From 05a97ff613e8a6cca45a4c22a079d796e9f7cf61 Mon Sep 17 00:00:00 2001
From: prise6 <vieille.francois@gmail.com>
Date: Wed, 10 Jun 2015 14:37:49 +0200
Subject: [PATCH] Update export/depends/suggests

---
 DESCRIPTION | 23 ++++++++++++++---------
 NAMESPACE   |  1 +
 R/predict.R | 13 +++++++------
 3 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 796568b..92c2ebe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,18 +1,22 @@
 Package: VirtualTwins
 Type: Package
-Title: What the package does (short line)
-Version: 1.0
+Title: Adaptation of Virtual Twins method from Jared Foster.
+Version: 0.0.0.1000
 Date: 2015-05-31
-Author: Who wrote it
-Maintainer: Who to complain to <yourfault@somewhere.net>
-Description: More about what it does (maybe more than one line)
-License: What license is it under?
+Author: François Vieille
+Maintainer: <vieille.francois@gmail.com>
+Description: Research of subgroups in random clinical trials with binary
+    outcome and two treatments groups.
+License: MIT
 Imports:
-    rpart
+    rpart,
+    party
 Suggests:
     randomForest,
-    caret,
-    party
+    caret
+Depends:
+    R (>= 3.2.0),
+    methods
 Collate:
     'VirtualTwins.R'
     'object.R'
@@ -23,6 +27,7 @@ Collate:
     'forest.double.R'
     'forest.fold.R'
     'forest.one.R'
+    'formatRCTDataset.R'
     'incidences.R'
     'tools.R'
     'tree.R'
diff --git a/NAMESPACE b/NAMESPACE
index c6fddc6..52fead9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,4 +1,5 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
+export(formatRCTDataset)
 import(methods)
 importClassesFrom(party,RandomForest)
diff --git a/R/predict.R b/R/predict.R
index 35fefdc..b42d233 100644
--- a/R/predict.R
+++ b/R/predict.R
@@ -17,6 +17,7 @@
 #'   
 #' @include setClass.R
 #' @importClassesFrom party RandomForest
+#' 
 setGeneric("VT.predict",
            function(rfor, newdata, type){standardGeneric("VT.predict")}
 )
@@ -29,7 +30,7 @@ setMethod(
     if(! type %in% c("binary", "continous")) stop("Type must be Binary or continous")
     if(type == "binary"){
       if(!requireNamespace("party", quietly = TRUE)) stop("Party package must be loaded.")
-      tmp <- predict.RandomForest(rfor, OOB = T, type = "prob")      
+      tmp <- party:::predict.RandomForest(rfor, OOB = T, type = "prob")      
       tmp <- unlist(tmp)
       tmp <- tmp[seq(2, length(tmp), 2)]      
     }else{
@@ -49,7 +50,7 @@ setMethod(
     if(! type %in% c("binary", "continous")) stop("Type must be Binary or continous")
     if(type == "binary"){
       if(!requireNamespace("party", quietly = TRUE)) stop("Party package must be loaded.")
-      tmp <- predict.RandomForest(rfor, newdata = newdata, type = "prob")
+      tmp <- party:::predict.RandomForest(rfor, newdata = newdata, type = "prob")
       tmp <- unlist(tmp)
       tmp <- tmp[seq(2, length(tmp), 2)]      
     }else{
@@ -71,7 +72,7 @@ setMethod(
       # no longer available in all version ?!
       # tmp <- rfor$vote[, 2] # get the "o" prob
       if(!requireNamespace("randomForest", quietly = TRUE)) stop("randomForest package must be loaded.")
-      tmp <- predict.randomForest(rfor, type = "prob")[, 2] # We want to get the "o" prob
+      tmp <- randomForest:::predict.randomForest(rfor, type = "prob")[, 2] # We want to get the "o" prob
     }else{
       message("continous is not done yet")
       tmp <- NULL
@@ -88,7 +89,7 @@ setMethod(
     if(! type %in% c("binary", "continous")) stop("Type must be Binary or continous")
     if(type == "binary"){
       if(!requireNamespace("randomForest", quietly = TRUE)) stop("randomForest package must be loaded.")
-      tmp <- predict.randomForest(rfor, newdata = newdata, type = "prob")[, 2] # We want to get the "o" prob
+      tmp <- randomForest:::predict.randomForest(rfor, newdata = newdata, type = "prob")[, 2] # We want to get the "o" prob
     }else{
       message("continous is not done yet")
       tmp <- NULL
@@ -102,7 +103,7 @@ setMethod(
   f = "VT.predict",
   signature = c(rfor = "train", newdata = "ANY", type = "character"),
   function(rfor, newdata, type = "binary"){
-    if(!requireNamespace("caret", quietly = TRUE)) stop("randomForest package must be loaded.")
+    if(!requireNamespace("caret", quietly = TRUE)) stop("caret package must be loaded.")
     return(VT.predict(rfor$finalModel, newdata, type))
   }
 )
@@ -112,7 +113,7 @@ setMethod(
   f = "VT.predict",
   signature = c(rfor = "train", newdata = "missing", type = "character"),
   function(rfor, type = "binary"){
-    if(!requireNamespace("caret", quietly = TRUE)) stop("randomForest package must be loaded.")
+    if(!requireNamespace("caret", quietly = TRUE)) stop("caret package must be loaded.")
     return(VT.predict(rfor=rfor$finalModel, type=type))
   }
 )
\ No newline at end of file