From 51b8a8d81fee8565d31a29715493aacf992edcea Mon Sep 17 00:00:00 2001
From: Thomas Guillerme <guillert@tcd.ie>
Date: Tue, 12 Nov 2024 16:42:30 +0000
Subject: [PATCH] 1.9 update

---
 DESCRIPTION |  2 +-
 NEWS.md     |  2 +-
 README.md   | 14 +++-----------
 3 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 412bc624..216cb463 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,7 +7,7 @@ Authors@R: c(person("Thomas", "Guillerme", role = c("aut", "cre", "cph"),
   			 person("Jack", "Hatfield",    role = c("aut", "cph"))
   			 )
 Maintainer: Thomas Guillerme <guillert@tcd.ie>
-Version: 1.8.12
+Version: 1.9
 Date: 2024-11-12
 Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
 Depends:
diff --git a/NEWS.md b/NEWS.md
index fb2de375..fdb1e0df 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-dispRity v1.8.12 (2024-11-12)  *distant update*
+dispRity v1.9 (2024-11-12)  *distant update*
 =========================
 
 ### NEW FEATURES
diff --git a/README.md b/README.md
index d97ac54b..b1d9f252 100755
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@ Release:
 [![R-CMD-check](https://github.com/TGuillerme/dispRity/workflows/R-CMD-check/badge.svg)](https://github.com/TGuillerme/dispRity/actions)
 [![codecov](https://codecov.io/gh/TGuillerme/dispRity/branch/release/graph/badge.svg)](https://codecov.io/gh/TGuillerme/dispRity)
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![develVersion](https://img.shields.io/badge/devel%20version-1.8.0-green.svg?style=flat)](https://github.com/TGuillerme/dispRity)
+[![develVersion](https://img.shields.io/badge/devel%20version-1.9.0-green.svg?style=flat)](https://github.com/TGuillerme/dispRity)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1186467.svg)](https://doi.org/10.5281/zenodo.1186467)
 
 Development (master):
@@ -75,22 +75,14 @@ Check out this paper on selecting the best metric for your specific question in
 You can also find more information in the [`dispRity` manual](https://rawcdn.githack.com/TGuillerme/dispRity/c94452e6877fbb274eb0a4ff1363272a6297a9ee/inst/gitbook/_book/details-of-specific-functions.html#disparity-metrics).
 
 ## Latest major patch highlights
-### dispRity v1.8 (2023-12-11) *dispRity.multi*
-<!-- ### dispRity v1.9 (2024-11-@@@) *distance update* -->
+### dispRity v1.9 (2024-11-12) *distance update*
 [Read the full patch note here](https://github.com/TGuillerme/dispRity/blob/master/NEWS.md).
 
- * Added the _dispRity.multi_ internal architecture now allowing users to work with different matrices **and** different trees as inputs for `custom.subsets`, `chrono.subsets`, `boot.matrix` and `dispRity`. This change is not affecting the user level appart from now allowing to bypass some error messages (thanks to Mario Corio for that obvious suggestion).
- * *New* statistical test: `pgls.dispRity` to run PGLS test on a `dispRity` object with a level-2 metric and a tree (using excellent [`phylolm`](https://CRAN.R-project.org/package=phylolm) algorithm). The new test comes with its own S3 print, summary and plot functions if the input `dispRity` data contains multiple trees or multiple matrices (running and handling the output of multiple `phylolm`).
- * *New vignette* compiling resources for developers to help people (and future me) to edit the package. 
- * And many more new additions, improvements and couple of bug fixes!
- * **NOTE** there are now changes in the following function names: `ellipse.volume` is now `ellipsoid.volume`; `rescale.dispRity` is now `scale.dispRity` and `randtest.dist` is now `distance.randtest` (the old aliases still work).
-
-<!-- 
  * `dispRity` has been not greatly optimised for using distance matrices: 1) it's now much faster thanks to the `dist.helper` new optional argument (storing the distance matrix in the cache) and 2) it now allows direct analyses of distance matrices in a dispRity pipeline.
  * `boot.matrix` function has now been generalised to be able to bootstrap any elements of a matrix. Previously it only allowed to bootstrap elements (rows) but now can work on dimensions (columns) or both (distances).
  * Redesigned `multi.ace` to be more modular and better handle both continuous and/or discrete characters. This is secretly a pre-release for a future version that will greatly improve pipelines with ancestral state estimations ;).
  * New utility functions (`set.root.time` to add root times to trees; `remove.dispRity` to cleanly remove parts of dispRity objects) and metrics (`count.neigbhours`).
- * Loads of minor improvements and couple of bug fixes! Yay! -->
+ * Loads of minor improvements and couple of bug fixes! Yay!
 
 Previous patch notes and notes for the *next version* can be seen [here](https://github.com/TGuillerme/dispRity/blob/master/NEWS.md).