diff --git a/NEWS.md b/NEWS.md index dd50ab627..a831e8252 100644 --- a/NEWS.md +++ b/NEWS.md @@ -16,6 +16,8 @@ ## Bug fixes +* Fixed bug in `p_value()` for objects of class `averaging`. + * Fixed bug when extracting 'pretty labels' for model parameters, which could fail when predictors were character vectors. diff --git a/R/methods_averaging.R b/R/methods_averaging.R index c2abcbf05..86eaf0cc4 100644 --- a/R/methods_averaging.R +++ b/R/methods_averaging.R @@ -66,9 +66,27 @@ p_value.averaging <- function(model, component = "conditional", ...) { s <- summary(model)$coefmat.subset } + # to data frame + s <- as.data.frame(s) + + # do we have a p-value column based on t? + pvcn <- which(colnames(s) == "Pr(>|t|)") + # if not, do we have a p-value column based on z? + if (length(pvcn) == 0) { + pvcn <- which(colnames(s) == "Pr(>|z|)") + } + # if not, default to ncol + if (length(pvcn) == 0) { + if (ncol(s) > 4) { + pvcn <- 5 + } else { + pvcn <- 4 + } + } + .data_frame( Parameter = .remove_backticks_from_string(params$Parameter), - p = as.vector(s[, 5]) + p = as.vector(s[, pvcn]) ) } diff --git a/tests/testthat/_snaps/averaging.md b/tests/testthat/_snaps/averaging.md new file mode 100644 index 000000000..2d4b11762 --- /dev/null +++ b/tests/testthat/_snaps/averaging.md @@ -0,0 +1,50 @@ +# MuMIn link functions + + Code + print(mp) + Output + Parameter | Log-Odds | SE | 95% CI | z | p + ---------------------------------------------------------------- + (Intercept) | -1.01 | 0.26 | [-1.51, -0.50] | 3.91 | < .001 + var cont | -0.42 | 0.25 | [-0.90, 0.07] | 1.70 | 0.090 + var binom [1] | -0.71 | 0.62 | [-1.92, 0.50] | 1.15 | 0.250 + Message + + Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed + using a Wald z-distribution approximation. + + The model has a log- or logit-link. Consider using `exponentiate = + TRUE` to interpret coefficients as ratios. + +# ggpredict, glmmTMB averaging + + Code + print(mp) + Output + Parameter | Coefficient | SE | 95% CI | z | p + --------------------------------------------------------------------------------- + cond((Int)) | -0.11 | 0.22 | [ -0.55, 0.32] | 0.52 | 0.605 + cond(income) | -0.01 | 3.20e-03 | [ -0.02, -0.01] | 4.07 | < .001 + zi((Int)) | -23.11 | 17557.33 | [-34434.85, 34388.63] | 1.32e-03 | 0.999 + Message + + Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed + using a Wald z-distribution approximation. + +# ggpredict, poly averaging + + Code + print(mp) + Output + Parameter | Coefficient | SE | 95% CI | z | p + ---------------------------------------------------------------------- + (Intercept) | 954.50 | 123.60 | [712.26, 1196.75] | 7.72 | < .001 + gear | -24.81 | 18.54 | [-61.14, 11.52] | 1.34 | 0.181 + mpg | -51.21 | 11.60 | [-73.96, -28.47] | 4.41 | < .001 + mpg^2 | 0.79 | 0.26 | [ 0.29, 1.30] | 3.07 | 0.002 + am [1] | -30.80 | 32.30 | [-94.11, 32.52] | 0.95 | 0.340 + Message + + Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed + using a Wald z-distribution approximation. + diff --git a/tests/testthat/test-averaging.R b/tests/testthat/test-averaging.R new file mode 100644 index 000000000..9eadb60fc --- /dev/null +++ b/tests/testthat/test-averaging.R @@ -0,0 +1,67 @@ +skip_on_cran() + +skip_if_not_installed("MuMIn") +skip_if_not_installed("withr") +skip_if_not_installed("glmmTMB") +skip_if_not_installed("betareg") + +withr::with_options( + list(na.action = "na.fail"), + test_that("MuMIn link functions", { + library(MuMIn) # nolint + set.seed(1234) + dat <- data.frame( + outcome = rbinom(n = 100, size = 1, prob = 0.35), + var_binom = as.factor(rbinom(n = 100, size = 1, prob = 0.2)), + var_cont = rnorm(n = 100, mean = 10, sd = 7), + group = sample(letters[1:4], size = 100, replace = TRUE), + stringsAsFactors = FALSE + ) + dat$var_cont <- as.vector(scale(dat$var_cont)) + m1 <- glm( + outcome ~ var_binom + var_cont, + data = dat, + family = binomial(link = "logit") + ) + out <- MuMIn::model.avg(MuMIn::dredge(m1), fit = TRUE) + mp <- model_parameters(out) + expect_snapshot(print(mp)) + }) +) + +test_that("ggpredict, glmmTMB averaging", { + library(MuMIn) # nolint + data(FoodExpenditure, package = "betareg") + m <- glmmTMB::glmmTMB( + I(food / income) ~ income + (1 | persons), + ziformula = ~1, + data = FoodExpenditure, + na.action = "na.fail", + family = glmmTMB::beta_family() + ) + set.seed(123) + dr <- MuMIn::dredge(m) + avg <- MuMIn::model.avg(object = dr, fit = TRUE) + mp <- model_parameters(avg) + expect_snapshot(print(mp)) +}) + + +withr::with_options( + list(na.action = "na.fail"), + test_that("ggpredict, poly averaging", { + library(MuMIn) + data(mtcars) + mtcars$am <- factor(mtcars$am) + + set.seed(123) + m <- lm(disp ~ mpg + I(mpg^2) + am + gear, mtcars) + dr <- MuMIn::dredge(m, subset = dc(mpg, I(mpg^2))) + dr <- subset(dr, !(has(mpg) & !has(I(mpg^2)))) + mod.avg.i <- MuMIn::model.avg(dr, fit = TRUE) + mp <- model_parameters(mod.avg.i) + expect_snapshot(print(mp)) + }) +) + +unloadNamespace("MuMIn") diff --git a/tests/testthat/test-marginaleffects.R b/tests/testthat/test-marginaleffects.R index ae1df673f..59882f8c0 100644 --- a/tests/testthat/test-marginaleffects.R +++ b/tests/testthat/test-marginaleffects.R @@ -1,5 +1,4 @@ -skip_if_not_installed("marginaleffects", minimum_version = "0.18.0") -skip_if_not_installed("insight", minimum_version = "0.19.9") +skip_if_not_installed("marginaleffects", minimum_version = "1.0.0") skip_if_not_installed("rstanarm") test_that("marginaleffects()", { diff --git a/tests/testthat/test-serp.R b/tests/testthat/test-serp.R index 3dbf04646..a09bb32df 100644 --- a/tests/testthat/test-serp.R +++ b/tests/testthat/test-serp.R @@ -1,5 +1,4 @@ skip_if_not_installed("serp") -skip_if_not_installed("insight", minimum_version = "0.20.0") skip_if_not_installed("withr") # make sure we have the correct interaction mark for tests