labels for pscl (#1131)

strengejacke · web-flow · commit 96eb264f334f · 2025-07-08T23:58:57.000+02:00
* labels for pscl Fixes #1126 * fix * fix rotten links * update workflow
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -8,4 +8,4 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    uses: easystats/workflows/.github/workflows/R-CMD-check.yaml@main
+    uses: easystats/workflows/.github/workflows/R-CMD-check-no-oldrel.yaml@main
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.26.0.14
+Version: 0.26.0.15
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
diff --git a/NEWS.md b/NEWS.md
@@ -35,6 +35,10 @@
 
 * `bootstrap_model()` did not work for intercept-only models. This has been fixed.
 
+* Fixed issue with printing labels as pretty names for models from package
+  *pscl*, i.e. `print(model_parameters(model), pretty_names = "labels")` now
+  works as expected.
+
 # parameters 0.26.0
 
 ## Changes
diff --git a/R/1_model_parameters.R b/R/1_model_parameters.R
@@ -358,7 +358,7 @@
 #'
 #'   - Lakens, D., Scheel, A. M., and Isager, P. M. (2018). Equivalence Testing
 #'     for Psychological Research: A Tutorial. Advances in Methods and Practices
-#'     in Psychological Science, 1(2), 259–269. \doi{10.1177/2515245918770963}
+#'     in Psychological Science, 1(2), 259–269.
 #'
 #'   - Makowski, D., Ben-Shachar, M. S., Chen, S. H. A., and Lüdecke, D. (2019).
 #'     Indices of Effect Existence and Significance in the Bayesian Framework.
diff --git a/R/equivalence_test.R b/R/equivalence_test.R
@@ -187,7 +187,7 @@ bayestestR::equivalence_test
 #'
 #'   - Lakens, D., Scheel, A. M., and Isager, P. M. (2018). Equivalence Testing
 #'     for Psychological Research: A Tutorial. Advances in Methods and Practices
-#'     in Psychological Science, 1(2), 259–269. \doi{10.1177/2515245918770963}
+#'     in Psychological Science, 1(2), 259–269.
 #'
 #'   - Makowski, D., Ben-Shachar, M. S., Chen, S. H. A., and Lüdecke, D. (2019).
 #'     Indices of Effect Existence and Significance in the Bayesian Framework.
diff --git a/R/format_parameters.R b/R/format_parameters.R
@@ -425,6 +425,16 @@ format_parameters.parameters_model <- function(model, ...) {
       unlist(preds, use.names = FALSE)
     ))
 
+    # for models from pscl, we have "count_" and "zero_" prefixes, which
+    # we need to add to the "pretty_labels" names, so that we can match
+    # them with the parameters
+    if (inherits(model, c("zeroinfl", "hurdle"))) {
+      pretty_labels <- c(
+        stats::setNames(pretty_labels, paste0("count_", names(pretty_labels))),
+        stats::setNames(pretty_labels, paste0("zero_", names(pretty_labels)))
+      )
+    }
+
     # retrieve pretty names attribute
     pn <- attributes(params)$pretty_names
     # replace former pretty names with labels, if we have any labels
diff --git a/R/p_direction.R b/R/p_direction.R
@@ -48,7 +48,7 @@ bayestestR::p_direction
 #'
 #'   - Lakens, D., Scheel, A. M., and Isager, P. M. (2018). Equivalence Testing
 #'     for Psychological Research: A Tutorial. Advances in Methods and Practices
-#'     in Psychological Science, 1(2), 259–269. \doi{10.1177/2515245918770963}
+#'     in Psychological Science, 1(2), 259–269.
 #'
 #'   - Makowski, D., Ben-Shachar, M. S., Chen, S. H. A., and Lüdecke, D. (2019).
 #'     Indices of Effect Existence and Significance in the Bayesian Framework.
diff --git a/R/p_significance.R b/R/p_significance.R
@@ -99,7 +99,7 @@ bayestestR::p_significance
 #'
 #'   - Lakens, D., Scheel, A. M., and Isager, P. M. (2018). Equivalence Testing
 #'     for Psychological Research: A Tutorial. Advances in Methods and Practices
-#'     in Psychological Science, 1(2), 259–269. \doi{10.1177/2515245918770963}
+#'     in Psychological Science, 1(2), 259–269.
 #'
 #'   - Makowski, D., Ben-Shachar, M. S., Chen, S. H. A., and Lüdecke, D. (2019).
 #'     Indices of Effect Existence and Significance in the Bayesian Framework.
diff --git a/README.md b/README.md
@@ -350,7 +350,6 @@ Lakens, D. (2024). *Improving Your Statistical Inferences*.
 Lakens, D., Scheel, A. M., & Isager, P. M. (2018). Equivalence testing
 for psychological research: A tutorial. *Advances in Methods and
 Practices in Psychological Science*, *1*(2), 259–269.
-<https://doi.org/10.1177/2515245918770963>
 
 </div>
 
@@ -385,7 +384,7 @@ science. *Journal of Statistical Planning and Inference*, *195*,
 Schweder, T., & Hjort, N. L. (2003). Frequentist Analogues of Priors and
 Posteriors. In B. Stigum (Ed.), *Econometrics and the Philosophy of
 Economics: Theory-Data Confrontations in Economics* (pp. 285–217).
-Retrieved from <https://www.duo.uio.no/handle/10852/10425>
+Princeton: Princeton University Press.
 
 </div>
 
diff --git a/man/equivalence_test.lm.Rd b/man/equivalence_test.lm.Rd
diff --git a/man/model_parameters.Rd b/man/model_parameters.Rd
diff --git a/man/p_direction.lm.Rd b/man/p_direction.lm.Rd
diff --git a/man/p_significance.lm.Rd b/man/p_significance.lm.Rd
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -54,8 +54,6 @@ @article{lakens2020equivalence
 	title = {Equivalence Testing for Psychological Research: A Tutorial},
 	volume = {1},
 	issn = {2515-2459, 2515-2467},
-	url = {https://journals.sagepub.com/doi/10.1177/2515245918770963},
-	doi = {10.1177/2515245918770963},
 	language = {en},
 	number = {2},
 	journal = {Advances in Methods and Practices in Psychological Science},
@@ -219,7 +217,6 @@ @article{schweder_confidence_2018
 @incollection{schweder_frequentist_2003,
 	address = {Princeton},
 	title = {Frequentist {Analogues} of {Priors} and {Posteriors}},
-	url = {https://www.duo.uio.no/handle/10852/10425},
 	language = {eng},
 	urldate = {2024-09-03},
 	booktitle = {Econometrics and the {Philosophy} of {Economics}: {Theory}-{Data} {Confrontations} in {Economics}},
diff --git a/tests/testthat/_snaps/pretty_names.md b/tests/testthat/_snaps/pretty_names.md
@@ -19,3 +19,24 @@
       The model has a log- or logit-link. Consider using `exponentiate =
         TRUE` to interpret coefficients as ratios.
 
+# pretty_labels, pscl
+
+    Code
+      print(model_parameters(model), pretty_names = "labels", zap_small = TRUE)
+    Output
+      # Fixed Effects
+      
+      Parameter           | Log-Mean |   SE |         95% CI |     z |      p
+      -----------------------------------------------------------------------
+      (Intercept)         |     0.85 | 0.06 | [ 0.72,  0.97] | 13.29 | < .001
+      MyGender [Women]    |    -0.24 | 0.06 | [-0.36, -0.11] | -3.70 | < .001
+      MyMarried [Married] |     0.01 | 0.07 | [-0.12,  0.14] |  0.17 | 0.868 
+      
+      # Zero-Inflation
+      
+      Parameter           | Log-Odds |   SE |         95% CI |     z |      p
+      -----------------------------------------------------------------------
+      (Intercept)         |    -1.32 | 0.24 | [-1.79, -0.86] | -5.55 | < .001
+      MyGender [Women]    |     0.02 | 0.24 | [-0.46,  0.50] |  0.08 | 0.939 
+      MyMarried [Married] |    -0.09 | 0.25 | [-0.58,  0.40] | -0.37 | 0.715 
+
diff --git a/tests/testthat/test-pretty_names.R b/tests/testthat/test-pretty_names.R
@@ -65,3 +65,21 @@ withr::with_options(
     expect_snapshot(print(p))
   })
 )
+
+
+withr::with_options(
+  list(parameters_exponentiate = FALSE, parameters_warning_exponentiate = FALSE),
+  {
+    test_that("pretty_labels, pscl", {
+      skip_if_not_installed("pscl")
+
+      mydf <- pscl::bioChemists
+      attr(mydf$art, "label") <- "MyCount"
+      attr(mydf$fem, "label") <- "MyGender"
+      attr(mydf$mar, "label") <- "MyMarried"
+
+      model <- pscl::zeroinfl(art ~ fem + mar, data = mydf)
+      expect_snapshot(print(model_parameters(model), pretty_names = "labels", zap_small = TRUE))
+    })
+  }
+)
