NEWS.md

In TGuillerme/mulTree: Performs MCMCglmm on Multiple Phylogenetic Trees

mulTree 1.3.7 (2020-04-12)

MINOR IMPROVEMENTS

• Updated package to R version 3.6.3
• Updated package to ape version 5.3

mulTree 1.3.6 (2019-05-08)

MINOR IMPROVEMENTS

• Updated package to R version 3.6.0

mulTree 1.3.5 (2019-03-04)

MINOR IMPROVEMENTS

• read.mulTree can now read more than 9 chains (following Hugo Gruson's contribution)

mulTree 1.3.4 (2018-08-08)

NEW FEATURES

• Increased test coverage for all functions.

MINOR IMPROVEMENTS

• Improved optional arguments handling for mulTree (following Eldar Rakhimberdiev's contribution)
• Fixed typos in the manual

mulTree 1.3.3 (2018-03-14)

MINOR IMPROVEMENTS

• Converted patch_notes.md into NEWS.md (with the correct standard format).

BUG FIXES

• Minor bug fix: the trees in data(lifespan) are now all ultrametric.

mulTree 1.3.2 (2017/10/19)

NEW FEATURES

• Complex formula management in mulTree and as.mulTree.

MINOR IMPROVEMENTS

• Added ask option to mulTree, whether to ask to overwrite files or not.
• Minor changes (internal) and code coverage increased for SIDER release.

mulTree 1.3.0 (2017-06-12)

BUG FIXES

• Minor fix to clean.data to properly deal with data frames.

mulTree 1.2.6 (2017/05/15)

NEW FEATURES

• Allows R-structure's standrad multi-response model in as.mulTree (e.g. rand.terms = ~taxa + specimen + us(trait):observation).

MINOR IMPROVEMENTS

• Removed caper dependencies.
• coda::gelman.diag in mulTree now only outputs a warning rather than a stop messag

BUG FIXES

• Minor fixes to code internal documentation.

mulTree 1.2.5 (2017/01/09)

MINOR IMPROVEMENTS

• Added minor sanitising function to mulTree the formula now has to match the data set column names.

BUG FIXES

• Fixed a bug with the parallel option in mulTree: only one cluster is now generated at the start of the function rather than one at each iteration.
• Fixed a minor bug with as.mulTree: the random terms formula's environment is not anymore exported by the function when set up by default.

mulTree 1.2.4 (2016/08/10)

MINOR IMPROVEMENTS

• Models memory management is now safer and is done only out of R environment leading to minor speed improvements in mulTree function.
• Some errors are now more verbose in mulTree and summary.mulTree.

BUG FIXES

• Fixed a bug in the convergence test where the convergence was not ran on the VCV matrix.
• Fixed bug with plot.mulTree that didn't allow to plot more than 5 parameters.

mulTree 1.2.3 (2016/07/06)

NEW FEATURES

• New phylogenetic analysis markdown vignette!

MINOR IMPROVEMENTS

• External functions are now properly imported via the NAMESPACE.

mulTree 1.2.2 (2016/02/19)

BUG FIXES

• major bug fix in mulTree where models saved out of R environment where accumulating data from former models (now fixed: each model saved out of the R environment contains only data for the target model).

mulTree 1.2.1 (2016/01/25)

BUG FIXES

• minor bug fix in summary.mulTree that can now deal with multiple hdr for each probabilities.
• minor bug fix in plot.mulTree with the number of terms used

mulTree 1.2.0 (2016/01/21)

NEW FEATURES

• complete new architectural structure!
• all the functions are now unit tested!
• all manuals are now written in Roxygen2 format!

DEPRECATED AND DEFUNCT

• many functions arguments names have been modified, please check individual functions manual.
• rTreeBind is renamed to tree.bind.
• In as.mulTree, the argument species is now taxa.
• mulTree output: when output chain name already exists in current directory, the function now asks if user wants to overwrite the existing files.
• In read.mulTree, the argument mulTree.mcmc is now mulTree.chain.
• In summary.mulTree, the argument mulTree.mcmc is now mulTree.results and the argument CI is now prob.
• summary.mulTree now outputs a c("matrix", "mulTree") class object.
• In plot.mulTree, the argument mulTree.mcmc must now be an object returned from summary.mulTree.

mulTree 1.1.2 (2015/11/05)

MINOR IMPROVMENTS

• added the extract option to read.mulTree to extract specific elements of each models.
• minor update on as.mulTree: can now intake single phylo objects.

BUG FIXES

• fixed bug with clean.data function

mulTree 1.1.1 (2015/10/02)

NEW FEATURES

• summary.mulTree and plot.mulTree have now an option whether to use hdrcde::hdr or not.

mulTree 1.1.0 (2015/08/17)

NEW FEATURES

• mulTree can now be run in parallel!

mulTree 1.0.6 (2015/07/25)

NEW FEATURES

• plot.mulTree has several more graphical options (see ?plot.mulTree).

mulTree 1.0.5 (2015/07/08)

BUG FIXES

• clean.data now properly cleans data.frames with multiple specimens entries.

mulTree 1.0.4 (2015/07/01)

MINOR IMPROVEMENTS

• improved formula management for as.mulTree and mulTree.

mulTree 1.0.3 (2015/06/03)

MINOR IMPROVEMENTS

• as.mulTree now deals properly with same taxa entries.
• updated examples for as.mulTree and mulTree on how to use specimen as a random term.

mulTree 1.0.2 (2015/05/17)

BUG FIXES

• Fixed bug in as.mulTree function with the random terms management.

mulTree 1.0.1 (2014/12/19)

NEW FEATURES

• NEW: clean.data function allows to match data and multiple trees and drop the non-shared taxa.
• as.mulTree function now allows multiple specimens for any taxa and allows the user to fix the random terms to be passed to the mulTree function.

Version in bold have a release back-up.

TGuillerme/mulTree documentation built on Feb. 21, 2024, 9:18 a.m.