Add documentation about forests

R/difft.R

@@ -12,7 +12,7 @@
 #'   
 #' @field vt.object VT.object (refClass) representing data
 #' @field twin1 vector of \eqn{E(Y|T = real treatment)}
-#' @field twin2 vector of \eqn{E(Y|T = anoher treatment)}
+#' @field twin2 vector of \eqn{E(Y|T = another treatment)}
 #' @field difft vector of difference between twin1 and twin2
 #'   
 #' @name VT.difft

R/forest.R

@@ -1,10 +1,20 @@
 # FORESTS -----------------------------------------------------------------
 
-#' A abstract reference class to compute twin via random forests
+#' Difft by Random Forest
 #' 
+#' An abstract reference class to compute twin via random forests
+#'  
+#' \code{VT.forest} extends \code{VT.difft}
+#' 
+#' @field ... see fields of \linkS4class{VT.difft}
+#'   
 #' @include difft.R predict.R
+#'   
+#' @name VT.forest
 #' 
-#' @import methods 
+#' @seealso \code{\link{VT.difft}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
+#'   
+#' @import methods
 VT.forest <- setRefClass(
   Class = "VT.forest",
   
@@ -12,7 +22,7 @@ VT.forest <- setRefClass(
   
   methods = list(  
     run = function(){
-      "Compute twin1 and twin2 computation. Switch treatment if necessary."
+      "Compute twin1 and twin2 estimation. Switch treatment if necessary."
       .self$computeTwin1()
       
       if(inherits(.self, "VT.forest.one")) .self$vt.object$switchTreatment() #if one forest

R/forest.double.R

@@ -1,13 +1,35 @@
 # VT.FOREST.DOUBLE --------------------------------------------------------
 # IF RUNNING DOUBLE FOREST COMPUTATION
 
+#' Difft by double random forest
+#' 
 #' A reference class to compute twins via double random forests
 #' 
+#' \code{VT.forest.double} extends \code{VT.forest}.
+#' 
+#' \eqn{E(Y|T = 1)} if \eqn{T_i = 1} is estimated by OOB predictions from
+#' \code{model_trt1}. 
+#' \eqn{E(Y|T = 0)} if \eqn{T_i = 0} is estimated by OOB predictions from
+#' \code{model_trt0}.
+#' This is what \code{computeTwin1()} does.
+#' 
+#' Then \eqn{E(Y|T = 1)} if \eqn{T_i = 0} is estimated by model_trt1.
+#' Then \eqn{E(Y|T = 0)} if \eqn{T_i = 1} is estimated by model_trt1.
+#' This is what \code{computeTwin2()} does.
+#' 
 #' @include forest.R
-#' 
-#' @field model_trt1 a caret/RandomForest/randomForest object for treatment T = 1
-#' @field model_trt0 a caret/RandomForest/randomForest object for treatment T = 0
-#' 
+#'   
+#' @field model_trt1 a caret/RandomForest/randomForest object for treatment T =
+#'   1
+#' @field model_trt0 a caret/RandomForest/randomForest object for treatment T =
+#'   0
+#' @field ... field from parent class : \linkS4class{VT.forest}
+#'   
+#' @seealso \code{\link{VT.difft}}, \code{\link{VT.forest}},
+#'   \code{\link{VT.forest.one}}
+#'   
+#' @name VT.forest.double
+#'   
 #' @import methods
 VT.forest.double <- setRefClass(
   Class = "VT.forest.double",
@@ -31,7 +53,7 @@ VT.forest.double <- setRefClass(
     },
     
     computeTwin1 = function(){
-      "Compute twin1 with OOB predictions from double forests"
+      "Compute twin1 with OOB predictions from double forests. See details."
       # Model with treatment (1)
       .self$twin1[.self$vt.object$data[, 2] == 1] <- VT.predict(rfor = .self$model_trt1, type = .self$vt.object$type)
       
@@ -42,7 +64,7 @@ VT.forest.double <- setRefClass(
     },
     
     computeTwin2 = function(){
-      "Compute twin2 by the other part of data in the other forest"
+      "Compute twin2 by the other part of data in the other forest. See details."
       # Model with treatment (1)
       .self$twin2[.self$vt.object$data[, 2] == 1] <- VT.predict(.self$model_trt0, newdata = .self$vt.object$getX(1, interactions = F), type = .self$vt.object$type)
       

R/forest.fold.R

@@ -1,14 +1,29 @@
 # VT.FOREST.FOLD ----------------------------------------------------------
 
+#' Difft via k random forests
+#' 
 #' A reference class to compute twins via k random forest
 #' 
+#' \code{VT.forest.fold} extends \code{VT.forest}
+#' 
+#' Twins are estimated by k-fold cross validation. A forest is computed on k-1/k
+#' of the data and then used to estimate twin1 and twin2 on 1/k of the left 
+#' data.
+#' 
 #' @include forest.R
-#' 
-#' @field interactions logical set TRUE if model has been computed with interactions 
-#' @field fold numeric Number of fold, i.e. number of forest
-#' @field ratio numeric 
-#' @field groups vector Define which observations belong to which group 
-#' 
+#'   
+#' @field interactions logical set TRUE if model has been computed with 
+#'   interactions
+#' @field fold numeric, number of fold, i.e. number of forest (k)
+#' @field ratio numeric experimental, use to balance sampsize. Defaut to 1.
+#' @field groups vector Define which observations belong to which group
+#' @field ... field from parent class : \linkS4class{VT.forest}
+#'   
+#' @name VT.forest.fold
+#'   
+#' @seealso \code{\link{VT.difft}}, \code{\link{VT.forest}}, 
+#'   \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
+#'   
 #' @import methods
 VT.forest.fold <- setRefClass(
   Class = "VT.forest.fold",
@@ -59,6 +74,7 @@ VT.forest.fold <- setRefClass(
         samp2 <- Yeff[2]
         samp1 <- sampmin
       }
+      if(!requireNamespace("randomForest", quietly = TRUE)) stop("randomForest package must be loaded.")
       rf <- randomForest(x = X, y = Y, sampsize = c(samp1, samp2), keep.forest = T, ...)
       
       .self$computeTwin1(rf, group)

R/forest.one.R

@@ -1,13 +1,26 @@
 # VT.FOREST.ONE -----------------------------------------------------------
 # IF RUNNING ONE FOREST COMPUTATION
 
+#' Difft by one random forest
+#' 
 #' A reference class to compute twins via one random forest
 #' 
+#' \code{VT.forest.one} extends \code{VT.forest}.
+#' 
+#' OOB predictions are used to estimate \eqn{E(Y|T = real treatment)}. Then, 
+#' treatement is switched, it means that 1 becomes 0 and 0 becomes 1. We use 
+#' again \code{model} to estimate \eqn{E(Y|T = the other treatment)}. This is
+#' what \code{computeTwin1()} and \code{computeTwin2()} functions do.
+#' 
 #' @include forest.R
 #' 
-#' @field model ANY a caret/RandomForest/randomForest class object
+#' @field model is a caret/RandomForest/randomForest class object
 #' @field interactions logical set TRUE if model has been computed with interactions 
-#' @field ... field from parent class : VT.forest
+#' @field ... field from parent class : \linkS4class{VT.forest}
+#' 
+#' @seealso \code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.double}}
+#' 
+#' @name VT.forest.one
 #' 
 #' @import methods
 VT.forest.one <- setRefClass(

man/VT.forest.Rd

@@ -1,13 +1,20 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/forest.R
 \docType{class}
-\name{VT.forest-class}
+\name{VT.forest}
 \alias{VT.forest}
-\alias{VT.forest-class}
-\title{A abstract reference class to compute twin via random forests}
+\title{Difft by Random Forest}
 \description{
-A abstract reference class to compute twin via random forests
+An abstract reference class to compute twin via random forests
 }
+\details{
+\code{VT.forest} extends \code{VT.difft}
+}
+\section{Fields}{
+
+\describe{
+\item{\code{...}}{see fields of \linkS4class{VT.difft}}
+}}
 \section{Methods}{
 
 \describe{
@@ -17,4 +24,7 @@ A abstract reference class to compute twin via random forests
 
 \item{\code{run()}}{Compute twin1 and twin2 computation. Switch treatment if necessary.}
 }}
+\seealso{
+\code{\link{VT.difft}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
+}
 

man/VT.forest.double-class.Rd

@@ -1,25 +0,0 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/forest.double.R
-\docType{class}
-\name{VT.forest.double-class}
-\alias{VT.forest.double}
-\alias{VT.forest.double-class}
-\title{A reference class to compute twins via double random forests}
-\description{
-A reference class to compute twins via double random forests
-}
-\section{Fields}{
-
-\describe{
-\item{\code{model_trt1}}{a caret/RandomForest/randomForest object for treatment T = 1}
-
-\item{\code{model_trt0}}{a caret/RandomForest/randomForest object for treatment T = 0}
-}}
-\section{Methods}{
-
-\describe{
-\item{\code{computeTwin1()}}{Compute twin1 with OOB predictions from double forests}
-
-\item{\code{computeTwin2()}}{Compute twin2 by the other part of data in the other forest}
-}}
-

man/VT.forest.double.Rd

@@ -0,0 +1,45 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/forest.double.R
+\docType{class}
+\name{VT.forest.double}
+\alias{VT.forest.double}
+\title{Difft by double random forest}
+\description{
+A reference class to compute twins via double random forests
+}
+\details{
+\code{VT.forest.double} extends \code{VT.forest}.
+
+\eqn{E(Y|T = 1)} if \eqn{T_i = 1} is estimated by OOB predictions from
+\code{model_trt1}.
+\eqn{E(Y|T = 0)} if \eqn{T_i = 0} is estimated by OOB predictions from
+\code{model_trt0}.
+This is what \code{computeTwin1()} does.
+
+Then \eqn{E(Y|T = 1)} if \eqn{T_i = 0} is estimated by model_trt1.
+Then \eqn{E(Y|T = 0)} if \eqn{T_i = 1} is estimated by model_trt1.
+This is what \code{computeTwin2()} does.
+}
+\section{Fields}{
+
+\describe{
+\item{\code{model_trt1}}{a caret/RandomForest/randomForest object for treatment T =
+1}
+
+\item{\code{model_trt0}}{a caret/RandomForest/randomForest object for treatment T =
+0}
+
+\item{\code{...}}{field from parent class : \linkS4class{VT.forest}}
+}}
+\section{Methods}{
+
+\describe{
+\item{\code{computeTwin1()}}{Compute twin1 with OOB predictions from double forests. See details.}
+
+\item{\code{computeTwin2()}}{Compute twin2 by the other part of data in the other forest. See details.}
+}}
+\seealso{
+\code{\link{VT.difft}}, \code{\link{VT.forest}},
+  \code{\link{VT.forest.one}}
+}
+

man/VT.forest.fold-class.Rd

@@ -1,27 +0,0 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/forest.fold.R
-\docType{class}
-\name{VT.forest.fold-class}
-\alias{VT.forest.fold}
-\alias{VT.forest.fold-class}
-\title{A reference class to compute twins via k random forest}
-\description{
-A reference class to compute twins via k random forest
-}
-\section{Fields}{
-
-\describe{
-\item{\code{interactions}}{logical set TRUE if model has been computed with interactions}
-
-\item{\code{fold}}{numeric Number of fold, i.e. number of forest}
-
-\item{\code{ratio}}{numeric}
-
-\item{\code{groups}}{vector Define which observations belong to which group}
-}}
-\section{Methods}{
-
-\describe{
-\item{\code{run()}}{Compute twin1 and twin2 computation. Switch treatment if necessary.}
-}}
-

man/VT.forest.fold.Rd

@@ -0,0 +1,40 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/forest.fold.R
+\docType{class}
+\name{VT.forest.fold}
+\alias{VT.forest.fold}
+\title{Difft via k random forests}
+\description{
+A reference class to compute twins via k random forest
+}
+\details{
+\code{VT.forest.fold} extends \code{VT.forest}
+
+Twins are estimated by k-fold cross validation. A forest is computed on k-1/k
+of the data and then used to estimate twin1 and twin2 on 1/k of the left
+data.
+}
+\section{Fields}{
+
+\describe{
+\item{\code{interactions}}{logical set TRUE if model has been computed with
+interactions}
+
+\item{\code{fold}}{numeric, number of fold, i.e. number of forest (k)}
+
+\item{\code{ratio}}{numeric experimental, use to balance sampsize. Defaut to 1.}
+
+\item{\code{groups}}{vector Define which observations belong to which group}
+
+\item{\code{...}}{field from parent class : \linkS4class{VT.forest}}
+}}
+\section{Methods}{
+
+\describe{
+\item{\code{run()}}{Compute twin1 and twin2 computation. Switch treatment if necessary.}
+}}
+\seealso{
+\code{\link{VT.difft}}, \code{\link{VT.forest}},
+  \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
+}
+

man/VT.forest.one-class.Rd

@@ -1,27 +0,0 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/forest.one.R
-\docType{class}
-\name{VT.forest.one-class}
-\alias{VT.forest.one}
-\alias{VT.forest.one-class}
-\title{A reference class to compute twins via one random forest}
-\description{
-A reference class to compute twins via one random forest
-}
-\section{Fields}{
-
-\describe{
-\item{\code{model}}{ANY a caret/RandomForest/randomForest class object}
-
-\item{\code{interactions}}{logical set TRUE if model has been computed with interactions}
-
-\item{\code{...}}{field from parent class : VT.forest}
-}}
-\section{Methods}{
-
-\describe{
-\item{\code{computeTwin1()}}{Compute twin1 with OOB predictions}
-
-\item{\code{computeTwin2()}}{Compute twin2 by switching treatment and applying random forest model}
-}}
-

man/VT.forest.one.Rd

@@ -0,0 +1,37 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/forest.one.R
+\docType{class}
+\name{VT.forest.one}
+\alias{VT.forest.one}
+\title{Difft by one random forest}
+\description{
+A reference class to compute twins via one random forest
+}
+\details{
+\code{VT.forest.one} extends \code{VT.forest}.
+
+OOB predictions are used to estimate \eqn{E(Y|T = real treatment)}. Then,
+treatement is switched, it means that 1 becomes 0 and 0 becomes 1. We use
+again \code{model} to estimate \eqn{E(Y|T = the other treatment)}. This is
+what \code{computeTwin1()} and \code{computeTwin2()} functions do.
+}
+\section{Fields}{
+
+\describe{
+\item{\code{model}}{is a caret/RandomForest/randomForest class object}
+
+\item{\code{interactions}}{logical set TRUE if model has been computed with interactions}
+
+\item{\code{...}}{field from parent class : \linkS4class{VT.forest}}
+}}
+\section{Methods}{
+
+\describe{
+\item{\code{computeTwin1()}}{Compute twin1 with OOB predictions}
+
+\item{\code{computeTwin2()}}{Compute twin2 by switching treatment and applying random forest model}
+}}
+\seealso{
+\code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.double}}
+}
+