tests/testthat/test-i2_ml.R

In daniel1noble/orchaRd: Orchard Plots and Prediction Intervals for Meta-analysis and Meta-regression

context("Checking i2_ml function..")

options(warn = -1)
data(lim)
lim$vi<-(1/sqrt(lim$N - 3))^2

# Check two types of model specification. One with formula and one without
lim_MR<-metafor::rma.mv(yi=yi, V=vi, mods=~Phylum-1, random=list(~1|Article, ~1|Datapoint), data = lim)

lim_MR2<-metafor::rma.mv(yi~1, V=vi, mods=~Phylum-1, random=list(~1|Article, ~1|Datapoint), data = lim)

# Check point estimates
 I2_lim_2 <- orchaRd::i2_ml(lim_MR)
I2_lim_22 <- orchaRd::i2_ml(lim_MR2)

# Checking boot
 I2_lim_2_boot <- orchaRd::i2_ml(lim_MR,  boot =10)
I2_lim_22_boot <- orchaRd::i2_ml(lim_MR2,  boot = 10)

# Check it works with robust models
lim_MR_robust <- metafor::robust(lim_MR, cluster=lim$Article)
I2_lim_robust <- orchaRd::i2_ml(lim_MR_robust)

testthat::test_that("Checking i2 has correct dimensions..", {
  testthat::expect_equal(
    length(I2_lim_2), 3,
    info = "i2 has correct dimensions")

  testthat::expect_equal(
    dim(I2_lim_2_boot)[1], 3,
    info = "i2 boot has correct dimensions")

  testthat::expect_equal(
    dim(I2_lim_22_boot)[1], 3,
    info = "i2 boot works with mod formula specification")

  testthat::expect_equal(
    length(I2_lim_robust), 3,
    info = "i2 on robust object has correct dimensions")

testthat::expect_equal(round(as.vector(I2_lim_2),2), round(c(84.32574, 48.19211, 36.13363), 2), info = "checking i2 estimates calculated correctly...")
})