Nothing
# LIBS
library(treeman)
library(testthat)
# DATA
data(mammals)
# ENSURE THIS FILE DOES NOT ALREADY EXIST
if(file.exists('testRData_ndmtrx')) {
file.remove('testRData_ndmtrx')
}
# RUNNING
context('Testing \'read-write-methods\'')
test_that('readTree([w/ spans]) works', {
text <- "(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);"
tree <- readTree(text=text, wndmtrx=sample(c(TRUE, FALSE), 1))
expect_that(tree['pd'], equals(0.1+0.2+0.3+0.4+0.5))
expect_that(tree['ntips'], equals(4))
expect_that(tree[['C']]['prdst'], equals(0.3+0.5))
})
test_that('readTree([w/o spans]) works', {
text <- "(A,B,(C,D));"
tree <- readTree(text=text, wndmtrx=sample(c(TRUE, FALSE), 1))
expect_that(tree['ntips'], equals(4))
expect_false(tree['wspn'])
})
test_that('readTree([w/ node labels]) works', {
text <- "(A,B,(C,D)0.9)0.8;"
tree <- readTree(text=text, spcl_slt_nm='bootstrap',
wndmtrx=sample(c(TRUE, FALSE), 1))
expect_that(tree['ntips'], equals(4))
expect_false(tree['wspn'])
})
test_that('writeTree() works', {
t1 <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
writeTree(t1, 'test.tre')
t2 <- readTree('test.tre', wndmtrx=sample(c(TRUE, FALSE), 1))
expect_that(t1['ntips'], equals(t2['ntips']))
expect_that(t1['nnds'], equals(t2['nnds']))
expect_that(t1['pd'], equals(t2['pd']))
t1_age <- getAge(t1)
t2_age <- getAge(t2)
expect_that(t1_age, equals(t2_age))
})
test_that('writeTrmn([for TreeMan]) works', {
t1 <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
writeTrmn(t1, 'test.trmn')
t2 <- readTrmn('test.trmn', wndmtrx=sample(c(TRUE, FALSE), 1))
expect_that(t1['ntips'], equals(t2['ntips']))
expect_that(t1['nnds'], equals(t2['nnds']))
expect_that(t1['pd'], equals(t2['pd']))
t1_age <- getAge(t1)
t2_age <- getAge(t2)
expect_that(t1_age, equals(t2_age))
# test example with taxonomy
data(mammals)
ape_id <- getPrnt(mammals, ids=c('Homo_sapiens', 'Hylobates_concolor'))
tree <- getSubtree(mammals, id=ape_id)
writeTrmn(tree, file='test.trmn')
tree <- readTrmn('test.trmn')
expect_true(tree@wtxnyms)
})
test_that('writeTrmn([for TreeMen]) works', {
t1 <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
ape_id <- getPrnt(mammals, ids=c('Homo_sapiens', 'Hylobates_concolor'))
t2 <- getSubtree(mammals, id=ape_id)
t3 <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
t3 <- setNdsSpn(t3, t3['all'], vals=0)
trs <- cTrees(t1, t2, t3)
writeTrmn(trs, file='test.trmn')
expect_error(writeTrmn('not_a_tree', file='test.trmn'))
})
test_that('readTrmn([for TreeMan]) works', {
tree <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
writeTrmn(tree, 'test.trmn')
t1 <- readTrmn('test.trmn', wndmtrx=sample(c(TRUE, FALSE), 1))
tree@wspn <- FALSE
writeTrmn(tree, 'test.trmn')
t2 <- readTrmn('test.trmn', wndmtrx=sample(c(TRUE, FALSE), 1))
expect_true(t1@wspn)
expect_true(!t2@wspn)
})
test_that('readTrmn([for TreeMen]) works', {
t1 <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
ape_id <- getPrnt(mammals, ids=c('Homo_sapiens', 'Hylobates_concolor'))
t2 <- getSubtree(mammals, id=ape_id)
t3 <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
t3 <- setNdsSpn(t3, t3['all'], vals=0)
trs <- cTrees(t1, t2, t3)
writeTrmn(trs, file='test.trmn')
remove(trs)
trs <- readTrmn(file='test.trmn')
expect_true(is(trs) == 'TreeMen')
expect_true(trs[[1]]['ntips'] == 100)
expect_true(trs[[1]]['wspn'])
expect_false(trs[[1]]['wtxnyms'])
expect_true(trs[[2]]['wspn'])
expect_true(trs[[2]]['wtxnyms'])
expect_true(trs[[3]]['ntips'] == 100)
expect_false(trs[[3]]['wspn'])
expect_false(trs[[3]]['wtxnyms'])
})
test_that('reading and writing with additional slots works', {
tree <- randTree(100, wndmtrx=sample(c(TRUE, FALSE), 1))
confndcs <- runif(min=0, max=1, n=tree['nall'])
tree <- setNdsOther(tree, ids=tree['all'], vals=confndcs,
slt_nm='confidences')
writeTrmn(tree, file='test.trmn')
tree <- readTrmn(file='test.trmn', wndmtrx=sample(c(TRUE, FALSE), 1))
expect_true(tree['othr_slt_nms'] == 'confidences')
})
test_that('saveTreeMan() works', {
tree <- randTree(100)
saveTreeMan(tree, file='test.RData')
expect_true(file.exists('test.RData'))
tree <- randTree(100, wndmtrx=TRUE)
saveTreeMan(tree, file='test.RData')
expect_true(file.exists('testRData_ndmtrx'))
file.remove('testRData_ndmtrx')
})
test_that('loadTreeMan() works', {
tree <- randTree(100)
saveTreeMan(tree, file='test.RData')
rm(tree)
tree <- loadTreeMan(file='test.RData')
expect_false(!is.null(tree@ndmtrx))
tree <- randTree(100, wndmtrx=TRUE)
saveTreeMan(tree, file='test.RData')
rm(tree)
tree <- loadTreeMan(file='test.RData')
expect_true(!is.null(tree@ndmtrx))
})
if(file.exists('test.tre')) {
file.remove('test.tre')
}
if(file.exists('test.trmn')) {
file.remove('test.trmn')
}
if(file.exists('test.RData')) {
file.remove('test.RData')
}
if(file.exists('testRData_ndmtrx')) {
file.remove('testRData_ndmtrx')
}
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