1.8.12 merge update

DESCRIPTION

@@ -7,8 +7,8 @@ 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: 1.8.11
-Date: 2024-10-25
+Version: 1.8.12
+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:
     R (>= 3.6.0),

NEWS.md

@@ -1,26 +1,11 @@
-dispRity v1.9 (2024-06-06)  *distant update*
+dispRity v1.8.12 (2024-11-12)  *distant update*
 =========================
 
-
-<!-- Blurb: 
- 
- * `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 ;).
- * Redesigned `dispRity.dtt` to be closely a 1 to 1 interface of `geiger::dtt` with default options.
- * 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!
-
- -->
-
 ### NEW FEATURES
  * Redesigned `multi.ace` to be more modular and handle both continuous and/or discrete characters. Changes include a **change in argument name** from `castor.options` to the generic `options.args` (the options can be provided the same way as before though); and a **change in default arguments** for `models` which can now be left missing (previously was `"ER"`) and applies `"ER"` and `"BM"` for respectively discrete and continuous characters by default.
  * New design when using distance matrices: `dist.helper` now allows to save distance matrices in the cache, saving a lot of RAM and speeding up calculations. You can use the helper using `dispRity(..., dist.helper = my_distance_function)` or `dispRity(..., dist.helper = my_distance_matrix)`.
- * *New dispRity, custom.subsets and chrono.subsets option*: these three functions can now use `dist.data = TRUE` to specify that the input data is a distance matrix (and handle it accordingly).
+ * *New `dispRity`, `custom.subsets` and `chrono.subsets` option*: these three functions can now use `dist.data = TRUE` to specify that the input data is a distance matrix (and handle it accordingly).
  * *New bootstrap options*: you can now use `boot.by` to specify whether bootstrap the rows (previous behaviour), the columns or both (for distance matrices).
-
- * Redesigned `dispRity.dtt` to be closely a 1 to 1 interface of `geiger::dtt` with default options.
-
  * *New utility function* `set.root.time` to add a root time to a tree (`"phylo"`), list of trees (`"multiPhylo"`) or `dispRity` object with trees.
  * *New utility function* `remove.dispRity` to cleanly remove specific parts of a `"dispRity"` object.
  * *New metric*: `count.neighbours` to count the number of neighbours for each elements within a certain radius (thanks to Rob MacDonald for the suggestion).

README.md

@@ -76,6 +76,7 @@ You can also find more information in the [`dispRity` manual](https://rawcdn.git
 
 ## Latest major patch highlights
 ### dispRity v1.8 (2023-12-11) *dispRity.multi*
+<!-- ### dispRity v1.9 (2024-11-@@@) *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).
@@ -84,6 +85,13 @@ You can also find more information in the [`dispRity` manual](https://rawcdn.git
  * 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! -->
+
 Previous patch notes and notes for the *next version* can be seen [here](https://github.com/TGuillerme/dispRity/blob/master/NEWS.md).
 
 Authors