From 85630d1e8365bbc9adf23ad10d2f171e574e785a Mon Sep 17 00:00:00 2001 From: Ben Bolker Date: Wed, 20 Mar 2024 09:23:29 -0400 Subject: [PATCH 1/5] updates for glmmTMB changes --- tests/testthat/test-get_variance.R | 1 + tests/testthat/test-glmmTMB.R | 9 +++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test-get_variance.R b/tests/testthat/test-get_variance.R index 9ca09ee4f..f3e38924b 100644 --- a/tests/testthat/test-get_variance.R +++ b/tests/testthat/test-get_variance.R @@ -364,6 +364,7 @@ test_that("fixed effects variance for rank-deficient models, #765", { mod_TMB <- glmmTMB::glmmTMB( z ~ x1 + x2 + x3 + x4 + (1 | re), data = dd, + start = list(theta = 3), control = glmmTMB::glmmTMBControl(rank_check = "adjust") ) }) diff --git a/tests/testthat/test-glmmTMB.R b/tests/testthat/test-glmmTMB.R index e5c7494f9..aaa28154d 100644 --- a/tests/testthat/test-glmmTMB.R +++ b/tests/testthat/test-glmmTMB.R @@ -617,7 +617,7 @@ test_that("get_data", { expect_null(get_data(m4, component = "disp", effects = "random", verbose = FALSE)) }) -test_that("find_paramaters", { +test_that("find_parameters", { expect_identical( find_parameters(m4), list( @@ -685,7 +685,7 @@ test_that("find_paramaters", { }) -test_that("get_paramaters", { +test_that("get_parameters", { expect_identical(nrow(get_parameters(m4)), 6L) expect_identical( colnames(get_parameters(m4)), @@ -880,7 +880,8 @@ d2$sd <- "five" dat <- rbind(d1, d2) m0 <- glmmTMB::glmmTMB(x ~ sd + (1 | t), dispformula = ~sd, data = dat) -test_that("get_paramaters", { + +test_that("get_parameters", { expect_identical(nrow(get_parameters(m0)), 4L) expect_identical( colnames(get_parameters(m0)), @@ -897,7 +898,7 @@ test_that("get_paramaters", { ) expect_equal( get_parameters(m0)$Estimate, - c(200.03431, -99.71491, 3.20287, 1.38648), + c(200.03431, -99.71491, 1.6014, 0.69323), tolerance = 1e-3 ) expect_identical( From b3c040965e9e0aa1c4ed8b8dbc9a13dd97ac582e Mon Sep 17 00:00:00 2001 From: Daniel Date: Wed, 20 Mar 2024 15:23:38 +0100 Subject: [PATCH 2/5] skip test for glmmTMB < 1.1.9 --- tests/testthat/test-glmmTMB.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-glmmTMB.R b/tests/testthat/test-glmmTMB.R index aaa28154d..54ad8644b 100644 --- a/tests/testthat/test-glmmTMB.R +++ b/tests/testthat/test-glmmTMB.R @@ -882,6 +882,7 @@ m0 <- glmmTMB::glmmTMB(x ~ sd + (1 | t), dispformula = ~sd, data = dat) test_that("get_parameters", { + skip_if_not_installed("glmmTMB", minimum_version = "1.1.9") expect_identical(nrow(get_parameters(m0)), 4L) expect_identical( colnames(get_parameters(m0)), From a864be51fcdad688d4ff1ba5839e97654ac09afe Mon Sep 17 00:00:00 2001 From: Daniel Date: Wed, 20 Mar 2024 15:38:53 +0100 Subject: [PATCH 3/5] lintr, accuracy of result --- tests/testthat/test-get_variance.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test-get_variance.R b/tests/testthat/test-get_variance.R index f3e38924b..207bb1f45 100644 --- a/tests/testthat/test-get_variance.R +++ b/tests/testthat/test-get_variance.R @@ -3,12 +3,12 @@ skip_if_not_installed("lme4") data(sleepstudy, package = "lme4") data("Penicillin", package = "lme4") set.seed(12345) -sleepstudy$grp <- sample(1:5, size = 180, replace = TRUE) +sleepstudy$grp <- sample.int(5, size = 180, replace = TRUE) sleepstudy$subgrp <- NA for (i in 1:5) { filter_group <- sleepstudy$grp == i sleepstudy$subgrp[filter_group] <- - sample(1:30, size = sum(filter_group), replace = TRUE) + sample.int(30, size = sum(filter_group), replace = TRUE) } study_data <<- sleepstudy @@ -286,7 +286,7 @@ test_that("get_variance-cat_random_slope", { data(sleepstudy, package = "lme4") set.seed(123) -sleepstudy$Months <- sample(1:4, nrow(sleepstudy), TRUE) +sleepstudy$Months <- sample.int(4, nrow(sleepstudy), TRUE) study_data3 <<- sleepstudy m2 <- lme4::lmer(Reaction ~ Days + (0 + Days | Subject), data = study_data3) @@ -369,5 +369,5 @@ test_that("fixed effects variance for rank-deficient models, #765", { ) }) out <- get_variance_fixed(mod_TMB) - expect_equal(out, 627.03661, tolerance = 1e-4, ignore_attr = TRUE) + expect_equal(out, 627.04511567, tolerance = 1e-4, ignore_attr = TRUE) }) From dba740a82baf7d3db7bc88e50360e9ab5d4f105c Mon Sep 17 00:00:00 2001 From: Daniel Date: Wed, 20 Mar 2024 15:57:50 +0100 Subject: [PATCH 4/5] styler --- tests/testthat/test-get_variance.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-get_variance.R b/tests/testthat/test-get_variance.R index 207bb1f45..534bb7e93 100644 --- a/tests/testthat/test-get_variance.R +++ b/tests/testthat/test-get_variance.R @@ -364,7 +364,7 @@ test_that("fixed effects variance for rank-deficient models, #765", { mod_TMB <- glmmTMB::glmmTMB( z ~ x1 + x2 + x3 + x4 + (1 | re), data = dd, - start = list(theta = 3), + start = list(theta = 3), control = glmmTMB::glmmTMBControl(rank_check = "adjust") ) }) From 0c36061fdbd6dad2ce8db3d47beb2d43ef00f52c Mon Sep 17 00:00:00 2001 From: Daniel Date: Wed, 20 Mar 2024 16:00:00 +0100 Subject: [PATCH 5/5] news, desc --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e9378b47c..075e95d40 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: insight Title: Easy Access to Model Information for Various Model Objects -Version: 0.19.9.1 +Version: 0.19.9.2 Authors@R: c(person(given = "Daniel", family = "Lüdecke", diff --git a/NEWS.md b/NEWS.md index ce5a59bed..2b4e9017e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,6 +5,8 @@ * Function like `find_variables()` or `clean_names()` now support multi-membership formulas for models from *brms*. +* Updated tests to work with the latest changes in *glmmTMBM 1.1.9*. + # insight 0.19.9 ## New supported models