p_adjust -> multcomp (#1300)

* p_adjust -> multcomp

* cruft

* multcomp works with raw models

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: marginaleffects
 Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests
-Version: 0.24.0.5
+Version: 0.24.0.6
 Authors@R:
     c(person(given = "Vincent",
              family = "Arel-Bundock",
@@ -123,6 +123,7 @@ Suggests:
     mlr3verse,
     modelbased,
     modelsummary,
+    multcomp,
     nlme,
     nnet,
     numDeriv,
@@ -200,7 +201,6 @@ Collate:
     'config.R'
     'conformal.R'
     'datagrid.R'
-    'deprecated.R'
     'equivalence.R'
     'get_coef.R'
     'get_contrast_data.R'
@@ -278,6 +278,7 @@ Collate:
     'methods_tidymodels.R'
     'methods_tobit1.R'
     'modelarchive.R'
+    'multcomp.R'
     'myTryCatch.R'
     'package.R'
     'plot.R'

NAMESPACE

@@ -195,8 +195,6 @@ export(avg_predictions)
 export(avg_slopes)
 export(comparisons)
 export(datagrid)
-export(datagridcf)
-export(deltamethod)
 export(expect_margins)
 export(expect_predictions)
 export(expect_slopes)
@@ -209,10 +207,6 @@ export(get_vcov)
 export(glance)
 export(hypotheses)
 export(inferences)
-export(marginal_means)
-export(marginaleffects)
-export(marginalmeans)
-export(meffects)
 export(plot_comparisons)
 export(plot_predictions)
 export(plot_slopes)

NEWS.md

@@ -2,13 +2,22 @@
 
 ## Development
 
-* Version 0.24.0 accidentally removed the "contrast" column from the output object in calls with only one focal predictor. This column is reinstated.
-* Reinstate some attributes lost with `marginaleffects_lean` but necessary for printing.
+Breaking changes:
+
+* `p_adjust` argument deprecated because of name-matching conflict with `p` argument in quantile regression and others. The recommended workflow is now to pass the object to the `hypotheses()` function and use its `multcomp` argument.
+* Removed long deprecated functions from the code base. These functions were already raising errors: `marginaleffects`, `meffects`, `marginal_means`, `deltamethod`, `datagridcf`. 
+
+New:
+
+* New `multcomp` argument for the `hypotheses()` function.
+* `hypotheses()` inherits the `conf_level` from `marginaleffects` objects when available. Otherwise, the default remains 0.95.
 * More informative warning for `lme4` and `glmmTMB` models with `re.form=NULL`
 * `df.residual()` methods tries to call `stats::df.residual()` on the "model" attribute. If that fails or returns `NULL`, we return `Inf`.
 
 Bugs:
 
+* Version 0.24.0 accidentally removed the "contrast" column from the output object in calls with only one focal predictor. This column is reinstated.
+* Reinstate some attributes lost with `marginaleffects_lean` but necessary for printing.
 * Encoding issue in bayesian models with `by`. Thanks to @Koalha for report #1290.
 * Retain necessary attribute information to ensure that "lean" return objects still print correctly #1295.
 

R/comparisons.R

@@ -243,7 +243,6 @@ comparisons <- function(model,
                         wts = FALSE,
                         hypothesis = NULL,
                         equivalence = NULL,
-                        p_adjust = NULL,
                         df = Inf,
                         eps = NULL,
                         numderiv = "fdforward",
@@ -287,7 +286,6 @@ comparisons <- function(model,
       wts = wts,
       hypothesis = hypothesis,
       equivalence = equivalence,
-      p_adjust = p_adjust,
       df = df),
     dots)
   if ("modeldata" %in% names(dots)) {
@@ -305,7 +303,6 @@ comparisons <- function(model,
   conf_level <- sanitize_conf_level(conf_level, ...)
   checkmate::assert_number(eps, lower = 1e-10, null.ok = TRUE)
   numderiv <- sanitize_numderiv(numderiv)
-  sanity_equivalence_p_adjust(equivalence, p_adjust)
   model <- sanitize_model(
     model = model,
     newdata = newdata,
@@ -511,7 +508,6 @@ comparisons <- function(model,
     draws = draws,
     estimate = "estimate",
     null_hypothesis = hypothesis_null,
-    p_adjust = p_adjust,
     model = model)
 
   # clean rows and columns
@@ -603,7 +599,6 @@ avg_comparisons <- function(model,
                             wts = FALSE,
                             hypothesis = NULL,
                             equivalence = NULL,
-                            p_adjust = NULL,
                             df = Inf,
                             eps = NULL,
                             numderiv = "fdforward",
@@ -638,7 +633,6 @@ avg_comparisons <- function(model,
     wts = wts,
     hypothesis = hypothesis,
     equivalence = equivalence,
-    p_adjust = p_adjust,
     df = df,
     eps = eps,
     ...)