Nothing
context("basic HMM functions in general RIL")
test_that("genril n_gen, n_alleles work", {
expect_equal(nalleles("genril38"), 38)
expect_equal(nalleles("genril6"), 6)
expect_equal(test_ngen("genril38", FALSE), 38)
expect_equal(test_ngen("genril8", FALSE), 8)
expect_equal(test_ngen("genril38", TRUE), 38)
expect_equal(test_ngen("genril8", TRUE), 8)
# throw error for "genril1"
expect_error(nalleles("genril1"))
})
test_that("genril possible_gen work", {
expect_equal(test_possible_gen("genril38", FALSE, FALSE, 1:38), 1:38)
})
# FIX_ME: test check_geno
test_that("genril init work", {
set.seed(20181105)
alpha <- sample(1:10, 38, replace=TRUE)
init<- alpha/sum(alpha)
expect_equal( sapply(1:38, function(i) test_init("genril38", i, FALSE, FALSE, c(8,alpha))), log(init))
expect_equal( sapply(1:38, function(i) test_init("genril38", i, FALSE, FALSE, c(8,alpha))), log(init))
})
# FIX_ME: test emit
test_that("genril step works", {
skip_on_cran()
nf <- 38
alpha_int <- sample(1:10, nf, replace=TRUE)
alpha <- alpha_int/sum(alpha_int)
for(rf in c(0.01, 0.1, 0.45)) {
for(ngen in c(3, 5)) {
expected <- matrix(rep(alpha*(1-(1-rf)^ngen),nf), ncol=nf, byrow=TRUE)
diag(expected) <- alpha + (1-alpha)*(1-rf)^ngen
result <- matrix(ncol=nf, nrow=nf)
for(i in 1:nf) {
for(j in 1:nf) {
result[i,j] <- test_step(paste0("genril",nf), i, j, rf, FALSE, FALSE, c(ngen, alpha_int))
}
}
# rows sum to 1?
expect_equal(rowSums(exp(result)), rep(1, nf))
# match what I expected?
expect_equal(result, log(expected))
}
}
})
test_that("genril geno_names work", {
# if 38 founders, using upper case and lower case letters. Ugh.
alleles <- c(LETTERS, letters[1:(38-26)])
expect_equal( geno_names("genril38", alleles, FALSE), paste0(alleles, alleles) )
# could also use two-letter allele codes, but ugly
alleles <- c(paste0("A",LETTERS), paste0("B", LETTERS[1:(38-26)]))
expect_equal( geno_names("genril38", alleles, FALSE), paste0(alleles, alleles) )
})
test_that("genril nrec work", {
skip_on_cran()
x <- matrix(ncol=38, nrow=38)
x <- matrix(as.numeric(col(x) != row(x)), ncol=38)
res38 <- matrix(ncol=38, nrow=38)
for(i in 1:38) {
for(j in 1:38) {
res38[i,j] <- test_nrec("genril38", i, j, FALSE, FALSE, c(3, rep(1, 38)))
}
}
expect_equal( res38, x )
})
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