very minor corrections in code

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
+export(fisher_mix)
 export(treediff)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,group_by)
 importFrom(dplyr,summarise)
 importFrom(limma,squeezeVar)
+importFrom(reshape2,colsplit)
 importFrom(stats,cophenetic)
 importFrom(stats,pt)
+importFrom(stats,rf)

R/treediff.R

@@ -17,7 +17,8 @@
 #' @param replicates A numeric vector of length 2 with the number of replicates
 #' for each condition.
 #'
-#' @return An object of class \code{treeTest} with the following entries: \itemize{
+#' @return An object of class \code{treeTest} with the following entries: 
+#' \itemize{
 #'   \item{p.value}{ the p-value for the treediff test.}
 #'   \item{statistic}{ the value of the Student's statistic of each leaf pair of
 #'   the tree test.}
@@ -29,10 +30,11 @@
 #'   conditions.}
 #' }
 #'
-#' @author Pierre Neuvial \email{pierre.neuvial@math.univ-toulouse.fr}\cr
-#' Nathanaël Randriamihamison\cr
+#' @author Gwendaelle Cardenac\cr
 #' Marie Chavent \email{marie.chavent@u-bordeaux.fr}\cr
 #' Sylvain Foissac \email{sylvain.foissac@inrae.fr}\cr
+#' Pierre Neuvial \email{pierre.neuvial@math.univ-toulouse.fr}\cr
+#' Nathanaël Randriamihamison\cr
 #' Nathalie Vialaneix \email{nathalie.vialaneix@inrae.fr}
 #'
 #' @references Neuvial Pierre, Randriamihamison Nathanaël, Chavent Marie,
@@ -52,11 +54,10 @@
 #'
 #'
 #' @examples
+#' leaves <- c(100, 120, 50, 80)
 #'
-#' leaves <- c(100,120,50,80)
-#'
-#' trees <- sapply(leaves, FUN = function(l){
-#'   base_data <- matrix(rnorm(2000), nrow = l, ncol = 200)
+#' trees <- sapply(leaves, FUN = function(leaf) {
+#'   base_data <- matrix(rnorm(2000), nrow = leaf, ncol = 200)
 #'
 #' ## generates two sets of trees with 4 clusters with 100, 120, 50 and 80
 #' ## leaves respectively
@@ -79,22 +80,22 @@
 #'   return(list("trees1" = trees1, "trees2" = trees2))
 #' })
 #'
-#' trees1 <- unlist(trees[1,], recursive = FALSE)
-#' trees2 <- unlist(trees[2,], recursive = FALSE)
-#' replicates = c(4, 6)
+#' trees1 <- unlist(trees[1, ], recursive = FALSE)
+#' trees2 <- unlist(trees[2, ], recursive = FALSE)
+#' replicates <- c(4, 6)
 #'
 #' tree_pvals <- treediff(trees1, trees2, replicates)
 #' ## 4 p-values, one for each cluster
 #' tree_pvals$p.value
 
-treediff <- function(trees1, trees2, replicates){
+treediff <- function(trees1, trees2, replicates) {
   # Check if `replicates` is numeric vector
-  if (inherits(replicates, "numeric") != TRUE){
+  if (inherits(replicates, "numeric") != TRUE) {
     stop("`replicates` is not a numeric vector")
   }
 
   # Check if the length of replicates is 2
-  if (length(replicates) != 2){
+  if (length(replicates) != 2) {
     stop("`replicates` must be a vector of length 2.")
   }
 
@@ -111,7 +112,7 @@ treediff <- function(trees1, trees2, replicates){
   tree_order2 <- lapply(trees2, "[[", "order")
   leaves2 <- sapply(tree_order2, length)
 
-  if (!identical(unique(leaves1), unique(leaves2))){
+  if (!identical(unique(leaves1), unique(leaves2))) {
     stop("the number of leaves in one or more clusters is different between ",
     "the two sets of trees.")
   }
@@ -230,7 +231,7 @@ compute_pvalue <- function(average_coph, squeezed_var, replicates) {
   cluster <- average_coph$cluster
 
   # Calculate the numerator for the t-statistic
-  numerator <- Reduce("-", average_coph[,-3])
+  numerator <- Reduce("-", average_coph[, -3])
 
   # Store replicates values for each group
   n1 <- replicates[1]

man/treediff.Rd

@@ -21,7 +21,8 @@ different from that of \code{trees1}.}
 for each condition.}
 }
 \value{
-An object of class \code{htest} with the following entries: \itemize{
+An object of class \code{treeTest} with the following entries:
+\itemize{
 \item{p.value}{ the p-value for the treediff test.}
 \item{statistic}{ the value of the Student's statistic of each leaf pair of
 the tree test.}
@@ -42,11 +43,10 @@ method. The p-values are obtained by the treediff method, as described in
 (Neuvial \emph{et al.}, 2023).
 }
 \examples{
+leaves <- c(100, 120, 50, 80)
 
-leaves <- c(100,120,50,80)
-
-trees <- sapply(leaves, FUN = function(l){
-  base_data <- matrix(rnorm(2000), nrow = l, ncol = 200)
+trees <- sapply(leaves, FUN = function(leaf) {
+  base_data <- matrix(rnorm(2000), nrow = leaf, ncol = 200)
 
 ## generates two sets of trees with 4 clusters with 100, 120, 50 and 80
 ## leaves respectively
@@ -69,9 +69,9 @@ trees <- sapply(leaves, FUN = function(l){
   return(list("trees1" = trees1, "trees2" = trees2))
 })
 
-trees1 <- unlist(trees[1,], recursive = FALSE)
-trees2 <- unlist(trees[2,], recursive = FALSE)
-replicates = c(4, 6)
+trees1 <- unlist(trees[1, ], recursive = FALSE)
+trees2 <- unlist(trees[2, ], recursive = FALSE)
+replicates <- c(4, 6)
 
 tree_pvals <- treediff(trees1, trees2, replicates)
 ## 4 p-values, one for each cluster
@@ -84,9 +84,10 @@ structure between families of trees. \emph{Preprint submitted for
 publication}.
 }
 \author{
-Pierre Neuvial \email{pierre.neuvial@math.univ-toulouse.fr}\cr
-Nathanaël Randriamihamison\cr
+Gwendaelle Cardenac\cr
 Marie Chavent \email{marie.chavent@u-bordeaux.fr}\cr
 Sylvain Foissac \email{sylvain.foissac@inrae.fr}\cr
+Pierre Neuvial \email{pierre.neuvial@math.univ-toulouse.fr}\cr
+Nathanaël Randriamihamison\cr
 Nathalie Vialaneix \email{nathalie.vialaneix@inrae.fr}
 }