Nothing
context("combi input")
data(Zhang)
test_that("combi throws warnings when ordination model is fitted", {
expect_warning(combi(data = list("microbiome" = zhangMicrobio), distributions = "quasi",
compositional = TRUE, maxIt = 2L))
})
test_that("combi throws error for wrong input type", {
expect_error(combi(data = zhangMicrobio, distributions = "quasi",
compositional = TRUE, M = 2))
})
n = 50; p = 100
tmpMat = matrix(rnbinom(n*p, mu = 5, size = 1),n,p)
test_that("combi throws errors when no row names provided", {
expect_error(
combi(list(tmpMat), distributions = "quasi", compositional = TRUE)
)
})
tmpMat2 = tmpMat
rownames(tmpMat2) = paste("sample", seq_len(n))
tmpMat2[1,1] = NA
test_that("combi throws errors when NAs present in data matrix", {
expect_error(
combi(list(tmpMat2), distributions = "quasi", compositional = TRUE)
)
})
test_that("combi runs when NAs present in data matrix
and allowMissingess = TRUE", {
expect_s3_class(
combi(list(tmpMat2), distributions = "quasi",
compositional = TRUE, allowMissingness = TRUE, maxIt = 2L),
"combi"
)
})
test_that("Polynomial mean-variance model works", {
expect_s3_class(combi(data = list("microbiome" = zhangMicrobio,
"metabo" = zhangMetabo),
distributions = c("quasi", "gaussian"),
compositional = c(TRUE, FALSE), maxIt = 2L,
meanVarFit = "cubic"), "combi")
})
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