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Added tests for learn_partition_modified

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This commit is contained in:
Waldir Leoncio 2019-12-16 16:56:41 +01:00
parent b5d99903d2
commit c630537516
2 changed files with 21 additions and 4 deletions
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3
R/admix1-learn_partition_modified.R
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@ -8,10 +8,9 @@
#' further combined. #' further combined.
learn_partition_modified <- function(ordered) { learn_partition_modified <- function(ordered) {
part <- learn_simple_partition(ordered, 0.05) part <- learn_simple_partition(ordered, 0.05)
# TODO: find learn_simple_partition
nclust <- length(unique(part)) nclust <- length(unique(part))
if (nclust == 3) { if (nclust == 3) {
mini_1 <- min(ordered(which(part == 1))) # ASK: what is ordered()? mini_1 <- min(ordered(which(part == 1)))
mini_2 <- min(ordered(which(part == 2))) mini_2 <- min(ordered(which(part == 2)))
mini_3 <- min(ordered(which(part == 3))) mini_3 <- min(ordered(which(part == 3)))
if (mini_1 > 0.9 & mini_2 > 0.9) { if (mini_1 > 0.9 & mini_2 > 0.9) {

22
tests/testthat/test-admix1.R
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@ -1,10 +1,14 @@
context("Admixture analysis") context("Admixture analysis")
test_that("learn_simple_partition behaves like Matlab", { test_that("learn*partition behaves like Matlab", {
# Test data
p1 <- c(0, .5, 1, 1.5) p1 <- c(0, .5, 1, 1.5)
p2 <- c(seq(0, .5, .1), 1, 1, 1, 2) p2 <- c(seq(0, .5, .1), 1, 1, 1, 2)
p3 <- c(.1, .1, .1, .5, .5, .5, 1, 1, 1) p3 <- c(.1, .1, .1, .5, .5, .5, 1, 1, 1)
p4 <- c(.7, 1, 1, 1)
# Testing learn_simple_partition
expect_equal( expect_equal(
object = learn_simple_partition(p1, 2), object = learn_simple_partition(p1, 2),
expected = matrix(c(1, 1, 2, 2)) expected = matrix(c(1, 1, 2, 2))
@ -17,4 +21,18 @@ test_that("learn_simple_partition behaves like Matlab", {
object = learn_simple_partition(p3, .5), object = learn_simple_partition(p3, .5),
expected = matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3)) expected = matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3))
) )
}) expect_equal(
object = learn_simple_partition(p4, 5),
expected = matrix(c(1, 1, 1, 1))
)
expect_equal(
object = learn_simple_partition(p4, .1),
expected = matrix(c(1, 2, 2, 2))
)
# Testing learn_partition_modified
expect_equal(
object = learn_partition_modified(p4),
expected = matrix(c(1, 2, 2, 2))
)
})