ -24,21 +24,21 @@
 #'   dimension. See 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
 #'   

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}{
+\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.
-}
-

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)
+ 
 
  
   

man/vt.data.Rd

@@ -27,9 +27,11 @@ interactions, set to TRUE (default value)}
 a VT.object object.
 }
 \examples{
-\dontrun{
+
- data(sepsis)
+data(sepsis)
- formatRCTdataset(sepsis, "survival", "THERAPY", T)
+vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
-}
   
 }
+\seealso{
+\code{\link{formatRCTDataset}}
+}

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)
+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)
-}   
+# ...
+   
 
 }

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)
- # 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) 
-}
 
 }

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)
- # 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)
   
 }