From b8fc9e76e318f3b8fc238c2e3d7708ee5f191e68 Mon Sep 17 00:00:00 2001 From: Thomas Guillerme Date: Tue, 12 Nov 2024 14:51:04 +0000 Subject: [PATCH] 1.8.12 merge update --- DESCRIPTION | 4 ++-- NEWS.md | 19 ++----------------- README.md | 8 ++++++++ 3 files changed, 12 insertions(+), 19 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6f8ebe7a..412bc624 100755 --- a/DESCRIPTION +++ b/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 -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), diff --git a/NEWS.md b/NEWS.md index e2bbb26c..fb2de375 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,26 +1,11 @@ -dispRity v1.9 (2024-06-06) *distant update* +dispRity v1.8.12 (2024-11-12) *distant update* ========================= - - - ### 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). diff --git a/README.md b/README.md index 80d09eaf..d97ac54b 100755 --- a/README.md +++ b/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* + [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). + + Previous patch notes and notes for the *next version* can be seen [here](https://github.com/TGuillerme/dispRity/blob/master/NEWS.md). Authors