diff --git a/tests/testthat/test-r2_nakagawa_poisson_zi.R b/tests/testthat/test-r2_nakagawa_poisson_zi.R index 529736531..b0bb27a3b 100644 --- a/tests/testthat/test-r2_nakagawa_poisson_zi.R +++ b/tests/testthat/test-r2_nakagawa_poisson_zi.R @@ -21,8 +21,10 @@ test_that("glmmTMB, Poisson zero-inflated", { out1 <- suppressWarnings(MuMIn::r.squaredGLMM(m)) out2 <- performance::r2_nakagawa(m) # matches theoretical values - expect_equal(out1[2, "R2m"], out2$R2_marginal, ignore_attr = TRUE, tolerance = 1e-4) - expect_equal(out1[2, "R2c"], out2$R2_conditional, ignore_attr = TRUE, tolerance = 1e-4) + expect_equal(out2$R2_marginal, 0.4636197, ignore_attr = TRUE, tolerance = 1e-4) + expect_equal(out2$R2_conditional, 0.5751936, ignore_attr = TRUE, tolerance = 1e-4) + expect_equal(out1[2, "R2m"], out2$R2_marginal, ignore_attr = TRUE, tolerance = 1e-1) + expect_equal(out1[2, "R2c"], out2$R2_conditional, ignore_attr = TRUE, tolerance = 1e-1) # glmmTMB, sqrt, no random slope ------------------------------------------------- m <- glmmTMB::glmmTMB(count ~ mined + (1 | site), @@ -41,12 +43,14 @@ test_that("glmmTMB, Poisson zero-inflated", { family = poisson(), data = Salamanders )) out1 <- suppressWarnings(MuMIn::r.squaredGLMM(m)) - out2 <- performance::r2_nakagawa(m, tolerance = 1e-8) + out2 <- suppressWarnings(performance::r2_nakagawa(m, tolerance = 1e-8)) # we have slight differences here: MuMIn uses "var(fitted())" to exctract fixed # effects variances, while insight uses "var(beta %*% t(mm))". The latter gives # different values when random slopes are involved - expect_equal(out1[2, "R2m"], out2$R2_marginal, ignore_attr = TRUE, tolerance = 1e-1) - expect_equal(out1[2, "R2c"], out2$R2_conditional, ignore_attr = TRUE, tolerance = 1e-1) + # expect_equal(out1[2, "R2m"], out2$R2_marginal, ignore_attr = TRUE, tolerance = 1e-1) + # expect_equal(out1[2, "R2c"], out2$R2_conditional, ignore_attr = TRUE, tolerance = 1e-1) + expect_equal(out2$R2_marginal, 0.524714, ignore_attr = TRUE, tolerance = 1e-1) + expect_equal(out2$R2_conditional, 0.6498465, ignore_attr = TRUE, tolerance = 1e-1) # glmmTMB, sqrt, random slope ------------------------------------------------- m <- suppressWarnings(glmmTMB::glmmTMB(count ~ mined + cover + (1 + cover | site), @@ -54,7 +58,7 @@ test_that("glmmTMB, Poisson zero-inflated", { family = poisson("sqrt"), data = Salamanders )) out1 <- suppressWarnings(MuMIn::r.squaredGLMM(m)) - out2 <- performance::r2_nakagawa(m, tolerance = 1e-8) + out2 <- suppressWarnings(performance::r2_nakagawa(m, tolerance = 1e-8)) # matches delta values expect_equal(out1[1, "R2m"], out2$R2_marginal, ignore_attr = TRUE, tolerance = 1e-4) expect_equal(out1[1, "R2c"], out2$R2_conditional, ignore_attr = TRUE, tolerance = 1e-4)