parameters() fails on binomial mgcv::gam (#1052)

* parameters() fails on binomial mgcv::gam Fixes #1051 * news. desc * fix * update snapshots * include performance remotes * styler
easystats · Dec 3, 2024 · eff54e5 · eff54e5
1 parent ac2eb02
commit eff54e5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.24.0.2
+Version: 0.24.0.3
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -224,4 +224,4 @@ Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/website: easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
-Remotes: easystats/datawizard
+Remotes: easystats/datawizard, easystats/performance
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# parameters 0.24.1
+
+## Bug fixes
+
+* Fixed issue when printing `model_parameters()` with models from `mgcv::gam()`.
+
+* Fixed issues due to breaking changes in the latest release of the *datawizard*
+  package.
+
 # parameters 0.24.0
 
 ## Breaking Changes

diff --git a/R/dominance_analysis.R b/R/dominance_analysis.R
@@ -571,7 +571,7 @@ dominance_analysis <- function(model, sets = NULL, all = NULL,
   }
 
   da_df_res <- datawizard::data_rename(
-  da_df_res,
+    da_df_res,
     replacement = c(
       "Parameter", "General_Dominance",
       "Percent", "Ranks", "Subset"

diff --git a/R/format.R b/R/format.R
@@ -887,9 +887,14 @@ format.parameters_sem <- function(x,
     logit_model <- isTRUE(.additional_arguments(x, "logit_link", FALSE)) ||
       isTRUE(attributes(x)$coefficient_name %in% c("Log-Odds", "Odds Ratio"))
 
+    # remove NA and infinite values from spurios coefficients
+    if (!is.null(spurious_coefficients)) {
+      spurious_coefficients <- spurious_coefficients[!is.na(spurious_coefficients) & !is.infinite(spurious_coefficients)] # nolint
+    }
+
     # check for complete separation coefficients or possible issues with
     # too few data points
-    if (!is.null(spurious_coefficients) && logit_model) {
+    if (!is.null(spurious_coefficients) && length(spurious_coefficients) && logit_model) {
       if (any(spurious_coefficients > 50)) {
         msg <- c(msg, "Some coefficients are very large, which may indicate issues with complete separation.") # nolint
       } else if (any(spurious_coefficients > 15)) {

diff --git a/tests/testthat/_snaps/printing.md b/tests/testthat/_snaps/printing.md
@@ -361,3 +361,24 @@
       Uncertainty intervals (equal-tailed) and p-values (two-tailed) computed
         using a Wald t-distribution approximation.
 
+# no fail for mgcv-binomial
+
+    Code
+      print(out)
+    Output
+      # Fixed Effects
+      
+      Parameter   | Log-Odds |   SE |        95% CI |     z |    df |     p
+      ---------------------------------------------------------------------
+      (Intercept) |    -0.20 | 0.50 | [-1.18, 0.79] | -0.39 | 29.98 | 0.695
+      
+      # Smooth Terms
+      
+      Parameter         |    z |   df |     p
+      ---------------------------------------
+      Smooth term (mpg) | 7.24 | 1.02 | 0.007
+    Message
+      
+      The model has a log- or logit-link. Consider using `exponentiate =
+        TRUE` to interpret coefficients as ratios.
+
diff --git a/tests/testthat/test-printing.R b/tests/testthat/test-printing.R
@@ -118,3 +118,13 @@ withr::with_options(
     expect_snapshot(print(out))
   })
 )
+
+withr::with_options(
+  list(parameters_warning_exponentiate = TRUE),
+  test_that("no fail for mgcv-binomial", {
+    skip_if_not_installed("mgcv")
+    m <- mgcv::gam(vs ~ s(mpg), data = mtcars, family = "binomial")
+    out <- model_parameters(m)
+    expect_snapshot(print(out))
+  })
+)