Nothing
context("alpha estimates")
library(breakaway)
library(phyloseq)
library(magrittr)
test_that("alpha_estimates works", {
data("GlobalPatterns")
# fix #77
my_alpha_estimates <- alpha_estimates(
alpha_estimate(estimate=1000, error=NULL, name = "tmp", model = "tmp", estimand = "tmp"),
alpha_estimate(estimate=1100, error=NULL, name = "tmp", model = "tmp", estimand = "tmp")
)
expect_is(summary(my_alpha_estimates), "data.frame")
expect_lt(object=summary(my_alpha_estimates)$estimate[1],
expected=summary(my_alpha_estimates)$estimate[2])
ba_raw <- GlobalPatterns %>%
subset_samples(SampleType == "Soil") %>%
breakaway
ba <- ba_raw %>%
summary
ba
expect_false(all(ba$estimate == ba$estimate[1]))
})
#
# test_that("breakaway runs on phyloseq objects", {
#
# expect_silent({y <- alpha_estimates(breakaway(apples),
# chao_bunge(apples))})
# expect_is(y, "alpha_estimates")
# expect_is(summary(y), "tbl")
# expect_is(plot(y), "ggplot")
# expect_is(plot(y, symmetric = FALSE), "ggplot")
# expect_is(plot(y, xaxis = 3:4, symmetric = FALSE), "ggplot")
# expect_equal(summary(y)[1,1] %>% unlist %>% unname,
# breakaway(apples)$estimate)
#
# ## this one
# expect_is(breakaway(GlobalPatterns %>%
# subset_samples(SampleType == "Mock")),
# "alpha_estimates")
# })
#
# test_that("breakaway runs on matrices objects", {
# # because it is a data frame
# expect_warning({y <- breakaway(toy_otu_table[, 1:2])})
# expect_is(y, "alpha_estimates")
# # bc it's a matrix
# expect_warning({y <- breakaway(as.matrix(toy_otu_table[, 1:2]))})
# expect_is(y, "alpha_estimates")
#
# })
#
#
# test_that("alpha_estimates is robust across taxonomy", {
#
# expect_silent({y <- GlobalPatterns %>%
# subset_samples(SampleType %in% c("Mock")) %>%
# tax_glom("Phylum") %>%
# sample_richness})
#
# expect_is(y, "alpha_estimates")
# expect_is(summary(y), "tbl")
# expect_is(plot(y), "ggplot")
#
# ps <- GlobalPatterns %>%
# subset_samples(SampleType %in% c("Mock")) %>%
# tax_glom("Order")
# expect_silent({z <- ps %>%
# breakaway})
# expect_is(z, "alpha_estimates")
# expect_is(summary(z), "tbl")
# expect_is(plot(z, physeq = ps, color = "SampleType"), "ggplot")
#
# expect_is(GlobalPatterns %>%
# subset_samples(X.SampleID %in% c("Even2")) %>%
# tax_glom("Order") %>% breakaway,
# "alpha_estimates")
#
# })
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