library("rEMM")
library("testthat")

data("16S")

data <- Mollicutes16S + 1
test <- Mollicutes16S[2:10, ] + 1

## create two EMMs for different data
emm <- EMM("Kullback", threshold = 0.1, data = data)
emm

context("remove states")

## remove two states
n <- nstates(emm)
e <- remove_clusters(emm, c("3", "4"))
n1 <- nstates(e)
expect_equal(n - 2L, n1)

## prune w/ copy and w/o copy
rare <- rare_clusters(emm, 5)
e <- prune(emm, 5)
expect_equal(nstates(e), nstates(emm) - length(rare))
expect_equal(clusters(e), setdiff(clusters(emm), rare))


prune(emm, 5, copy = FALSE)
expect_equal(e, emm)

## merge clusters
n <- nclusters(emm)
e <- merge_clusters(emm, c("2", "3", "4", "5"))
expect_equal(nclusters(emm) - 3L, nclusters(e))