From c71c68a5ecc45e16bc051fc57d3345e280140fb3 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 19:23:06 +0100
Subject: [PATCH 01/10] Draft marginalcontrasts

---
 R/estimate_contrasts.R    | 89 +++++++++++++++++++++++++--------------
 R/get_marginalcontrasts.R | 20 ++++++---
 man/estimate_contrasts.Rd |  4 ++
 man/get_marginalmeans.Rd  | 41 +++++++++++++-----
 4 files changed, 107 insertions(+), 47 deletions(-)

diff --git a/R/estimate_contrasts.R b/R/estimate_contrasts.R
index 407f7a42..b0f4ca5d 100644
--- a/R/estimate_contrasts.R
+++ b/R/estimate_contrasts.R
@@ -78,17 +78,64 @@ estimate_contrasts <- function(model,
                                ci = 0.95,
                                p_adjust = "holm",
                                method = "pairwise",
+                               backend = "emmeans",
                                ...) {
-  # Run emmeans
-  estimated <- get_emcontrasts(model,
-    contrast = contrast,
-    by = by,
-    transform = transform,
-    method = method,
-    adjust = p_adjust,
-    ...
+  if (backend == "emmeans") {
+    # Emmeans ------------------------------------------------------------------
+    estimated <- get_emcontrasts(model,
+      contrast = contrast,
+      by = by,
+      transform = transform,
+      method = method,
+      adjust = p_adjust,
+      ...
+    )
+    out <- .format_emmeans_contrasts(model, estimated, ci, transform, p_adjust, ...)
+  } else {
+    # Marginalmeans ------------------------------------------------------------
+    estimated <- get_marginalcontrasts(model,
+      contrast = contrast,
+      by = by,
+      transform = transform,
+      method = method,
+      adjust = p_adjust,
+      ...
+    )
+    out <- .format_marginaleffects_means(estimated, model, transform, ...)
+  }
+
+
+  # Table formatting
+  attr(out, "table_title") <- c("Marginal Contrasts Analysis", "blue")
+  attr(out, "table_footer") <- .estimate_means_footer(
+    out,
+    info$contrast,
+    type = "contrasts",
+    p_adjust = p_adjust
   )
 
+  # Add attributes
+  attr(out, "model") <- model
+  attr(out, "response") <- insight::find_response(model)
+  attr(out, "ci") <- ci
+  attr(out, "transform") <- transform
+  attr(out, "at") <- info$by
+  attr(out, "by") <- info$by
+  attr(out, "contrast") <- info$contrast
+  attr(out, "p_adjust") <- p_adjust
+
+
+  # Output
+  class(out) <- c("estimate_contrasts", "see_estimate_contrasts", class(out))
+  out
+}
+
+
+
+# Table formatting emmeans ----------------------------------------------------
+
+
+.format_emmeans_contrasts <- function(model, estimated, ci, transform, p_adjust, ...) {
   info <- attributes(estimated)
 
   # Summarize and clean
@@ -120,30 +167,10 @@ estimate_contrasts <- function(model,
 
   # Merge levels and rest
   out$contrast <- NULL
-  out <- cbind(level_cols, out)
-
-
-  # Table formatting
-  attr(out, "table_title") <- c("Marginal Contrasts Analysis", "blue")
-  attr(out, "table_footer") <- .estimate_means_footer(
-    out,
-    info$contrast,
-    type = "contrasts",
-    p_adjust = p_adjust
-  )
+  cbind(level_cols, out)
+}
 
-  # Add attributes
-  attr(out, "model") <- model
-  attr(out, "response") <- insight::find_response(model)
-  attr(out, "ci") <- ci
-  attr(out, "transform") <- transform
-  attr(out, "at") <- info$by
-  attr(out, "by") <- info$by
-  attr(out, "contrast") <- info$contrast
-  attr(out, "p_adjust") <- p_adjust
 
+.format_marginaleffects_means <- function() {
 
-  # Output
-  class(out) <- c("estimate_contrasts", "see_estimate_contrasts", class(out))
-  out
 }
diff --git a/R/get_marginalcontrasts.R b/R/get_marginalcontrasts.R
index c1444750..f8125536 100644
--- a/R/get_marginalcontrasts.R
+++ b/R/get_marginalcontrasts.R
@@ -1,24 +1,34 @@
 #' @rdname get_marginalmeans
 #'
 #' @param method Contrast method.
+#' @inheritParams get_emcontrasts
 #' @export
 get_marginalcontrasts <- function(model,
+                                  contrast = NULL,
                                   by = NULL,
-                                  ci = 0.95,
+                                  transform = "none",
                                   method = "pairwise",
+                                  ci = 0.95,
                                   ...) {
+  # check if available
+  insight::check_if_installed("marginaleffects")
+
+  # Guess arguments
+  my_args <- .guess_marginalcontrasts_arguments(model, contrast, by, ...)
+
   out <- estimate_means(
     model = model,
-    by = by,
+    by = my_args$by,
     ci = ci,
     hypothesis = method,
+    transform = transform,
     backend = "marginaleffects",
     ...
   )
 
-  attr(out, "table_title") <- c("Marginal Contrasts Analysis", "blue")
-  attr(out, "table_footer") <- .estimate_means_footer(out, by = by, type = "contrasts", p_adjust = NULL)
-
+  attr(out, "contrast") <- my_args$contrast
+  attr(out, "at") <- my_args$by
+  attr(out, "by") <- my_args$by
   out
 }
 
diff --git a/man/estimate_contrasts.Rd b/man/estimate_contrasts.Rd
index 105aa50c..7269373e 100644
--- a/man/estimate_contrasts.Rd
+++ b/man/estimate_contrasts.Rd
@@ -12,6 +12,7 @@ estimate_contrasts(
   ci = 0.95,
   p_adjust = "holm",
   method = "pairwise",
+  backend = "emmeans",
   ...
 )
 }
@@ -44,6 +45,9 @@ p-value adjustment section in the \code{emmeans::test} documentation.}
 
 \item{method}{Contrast method. See same argument in \link[emmeans:contrast]{emmeans::contrast}.}
 
+\item{backend}{Whether to use 'emmeans' or 'marginaleffects' as a backend.
+The latter is experimental and some features might not work.}
+
 \item{...}{Other arguments passed for instance to \code{\link[insight:get_datagrid]{insight::get_datagrid()}}.}
 }
 \value{
diff --git a/man/get_marginalmeans.Rd b/man/get_marginalmeans.Rd
index 3fb16250..fa12ea30 100644
--- a/man/get_marginalmeans.Rd
+++ b/man/get_marginalmeans.Rd
@@ -9,9 +9,25 @@
 \alias{model_marginalmeans}
 \title{Easy 'avg_predictions' and 'avg_slopes'}
 \usage{
-get_marginalcontrasts(model, by = NULL, ci = 0.95, method = "pairwise", ...)
-
-model_marginalcontrasts(model, by = NULL, ci = 0.95, method = "pairwise", ...)
+get_marginalcontrasts(
+  model,
+  contrast = NULL,
+  by = NULL,
+  transform = "none",
+  method = "pairwise",
+  ci = 0.95,
+  ...
+)
+
+model_marginalcontrasts(
+  model,
+  contrast = NULL,
+  by = NULL,
+  transform = "none",
+  method = "pairwise",
+  ci = 0.95,
+  ...
+)
 
 get_marginaleffects(model, trend = NULL, by = NULL, ...)
 
@@ -22,27 +38,30 @@ model_marginalmeans(model, by = "auto", transform = NULL, ci = 0.95, ...)
 \arguments{
 \item{model}{A statistical model.}
 
+\item{contrast}{A character vector indicating the name of the variable(s)
+for which to compute the contrasts.}
+
 \item{by}{The predictor variable(s) at which to evaluate the desired effect
 / mean / contrasts. Other predictors of the model that are not included
 here will be collapsed and "averaged" over (the effect will be estimated
 across them).}
 
-\item{ci}{Level for confidence intervals.}
+\item{transform}{Can be used to easily modulate the \code{type} argument in
+\code{marginaleffects::avg_predictions()}. Can be \code{"none"} or \code{"response"}.
+\code{"none"} will leave the values on scale of the linear predictors.
+\code{"response"} will transform them on scale of the response variable. Thus for
+a logistic model, \code{"none"} will give estimations expressed in log-odds
+(probabilities on logit scale) and \code{"response"} in terms of probabilities.}
 
 \item{method}{Contrast method.}
 
+\item{ci}{Level for confidence intervals.}
+
 \item{...}{Other arguments passed, for instance, to \code{\link[insight:get_datagrid]{insight::get_datagrid()}}
 or \code{\link[marginaleffects:predictions]{marginaleffects::avg_predictions()}}.}
 
 \item{trend}{A character indicating the name of the variable
 for which to compute the slopes.}
-
-\item{transform}{Can be used to easily modulate the \code{type} argument in
-\code{marginaleffects::avg_predictions()}. Can be \code{"none"} or \code{"response"}.
-\code{"none"} will leave the values on scale of the linear predictors.
-\code{"response"} will transform them on scale of the response variable. Thus for
-a logistic model, \code{"none"} will give estimations expressed in log-odds
-(probabilities on logit scale) and \code{"response"} in terms of probabilities.}
 }
 \description{
 The \code{get_marginalmeans()} function is a wrapper to facilitate the usage of

From c51a3a593e9c8fa59f451259cae700eb51f6ef53 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 21:13:30 +0100
Subject: [PATCH 02/10] draft

---
 R/estimate_contrasts.R    | 16 ++++++++++------
 R/get_marginalcontrasts.R | 11 +++--------
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/R/estimate_contrasts.R b/R/estimate_contrasts.R
index b0f4ca5d..0fbc45f7 100644
--- a/R/estimate_contrasts.R
+++ b/R/estimate_contrasts.R
@@ -91,6 +91,7 @@ estimate_contrasts <- function(model,
       ...
     )
     out <- .format_emmeans_contrasts(model, estimated, ci, transform, p_adjust, ...)
+    info <- attributes(estimated)
   } else {
     # Marginalmeans ------------------------------------------------------------
     estimated <- get_marginalcontrasts(model,
@@ -98,10 +99,13 @@ estimate_contrasts <- function(model,
       by = by,
       transform = transform,
       method = method,
-      adjust = p_adjust,
+      p_adjust = p_adjust,
+      ci = ci,
       ...
     )
-    out <- .format_marginaleffects_means(estimated, model, transform, ...)
+    out <- .format_marginaleffects_contrasts(model, estimated, ci, transform, p_adjust, ...)
+    ## TODO: needs to be fixed
+    info <- list(contrast = contrast, by = by)
   }
 
 
@@ -136,8 +140,6 @@ estimate_contrasts <- function(model,
 
 
 .format_emmeans_contrasts <- function(model, estimated, ci, transform, p_adjust, ...) {
-  info <- attributes(estimated)
-
   # Summarize and clean
   if (insight::model_info(model)$is_bayesian) {
     out <- cbind(estimated@grid, bayestestR::describe_posterior(estimated, ci = ci, verbose = FALSE, ...))
@@ -171,6 +173,8 @@ estimate_contrasts <- function(model,
 }
 
 
-.format_marginaleffects_means <- function() {
-
+.format_marginaleffects_contrasts <- function(model, estimated, ci, transform, p_adjust, ...) {
+  groups <- attributes(estimated)$by
+  contrast <- attributes(estimated)$contrast
+  estimated
 }
diff --git a/R/get_marginalcontrasts.R b/R/get_marginalcontrasts.R
index f8125536..1336b3d5 100644
--- a/R/get_marginalcontrasts.R
+++ b/R/get_marginalcontrasts.R
@@ -13,22 +13,17 @@ get_marginalcontrasts <- function(model,
   # check if available
   insight::check_if_installed("marginaleffects")
 
-  # Guess arguments
-  my_args <- .guess_marginalcontrasts_arguments(model, contrast, by, ...)
-
   out <- estimate_means(
     model = model,
-    by = my_args$by,
+    by = c(contrast, by),
     ci = ci,
     hypothesis = method,
-    transform = transform,
+    transform = "response",
     backend = "marginaleffects",
     ...
   )
 
-  attr(out, "contrast") <- my_args$contrast
-  attr(out, "at") <- my_args$by
-  attr(out, "by") <- my_args$by
+  attr(out, "contrast") <- contrast
   out
 }
 

From 1d041754dbd13956a12860665ca6eb37bd72d47f Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 21:18:41 +0100
Subject: [PATCH 03/10] fix

---
 R/get_marginalmeans.R | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/R/get_marginalmeans.R b/R/get_marginalmeans.R
index fc62be3f..95cc4c78 100644
--- a/R/get_marginalmeans.R
+++ b/R/get_marginalmeans.R
@@ -120,6 +120,13 @@ model_marginalmeans <- get_marginalmeans
   info <- insight::model_info(model, verbose = FALSE)
   non_focal <- setdiff(colnames(model_data), attr(means, "focal_terms"))
 
+  # do we have contrasts? For contrasts, we want to keep p-values
+  if (is.null(list(...)$hypothesis)) {
+    p_column <- "p"
+  } else {
+    p_column <- NULL
+  }
+
   # estimate name
   if (!identical(transform, "none") && (info$is_binomial || info$is_bernoulli)) {
     estimate_name <- "Probability"
@@ -129,9 +136,9 @@ model_marginalmeans <- get_marginalmeans
 
   # Format
   params <- suppressWarnings(parameters::model_parameters(means, verbose = FALSE))
-  params <- datawizard::data_relocate(params, c("Predicted", "SE", "CI_low", "CI_high"), after = -1, verbose = FALSE) # nolint
+  params <- datawizard::data_relocate(params, c("Predicted", "SE", "CI_low", "CI_high", "p"), after = -1, verbose = FALSE) # nolint
   params <- datawizard::data_rename(params, "Predicted", estimate_name)
-  params <- datawizard::data_remove(params, c("p", "Statistic", "s.value", "S", "CI", "df", "rowid_dedup", non_focal), verbose = FALSE) # nolint
+  params <- datawizard::data_remove(params, c(p_column, "Statistic", "s.value", "S", "CI", "df", "rowid_dedup", non_focal), verbose = FALSE) # nolint
   params <- datawizard::data_restoretype(params, model_data)
 
   # Store info

From e6aeb1be07a1bf6ccd92be083b41499b97ba3487 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 21:27:27 +0100
Subject: [PATCH 04/10] dev

---
 R/get_marginalmeans.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/get_marginalmeans.R b/R/get_marginalmeans.R
index 95cc4c78..1547f55f 100644
--- a/R/get_marginalmeans.R
+++ b/R/get_marginalmeans.R
@@ -123,15 +123,15 @@ model_marginalmeans <- get_marginalmeans
   # do we have contrasts? For contrasts, we want to keep p-values
   if (is.null(list(...)$hypothesis)) {
     p_column <- "p"
+    # estimate name
+    if (!identical(transform, "none") && (info$is_binomial || info$is_bernoulli)) {
+      estimate_name <- "Probability"
+    } else {
+      estimate_name <- "Mean"
+    }
   } else {
     p_column <- NULL
-  }
-
-  # estimate name
-  if (!identical(transform, "none") && (info$is_binomial || info$is_bernoulli)) {
-    estimate_name <- "Probability"
-  } else {
-    estimate_name <- "Mean"
+    estimate_name <- "Difference"
   }
 
   # Format

From ecbbf57a69f50360dc0f334c97e1e554dbb39e19 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 21:34:37 +0100
Subject: [PATCH 05/10] dev

---
 R/estimate_contrasts.R |  3 +++
 R/get_marginalmeans.R  | 18 +++++++++++-------
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/R/estimate_contrasts.R b/R/estimate_contrasts.R
index 0fbc45f7..9408a634 100644
--- a/R/estimate_contrasts.R
+++ b/R/estimate_contrasts.R
@@ -176,5 +176,8 @@ estimate_contrasts <- function(model,
 .format_marginaleffects_contrasts <- function(model, estimated, ci, transform, p_adjust, ...) {
   groups <- attributes(estimated)$by
   contrast <- attributes(estimated)$contrast
+
+  ## TODO: split Parameter column into levels indicated in "contrast", and filter by "by"
+
   estimated
 }
diff --git a/R/get_marginalmeans.R b/R/get_marginalmeans.R
index 1547f55f..878c8ca8 100644
--- a/R/get_marginalmeans.R
+++ b/R/get_marginalmeans.R
@@ -119,26 +119,30 @@ model_marginalmeans <- get_marginalmeans
   model_data <- insight::get_data(model)
   info <- insight::model_info(model, verbose = FALSE)
   non_focal <- setdiff(colnames(model_data), attr(means, "focal_terms"))
+  is_contrast_analysis <- !is.null(list(...)$hypothesis)
 
   # do we have contrasts? For contrasts, we want to keep p-values
-  if (is.null(list(...)$hypothesis)) {
-    p_column <- "p"
+  if (is_contrast_analysis) {
+    remove_column <- "SE"
+    estimate_name <- "Difference"
+  } else {
+    remove_column <- "p"
     # estimate name
     if (!identical(transform, "none") && (info$is_binomial || info$is_bernoulli)) {
       estimate_name <- "Probability"
     } else {
       estimate_name <- "Mean"
     }
-  } else {
-    p_column <- NULL
-    estimate_name <- "Difference"
   }
 
   # Format
   params <- suppressWarnings(parameters::model_parameters(means, verbose = FALSE))
-  params <- datawizard::data_relocate(params, c("Predicted", "SE", "CI_low", "CI_high", "p"), after = -1, verbose = FALSE) # nolint
+  params <- datawizard::data_relocate(params, c("Predicted", "SE", "CI_low", "CI_high"), after = -1, verbose = FALSE) # nolint
+  # move p to the end
+  params <- datawizard::data_relocate(params, "p", after = -1, verbose = FALSE)
   params <- datawizard::data_rename(params, "Predicted", estimate_name)
-  params <- datawizard::data_remove(params, c(p_column, "Statistic", "s.value", "S", "CI", "df", "rowid_dedup", non_focal), verbose = FALSE) # nolint
+  # remove redundant columns
+  params <- datawizard::data_remove(params, c(remove_column, "Statistic", "s.value", "S", "CI", "df", "rowid_dedup", non_focal), verbose = FALSE) # nolint
   params <- datawizard::data_restoretype(params, model_data)
 
   # Store info

From d59e6a0dfb31f6cd9d91336200aba52b97cb1e83 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 23:27:59 +0100
Subject: [PATCH 06/10] more

---
 R/get_marginalcontrasts.R | 56 +++++++++++++++++++++++++++++++++++++++
 R/get_marginalmeans.R     |  1 +
 man/get_marginalmeans.Rd  |  2 ++
 3 files changed, 59 insertions(+)

diff --git a/R/get_marginalcontrasts.R b/R/get_marginalcontrasts.R
index 1336b3d5..a5169b78 100644
--- a/R/get_marginalcontrasts.R
+++ b/R/get_marginalcontrasts.R
@@ -9,6 +9,7 @@ get_marginalcontrasts <- function(model,
                                   transform = "none",
                                   method = "pairwise",
                                   ci = 0.95,
+                                  p_adjust = "none",
                                   ...) {
   # check if available
   insight::check_if_installed("marginaleffects")
@@ -23,6 +24,8 @@ get_marginalcontrasts <- function(model,
     ...
   )
 
+  out <- .p_adjust(model, out, p_adjust, ...)
+
   attr(out, "contrast") <- contrast
   out
 }
@@ -30,3 +33,56 @@ get_marginalcontrasts <- function(model,
 #' @rdname get_marginalmeans
 #' @export
 model_marginalcontrasts <- get_marginalcontrasts
+
+
+# p-value adjustment -------------------
+
+.p_adjust <- function(model, params, p_adjust, ...) {
+  # extract information
+  datagrid <- attributes(params)$datagrid
+  focal <- attributes(params)$focal_terms
+  statistic <- insight::get_statistic(model)$Statistic
+  df <- insight::get_df(model)
+
+  # exit on NULL, or if no p-adjustment requested
+  if (is.null(p_adjust) || identical(p_adjust, "none")) {
+    return(params)
+  }
+
+  all_methods <- c(tolower(stats::p.adjust.methods), "tukey", "sidak")
+
+  # needed for rank adjustment
+  focal_terms <- datagrid[focal]
+  rank_adjust <- prod(vapply(focal_terms, insight::n_unique, numeric(1)))
+
+  # only proceed if valid argument-value
+  if (tolower(p_adjust) %in% all_methods) {
+    if (tolower(p_adjust) %in% tolower(stats::p.adjust.methods)) {
+      # base R adjustments
+      params[["p"]] <- stats::p.adjust(params[["p"]], method = p_adjust)
+    } else if (tolower(p_adjust) == "tukey") {
+      if (!is.null(statistic)) {
+        # tukey adjustment
+        params[["p"]] <- suppressWarnings(stats::ptukey(
+          sqrt(2) * abs(statistic),
+          rank_adjust,
+          df,
+          lower.tail = FALSE
+        ))
+        # for specific contrasts, ptukey might fail, and the tukey-adjustement
+        # could just be simple p-value calculation
+        if (all(is.na(params[["p"]]))) {
+          params[["p"]] <- 2 * stats::pt(abs(statistic), df = df, lower.tail = FALSE)
+        }
+      } else if (verbose) {
+        insight::format_alert("No test-statistic found. P-values were not adjusted.")
+      }
+    } else if (tolower(p_adjust) == "sidak") {
+      # sidak adjustment
+      params[["p"]] <- 1 - (1 - params[["p"]])^rank_adjust
+    }
+  } else if (verbose) {
+    insight::format_alert(paste0("`p_adjust` must be one of ", toString(all_methods)))
+  }
+  params
+}
diff --git a/R/get_marginalmeans.R b/R/get_marginalmeans.R
index 878c8ca8..37f6104f 100644
--- a/R/get_marginalmeans.R
+++ b/R/get_marginalmeans.R
@@ -102,6 +102,7 @@ get_marginalmeans <- function(model,
   attr(means, "at") <- my_args$by
   attr(means, "by") <- my_args$by
   attr(means, "focal_terms") <- at_specs$varname
+  attr(means, "datagrid") <- datagrid
   means
 }
 
diff --git a/man/get_marginalmeans.Rd b/man/get_marginalmeans.Rd
index fa12ea30..bc1d7396 100644
--- a/man/get_marginalmeans.Rd
+++ b/man/get_marginalmeans.Rd
@@ -16,6 +16,7 @@ get_marginalcontrasts(
   transform = "none",
   method = "pairwise",
   ci = 0.95,
+  p_adjust = "none",
   ...
 )
 
@@ -26,6 +27,7 @@ model_marginalcontrasts(
   transform = "none",
   method = "pairwise",
   ci = 0.95,
+  p_adjust = "none",
   ...
 )
 

From f8fda6133569cf9be9fb42c714e2205edd38ddc7 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 23:49:26 +0100
Subject: [PATCH 07/10] print

---
 R/estimate_contrasts.R    | 26 ++++++++++++++++++++------
 R/get_marginalcontrasts.R |  3 ---
 man/estimate_contrasts.Rd | 13 ++++++++++---
 man/get_marginalmeans.Rd  |  2 --
 4 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/R/estimate_contrasts.R b/R/estimate_contrasts.R
index 9408a634..aa25a58b 100644
--- a/R/estimate_contrasts.R
+++ b/R/estimate_contrasts.R
@@ -7,9 +7,14 @@
 #' @inheritParams estimate_means
 #' @inheritParams get_emcontrasts
 #' @param p_adjust The p-values adjustment method for frequentist multiple
-#'   comparisons. Can be one of `"holm"` (default), `"tukey"`, `"hochberg"`,
-#'   `"hommel"`, `"bonferroni"`, `"BH"`, `"BY"`, `"fdr"` or `"none"`. See the
-#'   p-value adjustment section in the `emmeans::test` documentation.
+#' comparisons.
+#' - For `backend = "emmeans"`, can be one of `"holm"` (default), `"tukey"`,
+#'   `"hochberg"`, `"hommel"`, `"bonferroni"`, `"BH"`, `"BY"`, `"fdr"` or
+#'   `"none"`. See the p-value adjustment section in the `emmeans::test`
+#'   documentation.
+#' - For `backend = "marginaleffects"`, can be one of `"holm"` (default),
+#'   `"hochberg"`, `"hommel"`, `"bonferroni"`, `"bh"`, `"by"`, `"fdr"`,
+#'   `"none"`, `"tukey"` or `"sidak"`.
 #'
 #' @inherit estimate_slopes details
 #'
@@ -103,7 +108,7 @@ estimate_contrasts <- function(model,
       ci = ci,
       ...
     )
-    out <- .format_marginaleffects_contrasts(model, estimated, ci, transform, p_adjust, ...)
+    out <- .format_marginaleffects_contrasts(model, estimated, p_adjust, method, ...)
     ## TODO: needs to be fixed
     info <- list(contrast = contrast, by = by)
   }
@@ -128,7 +133,6 @@ estimate_contrasts <- function(model,
   attr(out, "contrast") <- info$contrast
   attr(out, "p_adjust") <- p_adjust
 
-
   # Output
   class(out) <- c("estimate_contrasts", "see_estimate_contrasts", class(out))
   out
@@ -173,11 +177,21 @@ estimate_contrasts <- function(model,
 }
 
 
-.format_marginaleffects_contrasts <- function(model, estimated, ci, transform, p_adjust, ...) {
+.format_marginaleffects_contrasts <- function(model, estimated, p_adjust, method, ...) {
   groups <- attributes(estimated)$by
   contrast <- attributes(estimated)$contrast
+  focal_terms <- attributes(estimated)$focal_terms
+
+  estimated <- .p_adjust(model, estimated, p_adjust, ...)
 
+  valid_methods <- c(
+    "pairwise", "reference", "sequential", "meandev","meanotherdev",
+    "revpairwise", "revreference", "revsequential"
+  )
   ## TODO: split Parameter column into levels indicated in "contrast", and filter by "by"
+  if (!is.null(method) && is.character(method) && method %in% valid_methods) {
+
+  }
 
   estimated
 }
diff --git a/R/get_marginalcontrasts.R b/R/get_marginalcontrasts.R
index a5169b78..844fff51 100644
--- a/R/get_marginalcontrasts.R
+++ b/R/get_marginalcontrasts.R
@@ -9,7 +9,6 @@ get_marginalcontrasts <- function(model,
                                   transform = "none",
                                   method = "pairwise",
                                   ci = 0.95,
-                                  p_adjust = "none",
                                   ...) {
   # check if available
   insight::check_if_installed("marginaleffects")
@@ -24,8 +23,6 @@ get_marginalcontrasts <- function(model,
     ...
   )
 
-  out <- .p_adjust(model, out, p_adjust, ...)
-
   attr(out, "contrast") <- contrast
   out
 }
diff --git a/man/estimate_contrasts.Rd b/man/estimate_contrasts.Rd
index 7269373e..9361cdc8 100644
--- a/man/estimate_contrasts.Rd
+++ b/man/estimate_contrasts.Rd
@@ -39,9 +39,16 @@ probabilities.}
 \item{ci}{Confidence Interval (CI) level. Default to \code{0.95} (\verb{95\%}).}
 
 \item{p_adjust}{The p-values adjustment method for frequentist multiple
-comparisons. Can be one of \code{"holm"} (default), \code{"tukey"}, \code{"hochberg"},
-\code{"hommel"}, \code{"bonferroni"}, \code{"BH"}, \code{"BY"}, \code{"fdr"} or \code{"none"}. See the
-p-value adjustment section in the \code{emmeans::test} documentation.}
+comparisons.
+\itemize{
+\item For \code{backend = "emmeans"}, can be one of \code{"holm"} (default), \code{"tukey"},
+\code{"hochberg"}, \code{"hommel"}, \code{"bonferroni"}, \code{"BH"}, \code{"BY"}, \code{"fdr"} or
+\code{"none"}. See the p-value adjustment section in the \code{emmeans::test}
+documentation.
+\item For \code{backend = "marginaleffects"}, can be one of \code{"holm"} (default),
+\code{"hochberg"}, \code{"hommel"}, \code{"bonferroni"}, \code{"bh"}, \code{"by"}, \code{"fdr"},
+\code{"none"}, \code{"tukey"} or \code{"sidak"}.
+}}
 
 \item{method}{Contrast method. See same argument in \link[emmeans:contrast]{emmeans::contrast}.}
 
diff --git a/man/get_marginalmeans.Rd b/man/get_marginalmeans.Rd
index bc1d7396..fa12ea30 100644
--- a/man/get_marginalmeans.Rd
+++ b/man/get_marginalmeans.Rd
@@ -16,7 +16,6 @@ get_marginalcontrasts(
   transform = "none",
   method = "pairwise",
   ci = 0.95,
-  p_adjust = "none",
   ...
 )
 
@@ -27,7 +26,6 @@ model_marginalcontrasts(
   transform = "none",
   method = "pairwise",
   ci = 0.95,
-  p_adjust = "none",
   ...
 )
 

From e3ef3d16b7fc2f7b6983cb0fcee9f028fb8cf0af Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 23:55:29 +0100
Subject: [PATCH 08/10] fix

---
 R/get_marginalcontrasts.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_marginalcontrasts.R b/R/get_marginalcontrasts.R
index 844fff51..bc955b73 100644
--- a/R/get_marginalcontrasts.R
+++ b/R/get_marginalcontrasts.R
@@ -40,6 +40,7 @@ model_marginalcontrasts <- get_marginalcontrasts
   focal <- attributes(params)$focal_terms
   statistic <- insight::get_statistic(model)$Statistic
   df <- insight::get_df(model)
+  verbose <- isTRUE(list(...)$verbose)
 
   # exit on NULL, or if no p-adjustment requested
   if (is.null(p_adjust) || identical(p_adjust, "none")) {

From 0c54341c55ebe6166308553cc136070547905368 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 23:56:41 +0100
Subject: [PATCH 09/10] docs

---
 R/estimate_contrasts.R    | 11 +++--------
 man/estimate_contrasts.Rd | 13 +++----------
 2 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/R/estimate_contrasts.R b/R/estimate_contrasts.R
index aa25a58b..4d02a69d 100644
--- a/R/estimate_contrasts.R
+++ b/R/estimate_contrasts.R
@@ -7,14 +7,9 @@
 #' @inheritParams estimate_means
 #' @inheritParams get_emcontrasts
 #' @param p_adjust The p-values adjustment method for frequentist multiple
-#' comparisons.
-#' - For `backend = "emmeans"`, can be one of `"holm"` (default), `"tukey"`,
-#'   `"hochberg"`, `"hommel"`, `"bonferroni"`, `"BH"`, `"BY"`, `"fdr"` or
-#'   `"none"`. See the p-value adjustment section in the `emmeans::test`
-#'   documentation.
-#' - For `backend = "marginaleffects"`, can be one of `"holm"` (default),
-#'   `"hochberg"`, `"hommel"`, `"bonferroni"`, `"bh"`, `"by"`, `"fdr"`,
-#'   `"none"`, `"tukey"` or `"sidak"`.
+#' comparisons. Can be one of `"holm"` (default), `"tukey"`, `"hochberg"`,
+#' `"hommel"`, `"bonferroni"`, `"BH"`, `"BY"`, `"fdr"` or `"none"`. See the
+#' p-value adjustment section in the `emmeans::test` documentation.
 #'
 #' @inherit estimate_slopes details
 #'
diff --git a/man/estimate_contrasts.Rd b/man/estimate_contrasts.Rd
index 9361cdc8..7269373e 100644
--- a/man/estimate_contrasts.Rd
+++ b/man/estimate_contrasts.Rd
@@ -39,16 +39,9 @@ probabilities.}
 \item{ci}{Confidence Interval (CI) level. Default to \code{0.95} (\verb{95\%}).}
 
 \item{p_adjust}{The p-values adjustment method for frequentist multiple
-comparisons.
-\itemize{
-\item For \code{backend = "emmeans"}, can be one of \code{"holm"} (default), \code{"tukey"},
-\code{"hochberg"}, \code{"hommel"}, \code{"bonferroni"}, \code{"BH"}, \code{"BY"}, \code{"fdr"} or
-\code{"none"}. See the p-value adjustment section in the \code{emmeans::test}
-documentation.
-\item For \code{backend = "marginaleffects"}, can be one of \code{"holm"} (default),
-\code{"hochberg"}, \code{"hommel"}, \code{"bonferroni"}, \code{"bh"}, \code{"by"}, \code{"fdr"},
-\code{"none"}, \code{"tukey"} or \code{"sidak"}.
-}}
+comparisons. Can be one of \code{"holm"} (default), \code{"tukey"}, \code{"hochberg"},
+\code{"hommel"}, \code{"bonferroni"}, \code{"BH"}, \code{"BY"}, \code{"fdr"} or \code{"none"}. See the
+p-value adjustment section in the \code{emmeans::test} documentation.}
 
 \item{method}{Contrast method. See same argument in \link[emmeans:contrast]{emmeans::contrast}.}
 

From 9e9065f8207937a29f07d15f178d2b50be58b84c Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 16 Dec 2024 23:58:30 +0100
Subject: [PATCH 10/10] structure

---
 R/estimate_contrasts.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/estimate_contrasts.R b/R/estimate_contrasts.R
index 4d02a69d..c46f328b 100644
--- a/R/estimate_contrasts.R
+++ b/R/estimate_contrasts.R
@@ -172,6 +172,10 @@ estimate_contrasts <- function(model,
 }
 
 
+
+# Table formatting marginal effects -------------------------------------------
+
+
 .format_marginaleffects_contrasts <- function(model, estimated, p_adjust, method, ...) {
   groups <- attributes(estimated)$by
   contrast <- attributes(estimated)$contrast