library(DivNet)
context("Test utility functions")
data(Lee)
Lee_phylum <- phyloseq::tax_glom(Lee, taxrank="Phylum")
divnet_phylum_char <- divnet(Lee_phylum, X = "char", tuning = "test")
test_that("OLS function returns something reasonable",
{
expect_is(OLS(X = model.matrix(lm(as.numeric(sample_data(Lee_phylum)$type)~
sample_data(Lee_phylum)$char)),
Y = cbind(sapply(divnet_phylum_char$shannon,
function(x) x$estimate),
sapply(divnet_phylum_char$simpson,
function(x) x$estimate))),
"matrix")
})
test_that("pickbase() picks a base in Lee phylum data",
{
expect_is(pick_base(t(otu_table(Lee_phylum))),
"integer")
})
test_that("errors occur in OLS", {
X <- matrix(rnorm(30), nrow = 5)
Y <- rnorm(rnorm(6))
#expect_output(OLS(X, Y), "Tried to regress X on Y where X is")
#expect_output(OLS(X, Y), print(X))
expect_error(OLS(X, Y), "Non-conformable multiplication")
})
test_that("errors occur in pick_base", {
expect_error(pick_base(W = matrix(0, nrow = 3, ncol = 3)),
"Yikes! No taxa observed in all samples!\n Pick which taxon is to be the base")
})
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