fixed a few bugs in checks, improved documentation and added DESCRIPTION

DESCRIPTION

 Package: treediff
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
+Title: Testing Differences Between Families of Trees
+Version: 0.1
+Date: 2023-02-24
 Authors@R: 
-    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
-Imports: dplyr, limma, reshape2, stats
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+    c(person("Nathalie", "Vialaneix", , "nathalie.vialaneix@inrae.fr", 
+             role = c("aut", "cre"), 
+             comment = c(ORCID = "0000-0003-1156-0639")),
+      person("Gwendaelle", "Cardenac", , , role = "aut"),
+      person("Marie", "Chavent", , "marie.chavent@u-bordeaux.fr", role = "aut"),
+      person("Sylvain", "Foissac", , "sylvain.foissac@inrae.fr", role = "aut"),
+      person("Pierre", "Neuvial", , "pierre.neuvial@math.univ-toulouse.fr", 
+             role = "aut"),
+      person("Nathanael", "Randriamihamison", , , role = "aut"))
+Description: This package implements a method based on cophenetic distances
+             and designed to perform a test to detect differences in structure
+             between families of trees.
+Depends: R (>= 4.0.0)
+Imports: dplyr, limma, stats, reshape2, testthat, rlang
+Suggest: adjclust
+License: GPL (>= 3)
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
     knitr,
     rmarkdown
 VignetteBuilder: knitr
+URL: https://forgemia.inra.fr/scales/treediff
+BugReports: https://forgemia.inra.fr/scales/treediff/-/issues

NAMESPACE

@@ -3,10 +3,12 @@
 S3method(print,treeTest)
 S3method(summary,treeTest)
 export(treediff)
+import(testthat)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,group_by)
 importFrom(dplyr,summarise)
 importFrom(limma,squeezeVar)
 importFrom(reshape2,colsplit)
+importFrom(rlang,.data)
 importFrom(stats,cophenetic)
 importFrom(stats,pt)

R/treediff.R

@@ -19,10 +19,12 @@
 #' different from that of \code{trees1}.
 #' @param replicates A numeric vector of length 2 with the number of replicates
 #' for each condition.
-#' @param scale Logical. If \code{TRUE}, the trees are all rescalled to have a
-#' minimum height equal to 0 and a maximum height equal to 1.
-#' @param order_labels Logical. If \code{TRUE}, take a reference tree and keep
-#' track of leave order.
+#' @param scale Logical. If \code{TRUE}, the trees are all rescaled to have a
+#' minimum height equal to 0 and a maximum height equal to 1. Default to 
+#' \code{FALSE}.
+#' @param order_labels Logical. If \code{TRUE}, align leaves ordering in all 
+#' trees (required if your trees don't have their leaves ordered identically).
+#' Default to \code{FALSE}.
 #'
 #' @return An object of class \code{treeTest} with the following entries:
 #' \itemize{
@@ -58,6 +60,8 @@
 #' @importFrom reshape2 colsplit
 #' @importFrom stats cophenetic
 #' @importFrom stats pt
+#' @importFrom rlang .data
+#' @import testthat
 #'
 #' @examples
 #' leaves <- c(100, 120, 50, 80)
@@ -98,7 +102,7 @@ treediff <- function(trees1, trees2, replicates, scale = FALSE,
                      order_labels = FALSE) {
 
   # Check if `replicates` is numeric vector
-  if (inherits(replicates, "numeric") != TRUE) {
+  if (!is.numeric(replicates)) {
     stop("`replicates` is not a numeric vector")
   }
 
@@ -169,13 +173,14 @@ treediff <- function(trees1, trees2, replicates, scale = FALSE,
 
   # Aggregate p-values
   out_aggr <- suppressWarnings(outp %>%
-    group_by(cluster) %>%
-    summarise("p.value" = min(sort(p.value) / (1:p)) * p, .groups = "keep") %>%
+    group_by(.data$cluster) %>%
+    summarise("p.value" = min(sort(.data$p.value) / (1:.data$p)) * .data$p, 
+              .groups = "keep") %>%
     unique())
 
   # Store results in a list
   data_name <- paste(substitute(trees1), "and", substitute(trees2))
-  out <- list("method" = "Tree test based on t-test",
+  out <- list("method" = "Tree test based on aggregated t-tests",
               "data.name" = data_name,
               "p.value" = out_aggr$p.value,
               "statistic" = outp$statistics,
@@ -189,6 +194,8 @@ treediff <- function(trees1, trees2, replicates, scale = FALSE,
 }
 
 #' @export
+#' @param x a \code{treeTest} object to print
+#' @param ... not used
 #' @rdname treediff
 
 print.treeTest <- function(x, ...) {
@@ -199,17 +206,18 @@ print.treeTest <- function(x, ...) {
   cat("\n")
 
   # Print the name of the data used in the test
-  cat("data : ", x$data.name, "\n", sep = "")
+  cat("data: ", x$data.name, "\n", sep = "")
 
   # print alternative hypothesis
-  cat("alternative hypothesis : sets of trees are different.")
+  cat("alternative hypothesis: the two sets of trees have different structure.")
   cat ("\n\n")
 
   # print the first 5 p-values
-  print(colsplit(x$p.value, " ", "p.values :"), max = 5)
+  print(colsplit(x$p.value, " ", "p-values:"), max = 5)
 }
 
 #' @method summary treeTest
+#' @param object a \code{treeTest} object to print
 #' @export
 #' @rdname treediff
 
@@ -219,7 +227,7 @@ summary.treeTest <- function(object, ...) {
   cat("\nSummary\n")
 
   # Print the class of the object
-  cat("\tClass : ", class(object))
+  cat("\tClass: ", class(object))
   cat("\n")
 
   # Print the test output
@@ -227,13 +235,14 @@ summary.treeTest <- function(object, ...) {
   cat("\n")
 
   # Print a summary of the p.value
-  cat("p.value\n")
+  cat(" p-value summary:\n")
   print(summary(object$p.value))
   cat("\n")
 
   # Print a summary of the `statistic` and `p.value.indiv`
-  summary(data.frame("statistic" = object$statistic,
-                     "p.value.indiv" = object$p.value.indiv))
+  summary(data.frame("indiv. statistics" = object$statistic,
+                     "indiv. p-values" = object$p.value.indiv,
+                     check.names = FALSE))
 }
 
 compute_squeeze <- function(dist_coph, replicates) {

man/treediff.Rd

@@ -26,24 +26,32 @@ different from that of \code{trees1}.}
 \item{replicates}{A numeric vector of length 2 with the number of replicates
 for each condition.}
 
-\item{scale}{Logical. If \code{TRUE}, the trees are all rescalled to have a
-minimum height equal to 0 and a maximum height equal to 1.}
+\item{scale}{Logical. If \code{TRUE}, the trees are all rescaled to have a
+minimum height equal to 0 and a maximum height equal to 1. Default to 
+\code{FALSE}.}
 
-\item{order_labels}{Logical. If \code{TRUE}, take a reference tree and keep
-track of leave order.}
+\item{order_labels}{Logical. If \code{TRUE}, align leaves ordering in all 
+trees (required if your trees don't have their leaves ordered identically).
+Default to \code{FALSE}.}
+
+\item{x}{a \code{treeTest} object to print}
+
+\item{...}{not used}
+
+\item{object}{a \code{treeTest} object to print}
 }
 \value{
 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.}
-\item{p.value.indiv}{ the p-value of the Student's test for each leaf pair
-of the tree test.}
-\item{method}{ a character string indicating what type of test was
-performed.}
-\item{data.name}{ a character string giving the names of the tree
-conditions.}
+  \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.}
+  \item{p.value.indiv}{ the p-value of the Student's test for each leaf pair
+  of the tree test.}
+  \item{method}{ a character string indicating what type of test was
+  performed.}
+  \item{data.name}{ a character string giving the names of the tree
+  conditions.}
 }
 }
 \description{

tests/testthat/test-treediff.R

@@ -29,7 +29,7 @@ trees1 <- unlist(trees[1,], recursive = FALSE)
 trees2 <- unlist(trees[2,], recursive = FALSE)
 
 # Set the number of replicates
-replicates = c(4, 6)
+replicates <- c(4, 6)
 
 test_that("'treediff' works for simple cases", {
 
@@ -70,25 +70,24 @@ test_that("'treediff' works for simple cases", {
 })
 
 ## Test errors
-
-
 test_that("Test errors", {
   # Test if replicates is numeric vector
   expect_error(treediff(trees1 = trees1, trees2 = trees2, replicates = "abc"),
                "`replicates` is not a numeric vector")
 
   # Test if replicates is a vector of length 2
-  expect_error(treediff(trees1 = trees1, trees2 = trees2, replicates = c(1,2,3)),
+  expect_error(treediff(trees1 = trees1, trees2 = trees2, replicates = 1:3),
                "`replicates` must be a vector of length 2.")
 
   # Test if output is a list with class treeTest
-  out <- treediff(trees1, trees2, c(4,6))
+  out <- treediff(trees1, trees2, c(4, 6))
   expect_true(inherits(out, "treeTest"))
 
   # Test if the number of leaves in each cluster is the same between the two
   # sets of trees
   trees2[[5]]$order <- c(trees2[[5]]$order, 101)
-  expect_error(treediff(trees1, trees2, c(4, 6)), "the number of leaves in one or more clusters is different between the two sets of trees.")
+  expect_error(treediff(trees1, trees2, c(4, 6)), 
+               "the number of leaves in one or more clusters is different between the two sets of trees.")
 })