Nothing
context("breakaway")
library(breakaway)
library(phyloseq)
library(magrittr)
# library(testthat)
data("GlobalPatterns")
#### #### #### #### #### #### #### ####
#### All the datasets
#### #### #### #### #### #### #### ####
# see helper-data.R
gp_sub <- GlobalPatterns %>%
subset_samples(SampleType %in% c("Mock", "Even2"))
gp_order <- gp_sub %>%
tax_glom("Order")
gp_phylum <- gp_order %>%
tax_glom("Phylum")
datasets_ps <- list(GlobalPatterns,
gp_order %>%
subset_samples(X.SampleID %in% c("Even2")),
gp_order %>%
subset_samples(SampleType %in% c("Mock")),
gp_phylum %>%
subset_samples(X.SampleID %in% c("Even2")),
gp_phylum %>%
subset_samples(SampleType %in% c("Mock")),
gp_order)
#### #### #### #### #### #### #### ####
#### All the checks
#### #### #### #### #### #### #### ####
warnings_thrown <- function(est) {
working <- TRUE
if (is.nan(est$error) & is.null(est$warnings)) {
working <- FALSE
}
working
}
finite_ci <- function(est) {
working <- TRUE
if (is.nan(est$ci[2])) {
working <- FALSE
}
working
}
satisfies_bound <- function(est) {
working <- FALSE
if (est$estimate >= 0 | is.na(est$estimate)) {
working <- TRUE
}
working
}
test_that("All estimates", {
mm_ps <- lapply(X = datasets_ps, breakaway)
check_class <- lapply(X = mm_ps,
FUN = expect_is, class = "alpha_estimates")
# valid estimates
summaries <- lapply(X = mm_ps,
FUN = summary)
#
# # shouldn't be true for breakaway_nof1, the 9th estimate
# expect_true(lapply(X = lapply(mm,
# function(x) x$estimate), FUN = is.na) %>%
# lapply(function(x) !x) %>%
# unlist %>% all)
#
# expect_true(lapply(FUN = warnings_thrown, mm) %>%
# unlist %>% all)
#
# expect_true(lapply(FUN = satisfies_bound, mm) %>%
# unlist %>% all)
#
# ## dataset 4
# expect_true(lapply(FUN = finite_ci, mm) %>%
# unlist %>% all)
})
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