context("Merging operations")
test_that("Merging ok", {
data(dietswap)
ps <- dietswap
expect_equal(ntaxa(merge_taxa2(ps, pattern = "^Prevotella")), 127)
expect_equal(ntaxa(merge_taxa2(ps, taxa = taxa(ps)[grep("Prevotella", taxa(ps))])), 127)
expect_true("Prevotella" %in% taxa(merge_taxa2(ps, pattern = "^Prevotella", name = "Prevotella")))
expect_equal(abundances(aggregate_taxa(ps, level = "Phylum"))["Firmicutes", 2],
sum(abundances(ps)[rownames(tax_table(ps))[which(tax_table(ps)[, "Phylum"] == "Firmicutes")],2]))
#x <- dietswap
library(phyloseq)
data(GlobalPatterns)
x <- GlobalPatterns
a1 <- abundances(aggregate_taxa(x, level = "Genus"))
a2 <- colSums(abundances(x)[which(tax_table(x)[, "Genus"] == "Dialister"), ])
expect_equal(a1["Dialister",], a2)
})
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