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deprecated.R
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#' Deprecated function(s) in the MiscMetabar package
#'
#' These functions are provided for compatibility with older version of
#' the MiscMetabar package. They may eventually be completely
#' removed.
#' @rdname MiscMetabar-deprecated
#' @name MiscMetabar-deprecated
#' @param ... Parameters to be passed on to the modern version of the function
#' @return Depend on the functions.
#' @export physeq_graph_test adonis_phyloseq clean_physeq lulu_phyloseq otu_circle biplot_physeq read_phyloseq write_phyloseq sankey_phyloseq summary_plot_phyloseq plot_deseq2_phyloseq plot_edgeR_phyloseq venn_phyloseq ggVenn_phyloseq hill_tuckey_phyloseq hill_phyloseq
#' @aliases physeq_graph_test adonis_phyloseq clean_physeq lulu_phyloseq otu_circle biplot_physeq read_phyloseq write_phyloseq sankey_phyloseq summary_plot_phyloseq plot_deseq2_phyloseq plot_edgeR_phyloseq venn_phyloseq ggVenn_phyloseq hill_tuckey_phyloseq hill_phyloseq
#' @section Details:
#' \tabular{rl}{
#' [graph_test_pq] \tab now a synonym for `physeq_graph_test`\cr
#' [adonis_pq] \tab now a synonym for `adonis_phyloseq`\cr
#' [clean_pq] \tab now a synonym for `clean_physeq`\cr
#' [lulu_pq] \tab now a synonym for `lulu_phyloseq`\cr
#' [circle_pq] \tab now a synonym for `otu_circle`\cr
#' [biplot_pq] \tab now a synonym for `biplot_physeq`\cr
#' [read_pq] \tab now a synonym for `read_phyloseq`\cr
#' [write_pq] \tab now a synonym for `write_phyloseq`\cr
#' [sankey_pq] \tab now a synonym for `sankey_phyloseq`\cr
#' [summary_plot_pq] \tab now a synonym for `summary_plot_phyloseq`\cr
#' [plot_edgeR_pq] \tab now a synonym for `plot_edgeR_phyloseq`\cr
#' [plot_deseq2_pq] \tab now a synonym for `plot_deseq2_phyloseq`\cr
#' [venn_pq] \tab now a synonym for `venn_phyloseq`\cr
#' [ggvenn_pq] \tab now a synonym for `ggVenn_phyloseq`\cr
#' [hill_tuckey_pq] \tab now a synonym for `hill_tuckey_phyloseq`\cr
#' [hill_pq] \tab now a synonym for `hill_phyloseq`\cr
#' heat_tree_pq \tab now a synonym for `physeq_heat_tree`\cr
#' [compare_pairs_pq] \tab now a synonym for `multiple_share_bisamples`\cr
#' }
#'
physeq_graph_test <- function(...) {
.Deprecated("graph_test_pq", package = "MiscMetabar")
graph_test_pq(...)
}
adonis_phyloseq <- function(...) {
.Deprecated("adonis_pq", package = "MiscMetabar")
adonis_pq(...)
}
clean_physeq <- function(...) {
.Deprecated("clean_pq", package = "MiscMetabar")
clean_pq(...)
}
lulu_phyloseq <- function(...) {
.Deprecated("lulu_pq", package = "MiscMetabar")
lulu_pq(...)
}
otu_circle <- function(...) {
.Deprecated("circle_pq", package = "MiscMetabar")
circle_pq(...)
}
biplot_physeq <- function(...) {
.Deprecated("biplot_pq", package = "MiscMetabar")
biplot_pq(...)
}
read_phyloseq <- function(...) {
.Deprecated("read_pq", package = "MiscMetabar")
read_pq(...)
}
write_phyloseq <- function(...) {
.Deprecated("write_pq", package = "MiscMetabar")
write_pq(...)
}
sankey_phyloseq <- function(...) {
.Deprecated("sankey_pq", package = "MiscMetabar")
sankey_pq(...)
}
summary_plot_phyloseq <- function(...) {
.Deprecated("summary_plot_pq", package = "MiscMetabar")
summary_plot_pq(...)
}
plot_edgeR_phyloseq <- function(...) {
.Deprecated("plot_edgeR_pq", package = "MiscMetabar")
plot_edgeR_pq(...)
}
plot_deseq2_phyloseq <- function(...) {
.Deprecated("plot_deseq2_pq", package = "MiscMetabar")
plot_deseq2_pq(...)
}
venn_phyloseq <- function(...) {
.Deprecated("venn_pq", package = "MiscMetabar")
venn_pq(...)
}
ggVenn_phyloseq <- function(...) {
.Deprecated("ggvenn_pq", package = "MiscMetabar")
ggvenn_pq(...)
}
hill_tuckey_phyloseq <- function(...) {
.Deprecated("hill_tuckey_pq", package = "MiscMetabar")
hill_tuckey_pq(...)
}
hill_phyloseq <- function(...) {
.Deprecated("hill_pq", package = "MiscMetabar")
hill_pq(...)
}
# physeq_heat_tree <- function(...) {
# .Deprecated("heat_tree_pq", package = "MiscMetabar")
# heat_tree_pq(...)
# }
multiple_share_bisamples <- function(...) {
.Deprecated("compare_pairs_pq", package = "MiscMetabar")
compare_pairs_pq(...)
}
NULL