Updated patch note for pre-release

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Measuring disparity in R
 Author: Thomas Guillerme <guillert@tcd.ie>
 Maintainer: Thomas Guillerme <guillert@tcd.ie>
 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),

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

patch_notes.md

@@ -1,7 +1,7 @@
 Patch notes
 ----
 <!-- * 2017/10/18 - v1.0 *got you covered*  -->
-* 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`).