v1.3.7

mulTree 1.3.7 (2020-04-12)

MINOR IMPROVEMENTS

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

v1.3.1

• 2017/08/01 - 1.3.1
  • Minor changes (internal) and code coverage increased for SIDER release.
  • Added ask option to mulTree, whether to ask to overwrite files or not.
• 2017/06/12 - v1.3
  • Minor fix to clean.data to properly deal with data frames.

v1.3

• 2017/06/12 - v1.3
  • Minor fix to clean.data to properly deal with data frames.
• 2017/05/15 - v1.2.6
  • Removed caper dependencies.
  • Minor fixes to code internal documentation.
  • coda::gelman.diag in mulTree now only outputs a warning rather than a stop message
  • Allows R-structure's standrad multi-response model in as.mulTree (e.g. rand.terms = ~taxa + specimen + us(trait):observation).
• 2017/01/09 - v1.2.5
  • Added minor sanitising function to mulTree the formula now has to match the data set column names.
  • 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.
• 2016/08/10 - v1.2.4
  • Fixed a bug in the convergence test where the convergence was not ran on the VCV matrix.
  • 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.
  • Fixed bug with plot.mulTree that didn't allow to plot more than 5 parameters.
• 2016/07/06 - v1.2.3
  • External functions are now properly imported via the NAMESPACE.
  • New phylogenetic analysis markdown vignette!
• 2016/02/19 - v1.2.2
  • 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).
• 2016/01/25 - v1.2.1
  • 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

v1.2

• 2016/01/22 - v1.2
  • complete new architectural structure!
  • all the functions are now unit tested!
  • all manuals are now written in Roxygen2 format!
  • 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.

Version 1.1

New mulTree version 1.1

• mulTree can now be run in parallel!
• 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.
• plot.mulTree has several more graphical options (see ?plot.mulTree).

First released version [may contain minor bugs]

This is the first functional released version. The functions are tested and the examples provided work on both UNIX and Windows based machines. However, this version might contain minor bugs for other source data and/or typos in the function comments and manuals. Please report them.