context("breakaway_reasonable")
library(breakaway)
data("toy_otu_table")
set.seed(1)
test_that("breakaway gives reasonable std errors", {
### Sample 111 was a particular problem after change
selected_samples <- c(111, sample(1:143, size = 20, replace = F))
# this failed before any(is.infinite(ratiovars)) was added
for (i in selected_samples) {
y <- breakaway(toy_otu_table[, i])
expect_true(y$error >= 2 | is.na(y$estimate),
info = paste("std error is too small for Sample", i))
}
})
test_that("previously crazy estimates are fine", {
# this is fine: plot is just a disaster
library(phyloseq)
data(GlobalPatterns)
bad <- (GlobalPatterns %>% otu_table)[,1] %>% c
ba <- bad %>% breakaway
expect_true(ba$error >= 5 | is.na(ba$estimate),
info = paste("std error is too small for first GlobalPatterns"))
})
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