diff --git a/DESCRIPTION b/DESCRIPTION index b7f1b44e..7f55da79 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Title: Measuring disparity in R Author: Thomas Guillerme Maintainer: Thomas Guillerme Version: 0.4.1 -Date: 2017-10-30 +Date: 2017-11-13 Description: A modular package for measuring disparity from multidimensional matrices. 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 basic statistical tests for disparity analysis. Depends: R (>= 3.0.0), diff --git a/README.md b/README.md index a8e69cdf..45738244 100644 --- a/README.md +++ b/README.md @@ -19,9 +19,10 @@ library(dispRity) The following installs the latest release of dispRity (see patch notes below). For the piping hot development version (not recommended), replace the `ref = "release"` option with `ref = "master"`. If you're using the `master` branch, see the [patch notes](https://github.com/TGuillerme/dispRity/blob/master/patch_notes.md) for the latest developments. -> Installation problems? Make sure you're using the latest R version (or at least `> 4.0`) and try again. +> Installation problems? Make sure you're using the latest R version (or at least `> 3.3.0`) and try again. -> To optimise your `dispRity` usage and speed, make sure you have the last version of `ape` installed (`4.1` - [download here](https://cran.r-project.org/web/packages/ape/index.html))! +> To optimise your `dispRity` usage and speed, make sure you have the last version of `ape` installed (`5.0` - [download here](https://cran.r-project.org/web/packages/ape/index.html))! +If you get a corruption error while updateding your packages, remove both (`remove.packages(c("ape", "dispRity"))`), quit and relaunch `R` and simply reinstall `dispRity` (`ape` should update automatically). #### Vignettes @@ -30,24 +31,15 @@ See the package manual online [here](https://rawgit.com/TGuillerme/dispRity/mast Additionally, you can learn more about the structure of `dispRity` objects [here](https://github.com/TGuillerme/dispRity/blob/master/disparity_object.md). ##### Patch notes -* 2017/08/21 - v0.4.0 *user friendly* - * Entirely rewritten manual (in GitBook)! - * **Removed** `hyper.volume` metric for dependencies reasons - * **Removed** `parallel` option from `boot.matrix` (the new architecture is already super fast: >2sec for 5k taxa and 10k bootstraps!) - * *New* function: `Claddis.ordination` and `geomorph.ordination` for automatically ordinating data from `Claddis` and `geomorph` packages! - * *New* function: `char.diff` for calculating character differences and associated plot function (`plot.char.diff`) - * *New* utility function: `merge.subsamples` for... merging subsamples! - * *New* utility function: `size.subsamples` for... getting the size of subsamples in a disparity object! - * *New* wrapping functions: `dispRity.through.time` and `dispRity.per.group` now runs easy default disparity analysis. - * Input ordinated matrices do not need to be of maximum size `n*(n-1)`. Bigger matrices now only trigger a warning. - * **Changed name**: `series` as a part of `dispRity` objects is now changed to `subsamples` throughout the whole package. - * **Changed name**: `time.series` is now renamed `time.subsamples`, if dates are provided and method is `discrete`, this function doesn't need a phylogeny any more. - * **Changed name**: `get.subsamples.dispRity` is now renamed `get.subsamples`. - * **Modified function**: `cust.series` is now renamed `custom.subsamples` (to avoid confusion with `custard.subsamples`!). Its `factor` argument as been changed to `groups` and can now take a simple list. - * Added `dimensions` optional argument to `dispRity` to overwrite the number of dimensions generated by `boot.matrix`. - * `variances`, `ranges` and `centroids` are now simplified for speed. The optional arguments for data cleaning are now passed to `make.metric`. - * `space.maker` now allows to approximate the dimensions variance distribution with the `scree` option. - +* 2017/11/13 - v0.4.1 + * Added a **Making stuff up!** chapter to the manual + * *New* disparity metric: `ancestral.distance` to get the distance from taxa/nodes to their ancestors. + * *New* function: `random.circle` for generating random circle coordinates (see example in `space.maker` for creating doughnut spaces!). + * *New* function: `get.bin.ages` for getting the geological timescale of a tree (based on `geoscale`). + * Added a `t0` argument to `time.subsamples` allowing to set the start age of the first subsample. + * Allowing subsamples to contain less than three elements (up to 0!). + * Fixed fuzzy match issues in `slice.tree`. + Previous patch notes and notes for the *next version* can be seen [here](https://github.com/TGuillerme/dispRity/blob/master/patch_notes.md). Authors diff --git a/patch_notes.md b/patch_notes.md index 23dee08a..ed4d26c0 100644 --- a/patch_notes.md +++ b/patch_notes.md @@ -1,7 +1,7 @@ Patch notes ---- -* 2017/10/30 - v0.4.1 +* 2017/11/13 - v0.4.1 * *New* disparity metric: `ancestral.distance` to get the distance from taxa/nodes to their ancestors. * *New* function: `random.circle` for generating random circle coordinates (see example in `space.maker` for creating doughnut spaces!). * *New* function: `get.bin.ages` for getting the geological timescale of a tree (based on `geoscale`).