/usr/share/doc/r-cran-phangorn/tests/testthat/test_phyDat.R is in r-cran-phangorn 2.4.0-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 | context("conversion_and_subsetting")
# to test: phyDat.codon,
data(Laurasiatherian)
data(chloroplast)
set.seed(42)
tree <- rtree(10)
codon_align <- simSeq(tree, l=100, type = "CODON")
phy_matrix <- as.character(Laurasiatherian)
phy_df <- as.data.frame(Laurasiatherian)
phy_vec_dna <- phy_matrix[,1]
phy_vec_user <- sample(c("0","1"), 26, replace=TRUE)
names(phy_vec_user) <- letters
phy_dnabin <- as.DNAbin(Laurasiatherian)
phy_aabin <- as.AAbin(chloroplast)
phy_align <- phyDat2alignment(Laurasiatherian)
test_that("conversion work as expected", {
## skip_on_cran()
expect_is(phy_matrix, "matrix")
expect_is(phy_df, "data.frame")
expect_is(phy_dnabin, "DNAbin")
expect_is(phy_aabin, "AAbin")
expect_is(phy_align, "alignment")
expect_is(as.phyDat(phy_matrix), "phyDat")
expect_is(as.phyDat(phy_df), "phyDat")
expect_is(as.phyDat(phy_dnabin), "phyDat")
expect_equal(as.phyDat(phy_aabin), chloroplast)
expect_is(phyDat(phy_vec_dna), "phyDat")
expect_is(phyDat(phy_vec_user, type="USER", levels = c("0","1")), "phyDat")
expect_is(as.phyDat(phy_dnabin), "phyDat")
expect_is(as.phyDat(phy_align), "phyDat")
expect_is(c2d <- codon2dna(codon_align), "phyDat")
expect_equal(dna2codon(c2d), codon_align)
})
test_that("conversion with Biostrings work as expected", {
skip_on_cran()
if(require(Biostrings)){
expect_is(MA_AA <- as.MultipleAlignment(chloroplast), "AAMultipleAlignment")
expect_equal(as.phyDat(MA_AA), chloroplast)
expect_is(MA_DNA <- as.MultipleAlignment(Laurasiatherian), "DNAMultipleAlignment")
expect_equal(as.phyDat(MA_DNA), Laurasiatherian)
}
})
test_that("subsetting and combining work as expected", {
## skip_on_cran()
expect_is(subset_1 <- subset(Laurasiatherian, select = 1:1000, site.pattern = FALSE), "phyDat")
expect_is(subset_2 <- subset(Laurasiatherian, select = 1001:3179, site.pattern = FALSE), "phyDat")
expect_is(lauraCbind1 <- cbind(subset_1, subset_2), "phyDat")
expect_equal(baseFreq(lauraCbind1), baseFreq(Laurasiatherian))
expect_is(subset_3 <- subset(Laurasiatherian, select = 1:100), "phyDat")
expect_is(subset_4 <- subset(Laurasiatherian, select = 101:1605), "phyDat")
expect_is(lauraCbind2 <- cbind(subset_3, subset_4), "phyDat")
expect_equal(baseFreq(lauraCbind2), baseFreq(Laurasiatherian))
})
test_that("read and write work as expected", {
skip_on_cran()
write.phyDat(Laurasiatherian, "tmp1.txt")
expect_is(laura <- read.phyDat("tmp1.txt"), "phyDat")
expect_equal(laura, Laurasiatherian)
unlink("tmp1.txt")
write.phyDat(chloroplast, "tmp2.txt")
expect_is(chloro <- read.phyDat("tmp2.txt", type="AA"), "phyDat")
expect_equal(chloro, chloroplast)
unlink("tmp2.txt")
write.phyDat(chloroplast, "tmp.fas", format="fasta")
expect_is(chloro_fas <- read.phyDat("tmp.fas", type="AA", format = "fasta"), "phyDat")
expect_equal(chloro_fas, chloroplast)
unlink("tmp.fas")
})
test_that("removing duplicated sequences works", {
skip_on_cran()
tmp <- as.character(Laurasiatherian)
laura <- phyDat(rbind(phy_matrix, phy_matrix))
names(laura) <- paste0(names(laura), rep(c(1,2), each=47))
map1 <- map_duplicates(laura)
map2 <- map_duplicates(Laurasiatherian)
expect_null(map2)
expect_is(map1, "data.frame")
})
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