tests/testthat/test_model_tools.R

In hemoshear/assayr2: Tools for analyzing assay data

library(magrittr)
context("model_tools.R")

### makeCI() -------------------------------------------------------
# lm()
data(mtcars)
mtcars$cyl %<>% as.factor()
lm_model <- lm(log2(mpg) ~ 0 + cyl, data = mtcars)
ci <- suppressMessages(make_cis(lm_model))
ci2 <- suppressMessages(make_cis(lm_model, restore = FALSE))

stats_ci <- confint(lm_model)

test_that("confidence intervals work for lm()s", {
  expect_equal(names(ci), c("cyl", "est", "lwr", "upr"))
  expect_equal(ci$lwr, 2^unname(stats_ci[, 1]))
  expect_equal(ci2$lwr, unname(stats_ci[, 1]))
  expect_true(is.data.frame(ci))
})

# lmer()
data(iris)
iris %<>% dplyr::group_by(Species) %>% dplyr::mutate(site = rep(1:10, each = 5))
lmer_model <- lme4::lmer(log2(Sepal.Length) ~ 0 + Species + (1 | site), data = iris)
ci <- suppressMessages(make_cis(lmer_model))
ci2 <- suppressMessages(make_cis(lmer_model, restore = FALSE))

stats_ci <- suppressMessages(confint(lmer_model))

test_that("confidence intervals work for lm()s", {
  expect_equal(names(ci), c("Species", "est", "lwr", "upr"))
  expect_equal(ci$lwr, 2^unname(stats_ci[3:5, 1]))
  expect_equal(ci2$lwr, unname(stats_ci[3:5, 1]))
  expect_true(is.data.frame(ci))
})

# makeFC() -------------------------------------------------------------------

# lm()
fc <- suppressWarnings(make_fcs(lm_model))
fc2 <- suppressWarnings(make_fcs(lm_model, restore = FALSE))

test_that("fold changes work for lm()s", {
  expect_true(is.data.frame(fc))
  expect_equal(names(fc), c("cyl", "contrast", "baseline", "fc_est", "fc_lwr", "fc_upr", "pval", "pct_change", "log2_fc", "label"))
  expect_equal(fc$cyl, c("6", "8"))
  expect_equal(fc$fc_est, c(0.7482528, 0.5653657), tolerance = 0.001)
  expect_equal(fc2$fc_est, c(-0.4184022, -0.8227438), tolerance = 0.001)
  expect_equal(fc$pct_change, c(-25, -43))
})

# lmer()
data(iris)
iris %<>% dplyr::group_by(Species) %>% dplyr::mutate(site = rep(1:10, each = 5))
lmer_model <- lme4::lmer(log2(Sepal.Length) ~ 0 + Species + (1 | site), data = iris)
fc <- suppressWarnings(make_fcs(lmer_model))
fc2 <- suppressWarnings(make_fcs(lmer_model, restore = FALSE))

test_that("fold changes work for lmer()s", {
  expect_true(is.data.frame(fc))
  expect_equal(names(fc), c("Species", "contrast", "baseline", "fc_est", "fc_lwr", "fc_upr", "pval", "pct_change", "log2_fc", "label"))
  expect_equal(fc$Species, c("versicolor", "virginica"))
  expect_equal(fc$fc_est, c(1.184255, 1.313176), tolerance = 0.001)
  expect_equal(fc2$fc_est, c(0.2439793, 0.3930608), tolerance = 0.001)
  expect_equal(fc$pct_change, c(18, 31))
})