tests/testthat/test-alpha_estimates.R

In breakaway: Species Richness Estimation and Modeling

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")
#   
# })