Nothing
test_that("DriftTest returns resonable results",
{
skip_on_cran()
means <- array(rnorm(40*10), c(10, 40))
means.list <- alply(means, 1)
cov.matrix <- RandomMatrix(40, 1, 1, 10, LKJ = FALSE)
test.array <- DriftTest(means, cov.matrix, FALSE)
test.list <- DriftTest(means.list, cov.matrix, FALSE)
expect_equal(test.array[-6], test.list[-6])
expect_is(test.array, "list")
expect_is(test.array[[1]], "lm")
expect_is(test.array[[2]], "matrix")
expect_is(test.array[[3]], "numeric")
expect_is(test.array[[4]], "numeric")
expect_is(test.array[[5]], "logical")
expect_is(test.array[[6]], c("gg", "ggplot"))
expect_equal(names(test.array), c("regression",
"coefficient_CI_95",
"log.between_group_variance",
"log.W_eVals",
"drift_rejected",
"plot"))
expect_equal(length(test.array$log.between_group_variance), dim(means)[2])
expect_equal(length(test.array$log.W_eVals), dim(means)[2])
expect_equal(test.array$log.W_eVals, log(eigen(cov.matrix)$values))
})
test_that("TreeDriftTest returns resonable results",
{
library(ape)
data(bird.orders)
tree <- bird.orders
mean.list <- llply(tree$tip.label, function(x) rnorm(5))
names(mean.list) <- tree$tip.label
cov.matrix.list <- RandomMatrix(5, length(tree$tip.label))
names(cov.matrix.list) <- tree$tip.label
w.cov <- PhyloW(tree, cov.matrix.list)$'24'
test.list <- TreeDriftTest(tree, mean.list, cov.matrix.list)
expect_is(test.list, 'list')
expect_equal(length(test.list), 13)
expect_equal(test.list[[length(test.list)]][-6],
DriftTest(mean.list, w.cov, FALSE)[-6])
})
# gets descendant node numbers
# written by Liam Revell 2012, 2013, 2014
getDescendants<-function(tree,node,curr=NULL){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
if(is.null(curr)) curr<-vector()
daughters<-tree$edge[which(tree$edge[,1]==node),2]
curr<-c(curr,daughters)
if(length(curr)==0&&node<=length(tree$tip.label)) curr<-node
w<-which(daughters>length(tree$tip.label))
if(length(w)>0) for(i in 1:length(w))
curr<-getDescendants(tree,daughters[w[i]],curr)
return(curr)
}
test_that("TreeDriftTest returns resonable results",
{
library(ape)
data(bird.orders)
tree <- bird.orders
mean.list <- llply(tree$tip.label, function(x) rnorm(5))
names(mean.list) <- tree$tip.label
cov.matrix.list <- RandomMatrix(5, length(tree$tip.label))
names(cov.matrix.list) <- tree$tip.label
cov.matrix.list = cov.matrix.list[sample(1:length(cov.matrix.list))]
mean.list_2 = mean.list[sample(1:length(mean.list))]
w.cov <- PhyloW(tree, cov.matrix.list)$'32'
test.list <- TreeDriftTest(tree, mean.list_2, cov.matrix.list)
expect_is(test.list, 'list')
expect_equal(length(test.list), 13)
expect_equal(test.list[["32"]][-6],
DriftTest(mean.list[na.omit(tree$tip.label[getDescendants(tree, "32")])],
w.cov, FALSE)[-6])
})
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