diff --git a/DESCRIPTION b/DESCRIPTION
index 6cb44998bda58e6edb201fbfa4cb85c5b53f589f..2979226873e8f7af4d3ddf5701a4cd1f9b78947e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,17 +1,29 @@
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
diff --git a/NAMESPACE b/NAMESPACE
index 7f888e928e5570d110cdd179de7d53082834cc7d..748984ddc57c316e7ded57dac0fbf229b86d8097 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/treediff.R b/R/treediff.R
index 325d8c51631b68e74e0b995003fa346c87a7ca6d..2d149b2f81e16d4832bce335595532cfdaeb94c4 100644
--- a/R/treediff.R
+++ b/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) {
diff --git a/man/treediff.Rd b/man/treediff.Rd
index ac0df8afdfd40259c89f0985a3dbad782bbf469b..6c2b37755fcf9a34618a99f738af49da70c6f370 100644
--- a/man/treediff.Rd
+++ b/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{
diff --git a/tests/testthat/test-treediff.R b/tests/testthat/test-treediff.R
index cacb50d1bfe867d1c7b1e2900c71d8770172506f..41559ce2eee6b39fa8a8774b44ff100799b076aa 100644
--- a/tests/testthat/test-treediff.R
+++ b/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.")
})