From 8f704ec5d6c05833b2981ddf25f3f04027de2fed Mon Sep 17 00:00:00 2001
From: nfrerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Date: Mon, 16 Dec 2024 18:45:33 +0100
Subject: [PATCH] Remove deprecated methods

---
 R/tabula-deprecated.R    | 56 ----------------------------------------
 man/tabula-deprecated.Rd | 11 --------
 2 files changed, 67 deletions(-)

diff --git a/R/tabula-deprecated.R b/R/tabula-deprecated.R
index 3efbf22f..745c16bf 100644
--- a/R/tabula-deprecated.R
+++ b/R/tabula-deprecated.R
@@ -4,59 +4,3 @@
 #' @name tabula-deprecated
 #' @keywords internal
 NULL
-
-#' @rdname tabula-deprecated
-#' @aliases test_diversity-method
-setGeneric(
-  name = "test_diversity",
-  def = function(object, ...) standardGeneric("test_diversity")
-)
-
-#' @export
-#' @rdname tabula-deprecated
-#' @aliases test_diversity,matrix-method
-setMethod(
-  f = "test_diversity",
-  signature = signature(object = "matrix"),
-  definition = function(object, adjust = "holm", ...) {
-    .Deprecated(new = "test_shannon()", old = "test_diversity()")
-
-    # Calculate the number of individuals
-    N <- rowSums(object)
-    # Calculate Shannon diversity
-    H <- apply(X = object, MARGIN = 1, FUN = index_shannon, ...)
-    # Calculate Shannon variance
-    V <- apply(X = object, MARGIN = 1, FUN = variance_shannon, ...)
-    # Get the names of the assemblages
-    row_names <- rownames(object)
-    if (length(row_names) != 0) {
-      row_names <- factor(row_names, levels = unique(row_names))
-    } else {
-      row_names <- factor(seq_len(nrow(object)))
-    }
-    # Compute t test
-    compare <- function(i, j) {
-      tt <- (H[i] - H[j]) / sqrt(V[i] + V[j])
-      df <- (V[i] + V[j])^2 / sum(V[c(i, j)]^2 / N[c(i, j)])
-      2 * (1 - stats::pt(q = abs(tt), df = df))
-    }
-    result <- stats::pairwise.table(
-      compare.levels = compare,
-      level.names = row_names,
-      p.adjust.method = adjust
-    )
-    return(result)
-  }
-)
-
-#' @export
-#' @rdname tabula-deprecated
-#' @aliases test_diversity,data.frame-method
-setMethod(
-  f = "test_diversity",
-  signature = signature(object = "data.frame"),
-  definition = function(object, adjust = "holm", ...) {
-    object <- data.matrix(object)
-    methods::callGeneric(object, adjust = adjust)
-  }
-)
diff --git a/man/tabula-deprecated.Rd b/man/tabula-deprecated.Rd
index 1a6a9d89..f2a78ba3 100644
--- a/man/tabula-deprecated.Rd
+++ b/man/tabula-deprecated.Rd
@@ -2,18 +2,7 @@
 % Please edit documentation in R/tabula-deprecated.R
 \name{tabula-deprecated}
 \alias{tabula-deprecated}
-\alias{test_diversity}
-\alias{test_diversity-method}
-\alias{test_diversity,matrix-method}
-\alias{test_diversity,data.frame-method}
 \title{Deprecated Functions in tabula}
-\usage{
-test_diversity(object, ...)
-
-\S4method{test_diversity}{matrix}(object, adjust = "holm", ...)
-
-\S4method{test_diversity}{data.frame}(object, adjust = "holm", ...)
-}
 \description{
 These functions still work but will be removed (defunct) in the next version.
 }