From cc8570ca9ea7408f5558ea0b05ef61a755333bea Mon Sep 17 00:00:00 2001
From: Pierre Santagostini <pierre.santagostini@agrocampus-ouest.fr>
Date: Thu, 14 Dec 2023 17:54:09 +0100
Subject: [PATCH] Documentation: deprecated functions

---
 R/deprecated.R    | 25 ++++++++++++++++++++++---
 man/deprecated.Rd | 43 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 3 deletions(-)

diff --git a/R/deprecated.R b/R/deprecated.R
index f168c89..9893af4 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -4,9 +4,6 @@
 #' `r lifecycle::badge("deprecated")`
 #'
 #' Use [dmcd()] instead of `mvdcd()`.
-#' Use [rmcd()] instead of `mvrcd()`.
-#' Use [plotmcd()] instead of `plotmvcd()`.
-#' Use [contourmcd()] instead of `contourmvcd()`.
 #'
 #' @importFrom lifecycle deprecate_soft
 #' @export
@@ -19,12 +16,27 @@ mvdcd <- function(x, mu, Sigma, tol = 1e-6) {
   dmcd(x, mu, Sigma, tol)
 }
 
+#' @description
+#' Use [rmcd()] instead of `mvrcd()`.
+#'
+#' @importFrom lifecycle deprecate_soft
+#' @export
+#' @keywords internal
+#' @rdname deprecated
 mvrcd <- function(n, mu, Sigma, tol = 1e-6) {
   deprecate_soft("1.2.0", "mvrcd()", "rmcd()")
   
   rmcd(n, mu, Sigma, tol)
 }
 
+#' @description
+#' Use [plotmcd()] instead of `plotmvcd()`.
+#' Use [contourmcd()] instead of `contourmvcd()`.
+#'
+#' @importFrom lifecycle deprecate_soft
+#' @export
+#' @keywords internal
+#' @rdname deprecated
 plotmvcd <- function(mu, Sigma, xlim = c(mu[1] + c(-10, 10)*Sigma[1, 1]),
                      ylim = c(mu[2] + c(-10, 10)*Sigma[2, 2]), n = 101,
                      xvals = NULL, yvals = NULL, xlab = "x", ylab = "y",
@@ -35,6 +47,13 @@ plotmvcd <- function(mu, Sigma, xlim = c(mu[1] + c(-10, 10)*Sigma[1, 1]),
           col, tol, ...)
 }
 
+#' @description
+#' Use [contourmcd()] instead of `contourmvcd()`.
+#'
+#' @importFrom lifecycle deprecate_soft
+#' @export
+#' @keywords internal
+#' @rdname deprecated
 contourmvcd <- function(mu, Sigma, beta,
                          xlim = c(mu[1] + c(-10, 10)*Sigma[1, 1]),
                          ylim = c(mu[2] + c(-10, 10)*Sigma[2, 2]),
diff --git a/man/deprecated.Rd b/man/deprecated.Rd
index 47e469d..cca8332 100644
--- a/man/deprecated.Rd
+++ b/man/deprecated.Rd
@@ -3,16 +3,59 @@
 \name{deprecated}
 \alias{deprecated}
 \alias{mvdcd}
+\alias{mvrcd}
+\alias{plotmvcd}
+\alias{contourmvcd}
 \title{Deprecated functions}
 \usage{
 mvdcd(x, mu, Sigma, tol = 1e-06)
+
+mvrcd(n, mu, Sigma, tol = 1e-06)
+
+plotmvcd(
+  mu,
+  Sigma,
+  xlim = c(mu[1] + c(-10, 10) * Sigma[1, 1]),
+  ylim = c(mu[2] + c(-10, 10) * Sigma[2, 2]),
+  n = 101,
+  xvals = NULL,
+  yvals = NULL,
+  xlab = "x",
+  ylab = "y",
+  zlab = "f(x,y)",
+  col = "gray",
+  tol = 1e-06,
+  ...
+)
+
+contourmvcd(
+  mu,
+  Sigma,
+  beta,
+  xlim = c(mu[1] + c(-10, 10) * Sigma[1, 1]),
+  ylim = c(mu[2] + c(-10, 10) * Sigma[2, 2]),
+  zlim = NULL,
+  npt = 30,
+  nx = npt,
+  ny = npt,
+  main = "Multivariate generalised Gaussian density",
+  sub = NULL,
+  nlevels = 10,
+  levels = pretty(zlim, nlevels),
+  tol = 1e-06,
+  ...
+)
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
 Use \code{\link[=dmcd]{dmcd()}} instead of \code{mvdcd()}.
+
 Use \code{\link[=rmcd]{rmcd()}} instead of \code{mvrcd()}.
+
 Use \code{\link[=plotmcd]{plotmcd()}} instead of \code{plotmvcd()}.
+Use \code{\link[=contourmcd]{contourmcd()}} instead of \code{contourmvcd()}.
+
 Use \code{\link[=contourmcd]{contourmcd()}} instead of \code{contourmvcd()}.
 }
 \keyword{internal}
-- 
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