tests/testthat/test-calculate.R

In SchlossLab/mothuR: Schloss Lab Tools for Reproducible Microbiome Research

library(dplyr)
library(tidyr)
shared_dat <- data.frame(
  label = rep.int(0.03, 3),
  Group = glue::glue("p{seq.int(1, 3, 1)}") %>% as.character(),
  numOtus = 3,
  Otu00001 = c(10, 0, 0), # 10
  Otu00002 = c(2, 10, 2), # 14
  Otu00003 = c(2, 1, 10), # 13
  Otu00004 = c(2, 2, 0), # 04
  Otu00005 = c(2, 0, 10), # 12
  Otu00006 = c(0, 11, 12) # 23
)
test_that("calc_rel_abun works", {
  expect_equal( # rows sum to 1
    calc_relabun(shared_dat) %>%
      pivot_wider(names_from = "otu", values_from = "rel_abun") %>%
      select(starts_with("Otu")) %>%
      rowSums(),
    rep(1, 3)
  )
  expect_equal(
    calc_relabun(shared_dat),
    structure(
      list(
        sample = c(
          "p1",
          "p1",
          "p1",
          "p1",
          "p1",
          "p1",
          "p2",
          "p2",
          "p2",
          "p2",
          "p2",
          "p2",
          "p3",
          "p3",
          "p3",
          "p3",
          "p3",
          "p3"
        ),
        otu = c(
          "Otu00001",
          "Otu00002",
          "Otu00003",
          "Otu00004",
          "Otu00005",
          "Otu00006",
          "Otu00001",
          "Otu00002",
          "Otu00003",
          "Otu00004",
          "Otu00005",
          "Otu00006",
          "Otu00001",
          "Otu00002",
          "Otu00003",
          "Otu00004",
          "Otu00005",
          "Otu00006"
        ),
        rel_abun = c(
          0.555555555555556,
          0.111111111111111,
          0.111111111111111,
          0.111111111111111,
          0.111111111111111,
          0,
          0,
          0.416666666666667,
          0.0416666666666667,
          0.0833333333333333,
          0,
          0.458333333333333,
          0,
          0.0588235294117647,
          0.294117647058824,
          0,
          0.294117647058824,
          0.352941176470588
        )
      ),
      row.names = c(NA, -18L),
      class = c("tbl_df", "tbl", "data.frame")
    )
  )
})