tests/testthat/test_mut.R
In iferres/simba: simurg: Simulate Bacterial Pangenomes
context('Simulating mutations.')
# library(ape)
phy <- structure(list(edge = structure(c(11L, 13L, 19L, 19L, 13L, 18L,
18L, 11L, 12L, 15L, 15L, 16L, 16L, 12L, 14L, 14L, 17L, 17L, 13L,
19L, 1L, 2L, 18L, 3L, 4L, 12L, 15L, 5L, 16L, 6L, 7L, 14L, 8L,
17L, 9L, 10L), .Dim = c(18L, 2L)),
edge.length = c(0.570743614638502, 0.743533392747197, 0.00315730974266033, 0.00315730974266033,
0.718087960984797, 0.028602741505061, 0.028602741505061, 0.226254712324589,
0.961297501178038, 0.129882103625732, 0.0568438422459096, 0.0730382613798221,
0.0730382613798221, 0.924327430521649, 0.166852174282121, 0.116060928134785,
0.0507912461473357, 0.0507912461473357),
tip.label = c("genome10","genome6", "genome5", "genome7", "genome9", "genome4", "genome1",
"genome2", "genome8", "genome3"), Nnode = 9L),
class = "phylo", order = "cladewise")
m <- as.data.frame(phy$edge)
m$length <- phy$edge.length
norg <- 10
depth <- coalescent.intervals(phy)$total.depth
brti <- c(structure(rep(0, norg), names=1:norg), branching.times(phy))
ne <- 1e10
mu <- 5e-12
smat <- simurg:::.codon.subst.mat
pm <- structure(c(0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1,
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0,
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0, 0, 0), .Dim = c(10L, 359L), .Dimnames = list(c("genome1",
"genome2", "genome3", "genome4", "genome5", "genome6", "genome7",
"genome8", "genome9", "genome10"), c("gene1", "gene2", "gene3",
"gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10",
"gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17",
"gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24",
"gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31",
"gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38",
"gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45",
"gene46", "gene47", "gene48", "gene49", "gene50", "gene51", "gene52",
"gene53", "gene54", "gene55", "gene56", "gene57", "gene58", "gene59",
"gene60", "gene61", "gene62", "gene63", "gene64", "gene65", "gene66",
"gene67", "gene68", "gene69", "gene70", "gene71", "gene72", "gene73",
"gene74", "gene75", "gene76", "gene77", "gene78", "gene79", "gene80",
"gene81", "gene82", "gene83", "gene84", "gene85", "gene86", "gene87",
"gene88", "gene89", "gene90", "gene91", "gene92", "gene93", "gene94",
"gene95", "gene96", "gene97", "gene98", "gene99", "gene100",
"gene101", "gene102", "gene103", "gene104", "gene105", "gene106",
"gene107", "gene108", "gene109", "gene110", "gene111", "gene112",
"gene113", "gene114", "gene115", "gene116", "gene117", "gene118",
"gene119", "gene120", "gene121", "gene122", "gene123", "gene124",
"gene125", "gene126", "gene127", "gene128", "gene129", "gene130",
"gene131", "gene132", "gene133", "gene134", "gene135", "gene136",
"gene137", "gene138", "gene139", "gene140", "gene141", "gene142",
"gene143", "gene144", "gene145", "gene146", "gene147", "gene148",
"gene149", "gene150", "gene151", "gene152", "gene153", "gene154",
"gene155", "gene156", "gene157", "gene158", "gene159", "gene160",
"gene161", "gene162", "gene163", "gene164", "gene165", "gene166",
"gene167", "gene168", "gene169", "gene170", "gene171", "gene172",
"gene173", "gene174", "gene175", "gene176", "gene177", "gene178",
"gene179", "gene180", "gene181", "gene182", "gene183", "gene184",
"gene185", "gene186", "gene187", "gene188", "gene189", "gene190",
"gene191", "gene192", "gene193", "gene194", "gene195", "gene196",
"gene197", "gene198", "gene199", "gene200", "gene201", "gene202",
"gene203", "gene204", "gene205", "gene206", "gene207", "gene208",
"gene209", "gene210", "gene211", "gene212", "gene213", "gene214",
"gene215", "gene216", "gene217", "gene218", "gene219", "gene220",
"gene221", "gene222", "gene223", "gene224", "gene225", "gene226",
"gene227", "gene228", "gene229", "gene230", "gene231", "gene232",
"gene233", "gene234", "gene235", "gene236", "gene237", "gene238",
"gene239", "gene240", "gene241", "gene242", "gene243", "gene244",
"gene245", "gene246", "gene247", "gene248", "gene249", "gene250",
"gene251", "gene252", "gene253", "gene254", "gene255", "gene256",
"gene257", "gene258", "gene259", "gene260", "gene261", "gene262",
"gene263", "gene264", "gene265", "gene266", "gene267", "gene268",
"gene269", "gene270", "gene271", "gene272", "gene273", "gene274",
"gene275", "gene276", "gene277", "gene278", "gene279", "gene280",
"gene281", "gene282", "gene283", "gene284", "gene285", "gene286",
"gene287", "gene288", "gene289", "gene290", "gene291", "gene292",
"gene293", "gene294", "gene295", "gene296", "gene297", "gene298",
"gene299", "gene300", "gene301", "gene302", "gene303", "gene304",
"gene305", "gene306", "gene307", "gene308", "gene309", "gene310",
"gene311", "gene312", "gene313", "gene314", "gene315", "gene316",
"gene317", "gene318", "gene319", "gene320", "gene321", "gene322",
"gene323", "gene324", "gene325", "gene326", "gene327", "gene328",
"gene329", "gene330", "gene331", "gene332", "gene333", "gene334",
"gene335", "gene336", "gene337", "gene338", "gene339", "gene340",
"gene341", "gene342", "gene343", "gene344", "gene345", "gene346",
"gene347", "gene348", "gene349", "gene350", "gene351", "gene352",
"gene353", "gene354", "gene355", "gene356", "gene357", "gene358",
"gene359")))
nsites <- rep(100, dim(pm)[2])
muts <- simurg:::.sim_mut(pm = pm,
phy = phy,
nsites = nsites,
m = m,
depth = depth,
brti = brti,
ne = ne,
norg = norg,
mu = mu,
smat = smat)
segments <- apply(phy$edge, 1, paste, collapse = '-')
test_that('.sim_mut works',{
expect_is(muts, 'list')
expect_true(all(sapply(muts, class)=='list'))
expect_true(class(unlist(muts))=='integer')
sg <- unique(unlist(lapply(muts, names)))
expect_true(all(sg%in%segments))
})
iferres/simba documentation built on July 31, 2019, 10:25 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context('Simulating mutations.')
# library(ape)
phy <- structure(list(edge = structure(c(11L, 13L, 19L, 19L, 13L, 18L,
18L, 11L, 12L, 15L, 15L, 16L, 16L, 12L, 14L, 14L, 17L, 17L, 13L,
19L, 1L, 2L, 18L, 3L, 4L, 12L, 15L, 5L, 16L, 6L, 7L, 14L, 8L,
17L, 9L, 10L), .Dim = c(18L, 2L)),
edge.length = c(0.570743614638502, 0.743533392747197, 0.00315730974266033, 0.00315730974266033,
0.718087960984797, 0.028602741505061, 0.028602741505061, 0.226254712324589,
0.961297501178038, 0.129882103625732, 0.0568438422459096, 0.0730382613798221,
0.0730382613798221, 0.924327430521649, 0.166852174282121, 0.116060928134785,
0.0507912461473357, 0.0507912461473357),
tip.label = c("genome10","genome6", "genome5", "genome7", "genome9", "genome4", "genome1",
"genome2", "genome8", "genome3"), Nnode = 9L),
class = "phylo", order = "cladewise")
m <- as.data.frame(phy$edge)
m$length <- phy$edge.length
norg <- 10
depth <- coalescent.intervals(phy)$total.depth
brti <- c(structure(rep(0, norg), names=1:norg), branching.times(phy))
ne <- 1e10
mu <- 5e-12
smat <- simurg:::.codon.subst.mat
pm <- structure(c(0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1,
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0,
0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,
1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0,
0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0,
0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1,
1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0,
1, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0,
0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0,
0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0,
0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1,
1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0,
1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1,
0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1,
1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1,
1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1,
0, 1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1,
0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0,
1, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1,
1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1,
0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0,
0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0,
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1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0,
1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1,
0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0,
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0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1,
0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1,
1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 1,
0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0,
1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1,
0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0,
0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1,
0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1,
1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1,
1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0,
0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
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0, 0, 0), .Dim = c(10L, 359L), .Dimnames = list(c("genome1",
"genome2", "genome3", "genome4", "genome5", "genome6", "genome7",
"genome8", "genome9", "genome10"), c("gene1", "gene2", "gene3",
"gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10",
"gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17",
"gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24",
"gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31",
"gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38",
"gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45",
"gene46", "gene47", "gene48", "gene49", "gene50", "gene51", "gene52",
"gene53", "gene54", "gene55", "gene56", "gene57", "gene58", "gene59",
"gene60", "gene61", "gene62", "gene63", "gene64", "gene65", "gene66",
"gene67", "gene68", "gene69", "gene70", "gene71", "gene72", "gene73",
"gene74", "gene75", "gene76", "gene77", "gene78", "gene79", "gene80",
"gene81", "gene82", "gene83", "gene84", "gene85", "gene86", "gene87",
"gene88", "gene89", "gene90", "gene91", "gene92", "gene93", "gene94",
"gene95", "gene96", "gene97", "gene98", "gene99", "gene100",
"gene101", "gene102", "gene103", "gene104", "gene105", "gene106",
"gene107", "gene108", "gene109", "gene110", "gene111", "gene112",
"gene113", "gene114", "gene115", "gene116", "gene117", "gene118",
"gene119", "gene120", "gene121", "gene122", "gene123", "gene124",
"gene125", "gene126", "gene127", "gene128", "gene129", "gene130",
"gene131", "gene132", "gene133", "gene134", "gene135", "gene136",
"gene137", "gene138", "gene139", "gene140", "gene141", "gene142",
"gene143", "gene144", "gene145", "gene146", "gene147", "gene148",
"gene149", "gene150", "gene151", "gene152", "gene153", "gene154",
"gene155", "gene156", "gene157", "gene158", "gene159", "gene160",
"gene161", "gene162", "gene163", "gene164", "gene165", "gene166",
"gene167", "gene168", "gene169", "gene170", "gene171", "gene172",
"gene173", "gene174", "gene175", "gene176", "gene177", "gene178",
"gene179", "gene180", "gene181", "gene182", "gene183", "gene184",
"gene185", "gene186", "gene187", "gene188", "gene189", "gene190",
"gene191", "gene192", "gene193", "gene194", "gene195", "gene196",
"gene197", "gene198", "gene199", "gene200", "gene201", "gene202",
"gene203", "gene204", "gene205", "gene206", "gene207", "gene208",
"gene209", "gene210", "gene211", "gene212", "gene213", "gene214",
"gene215", "gene216", "gene217", "gene218", "gene219", "gene220",
"gene221", "gene222", "gene223", "gene224", "gene225", "gene226",
"gene227", "gene228", "gene229", "gene230", "gene231", "gene232",
"gene233", "gene234", "gene235", "gene236", "gene237", "gene238",
"gene239", "gene240", "gene241", "gene242", "gene243", "gene244",
"gene245", "gene246", "gene247", "gene248", "gene249", "gene250",
"gene251", "gene252", "gene253", "gene254", "gene255", "gene256",
"gene257", "gene258", "gene259", "gene260", "gene261", "gene262",
"gene263", "gene264", "gene265", "gene266", "gene267", "gene268",
"gene269", "gene270", "gene271", "gene272", "gene273", "gene274",
"gene275", "gene276", "gene277", "gene278", "gene279", "gene280",
"gene281", "gene282", "gene283", "gene284", "gene285", "gene286",
"gene287", "gene288", "gene289", "gene290", "gene291", "gene292",
"gene293", "gene294", "gene295", "gene296", "gene297", "gene298",
"gene299", "gene300", "gene301", "gene302", "gene303", "gene304",
"gene305", "gene306", "gene307", "gene308", "gene309", "gene310",
"gene311", "gene312", "gene313", "gene314", "gene315", "gene316",
"gene317", "gene318", "gene319", "gene320", "gene321", "gene322",
"gene323", "gene324", "gene325", "gene326", "gene327", "gene328",
"gene329", "gene330", "gene331", "gene332", "gene333", "gene334",
"gene335", "gene336", "gene337", "gene338", "gene339", "gene340",
"gene341", "gene342", "gene343", "gene344", "gene345", "gene346",
"gene347", "gene348", "gene349", "gene350", "gene351", "gene352",
"gene353", "gene354", "gene355", "gene356", "gene357", "gene358",
"gene359")))
nsites <- rep(100, dim(pm)[2])
muts <- simurg:::.sim_mut(pm = pm,
phy = phy,
nsites = nsites,
m = m,
depth = depth,
brti = brti,
ne = ne,
norg = norg,
mu = mu,
smat = smat)
segments <- apply(phy$edge, 1, paste, collapse = '-')
test_that('.sim_mut works',{
expect_is(muts, 'list')
expect_true(all(sapply(muts, class)=='list'))
expect_true(class(unlist(muts))=='integer')
sg <- unique(unlist(lapply(muts, names)))
expect_true(all(sg%in%segments))
})
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