Update documentation and deprecation warnings in preparation for merg…

…e to main

CHANGELOG.md

@@ -1,21 +1,19 @@
-* 2023-08-03 v0.0.1.9002 (development update)
+* 2023-11-21 v0.1.0
 	* **BREAKING CHANGES**
-		* Completely re-writes `plot_read_depth()`. 
+		* **Completely re-writes `plot_read_depth()`.** 
 			* allows users to plot read depth with a variable on the X axis and
 			a colour parameter
 			* users can access the old function with `plt_read_depth()`
 			temporarily, but this will be removed before the next full release.
-		* `rank_abund()` is broken and is no longer exported. Please file a bug
-		report if you were using this function.
+		* **`rank_abund()` is broken and is no longer exported.** Please file a
+		bug report if you were using this function.
 	* exports `order_taxa()`, by request 
 	* makes `prop_tax_down()` slightly more efficient by checking up front if
 	there is nothing to do.
 	* deprecates `order_levs()` because it isn't used anywhere. Its intended
 	function is performed by `order_taxa()`.
 	* introduces visual and automatic testing of the new `plot_read_depth()`
 	function.
-
-* 2023-04-25 v0.0.1.9001 (development update)
 	* in `plot_tax_bar()` 
 		* the `legloc` argument is now passed directly to
 		`ggplot2::theme(legend.position)` and can take any value that can take.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: AfterSl1p
 Type: Package
 Title: Generate Summary Graphics and Basic Analysis of 16s Data
-Version: 0.0.1.9001
+Version: 0.1.0
 Author: J. C. Szamosi and Shahrokh Shekarriz
 Authors@R: c(person("JC", "Szamosi", email = "[email protected]",
                   role = c('aut','cre')), 

R/plot_read_depth.R

@@ -178,7 +178,7 @@ prd_clrs = function(sample_sum_df, cvar, clrs){
 #' @param physeq A phyloseq object
 #' @export
 plt_read_depth = function(physeq){
-    lifecycle::deprecate_soft('0.0.1.9002', 'plt_read_depth()',
+    lifecycle::deprecate_soft('0.1.0.', 'plt_read_depth()',
                               'plot_read_depth()',
                               details = paste("This is the old version of",
                                               "plot_read_depth(), and will be",

R/plot_tax_bar.R

@@ -45,7 +45,7 @@ plot_tax_bar = function(taxa_df,rank,colours = NULL,
 					 means = FALSE, r_ticks = FALSE, leglen = NULL){
    # Lifecycle Management
     if (yscale != 'lin'){
-        lifecycle::deprecate_warn('0.0.1', 'plot_tax_bar(yscale)',
+        lifecycle::deprecate_warn('0.1.0', 'plot_tax_bar(yscale)',
                         details = paste('The ability to set non-linear y-axis',
                                         'scaling will be removed soon.'))
     }

R/utils.R

@@ -21,7 +21,7 @@
 #' @param f2 The factor to use when re-ordering `f1`.
 #' @export
 order_levs = function(f1,...){
-    lifecycle::deprecate_warn('0.0.2', 'order_levs()')
+    lifecycle::deprecate_warn('0.1.0', 'order_levs()')
 
     # if (is.numeric(f2)){
     #     ord = order(...)