Update data and test

NEWS.md

@@ -16,16 +16,8 @@ dispRity v1.9 (2024-06-06)  *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)`.
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- * *New bootstrap options*
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- * Redesigned `dispRity` and associated functions to now work on distance matrices while keeping the distance matrix properties (using `keep.distance = TRUE` as a default option - toggle back to `FALSE` to use previous behaviour).
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+ * *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.
 

TODO.md

@@ -5,7 +5,7 @@
  - [ ] run test
  - [ ] compile function index
  - [ ] run CRAN check
- - [ ] RECOMPILE ALL INTERNAL DATASETS
+ - [x] RECOMPILE ALL INTERNAL DATASETS
 
 ## bootstrapping dimensions
 
@@ -51,12 +51,17 @@
 
 ## Vignettes and manual
 
- - [ ] make a MCMCglmm related standalone vignette
- - [ ] make a morpho disparity (Claddis) standalone vignette
+ - [ ] add a summary of specific methods.
+ - [ ] make a dispRity.multi vignette
  - [ ] make a dist.help section in the manual
  - [ ] update the bootstrap section in the manual with the dimensions
  - [x] add `count.neigbhours` to the metrics section (*New metric*: `count.neighbours` to count the number of neighbours for each elements within a certain radius (thanks to Rob MacDonald for the suggestion).)
 
+ - [ ] make a MCMCglmm related standalone vignette
+ - [ ] make a morpho disparity (Claddis) standalone vignette
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 ## Minor improvements:
   * Make roundness work for non-VCV matrices (specify the axis function, e.g. variances or quantiles).
   - [ ] TODO