Version 3.44 - CRAN Release (04-25-22)

Submitted and accepted to CRAN in April, 2022.

CRAN Release - paleotree v3.3.25

A new version with some small changes, in particular a change to how taxon labeling is done with timeSliceTree and many many spelling fixes, for use with an incoming R version that will require using inherits for checking object classes.

Here's the tarball:
paleotree_3.3.25.tar.gz

Here's the zipped Windows binary, from Win-Builder:
paleotree_3.3.25.zip

Enjoy, and happy holidays! 🎄 ☃️

PS: Yes, lol, I named the commit this release is attached to wrong...

paleotree v3.3.0 CRAN Release (06-04-19)

Here's the most recent CHANGELOG:

Version - 3.3.0 - 06-03-19

• Lots of style edits to doc and examples in many places.
• Released to CRAN!

Version - 3.2.8 - 06-02-19 (Not Released to CRAN)

• Fixed bug communicated by user Armin Elsler in October 2018 in cal3TimePaleoPhy where if dateTreatment = 'minMax' was used, the output trees would have tips at the same absolute time, as the generating time-tree used for cal3 inference was generated using the input fixed first and last dates as if they were FAD and LAD, with the upper age constraint treated as fixed LAD and time of observation for each tip. This has the effect of making 'minMax' treatment with cal3 nearly identical to using 'firstLast'. This is now fixed by creating a new new basic-time-scaled tree using the randomly generated set of point occurrence times within each iteration under 'minMax', such that the resulting tip dates are always different.
• Also fixed tests for variance in cal3 tree calculations that were not properly sorting time data before comparing it against the time-scaled tree.

Version - 3.2.4 - 05-30-19 (Not Released to CRAN)

• Noted that functions for processing MrBayes trees was not checking if names for NEXUS files included .nex or not - added a test for this, so that .nex would be added if it wasn't present
• Anat Shafir reported that paleotree's obtainDatedPosteriorTreesMrB was inappropriately using the prior probability, not the posterior probability, for finding the Maximum A Posterior tree (and thus was presumably returning the Maximum A Priori tree). This was fixed and the help was greatly clarified. For many paleotree users tip-dating with an empty matrix, however, the log-likelihood of the character data is always zero, and thus the posterior probability in those cases was always identical to the prior probability. Regardless, point estimates of topologies are always to be less preferred than looking at samples of trees from the posterior.

Version - 3.2.0 - 04-14-19 (Not Released to CRAN)
-Replaced all instances of is.binary.tree with ape::is.binary.phylo
-Updated all PBDB-dependent functions to use the current 2019 specifications of the v1.2 API for the PBDB
-Phylopic plotting functions refined, with more user control of the resulting plot.
-Numerous fixes to how making taxon trees are created.

Version - 3.1.9 - 02-15-19 (Not Released to CRAN)
-Updates to timePaleoPhy and cal3 documentation for dateTreatment argument, thanks to Armin Elsler for pointing out some inaccuracies in the text.
-Updated some (but not all) functions related to use of PBDB data to use the proper 1.2 API, and made sure usage was properly accounted for.
-Added functions for getting taxonomic data for clades, or for a specific list of taxa from the PBDB, which previously had existed in proto form in examples.
-Added a function for plotting a tree with phylopics from the PBDB - this function currently does not allow for a lot of flexibility and is a work in progress.

Version - 3.1.3 - 10-01-18
-Added function twoWayEcologyCluster for doing two-way R-mode & Q-mode cluster analyses of proportional abundance datasets from community ecology

CRAN Release v3.1.3

In particular, this release contains the new functions for character compatibility from Pete Wagner, a new function for plotting two-way cluster analyses of community ecology data, and some bug fixes related to functions for MrBayes-prep functions.

Here's the full CHANGELOG since the last version:

Version - 3.1.3 - 10-01-18
-Added function twoWayEcologyCluster for doing two-way R-mode & Q-mode cluster analyses of proportional abundance datasets from community ecology

Version - 3.1.1 - 07-05-18
-Fixed bug with createMrBayesTipDatingNexus to avoid 'morphNexus not found error' when a pre-existing NEXUS file is used but the morphological matrix doesn't need to be entirely reconstituted. Thanks to Struan Henderson for finding this bug.

Version - 3.1.0 - 07-02-18 (Released to CRAN)
-CRAN release
-Modified code checking for unique solutions in minCharChange on advice of Uwe Ligges, to avoid timing-out when tested on openBLAS systems

Version - 3.0.2 - 06-27-18 (Not Released to CRAN)
-Added new function nodeDates2branchLengths, so that node and tip ages can be used to obtain edge lengths, in absolute time, for undated trees, at suggestion of Struan Henderson
-Bumped version number, merged to master branch.

Version - 3.0.1 - 05-03-18 (Not Released to CRAN)
-Added Pete Wagner's functions relating to measuring character exhaustation, added Pete to the authors for paleotree.
-Added another cladogram (an MPT from a 13-taxon analysis) to SongZhangDicrano example dataset
-Added argument verboseWarnings to cal3 functions, modified previous 'warnings' (actually used function for messages) to warnings

CRAN Release v3.0.0 10-20-17

The version released to CRAN on October 20th, 2017. Here is the relevant changes since the last CRAN release (see CHANGELOG for a full CHANGELOG):

-Added additional checks so that helpful error messages are given if species names are accidentally left in as a column in timeList for bin_cal3TimePaleoPhy and bin_timePaleoPhy, thanks Victoria Arbour for this bug report
-Added informative error message if sliceTime is later in time than the lattest (most recent) tip (thanks Graeme Lloyd for reporting this)
-Merged two taxa due to an accidental taxon name mis-spelling in the kanto dataset
-Fixed a missing line in the example code for perCapitaRates
-Added argument 'yAxisLims' to multiDiv functions so that the y axis (richness) can be constrained by the user, thanks to Robin Beck for suggestion (01-23-17)
-Added examples of using simFossilRecord with randomly-sampled rate variation, thanks to Laura Soul for making me realize I'd already made this possible! (03-20-17)
-Small edit to createMrBayesConstraints documentation
-Added example of a two-way cluster analysis (sensu Miller 1988) to examples for kanto data, based on code provided by Max Christie (Thanks!)
-Added new function: createMrBayesTipCalibrations, which creates a block of MrBayes codes for calibrating tip ages in a tip-dating analysis
-Added function createMrBayesTipDatingNexus, which creates a full NEXUS script for doing tip-dating analyses in MrBayes.
-Added function obtainDatedPosteriorTreesMrB, which will get the dated trees from the posterior of a MrBayes analysis (or provide an otherwise difficult to obtain summary tree, appropriate for dated analyses).
-Added function treeContradiction, which gives the contradiction difference (CD) value between two topologies, as described in Bapst et al. in press (Syst Biol).
-Added function setRootAge which will add a $root.time element to a tree, given a set of ages for tip taxa, using the age for the youngest matching taxon name,
-Added function setRootAges for setting root ages for a set of many trees as a multiPhylo object,
-Tried changing changelog.txt to .md, then changed it back.
-So, it turns out that ACCTRAN in phangorn was never converted from Fitch algorithm to Sankoff, and thus it was inappropriate for ACCTRAN to be applied to trees with multifurcations. This now results in an error if attempted by a user. Many apologies!
-Added new dataset RaiaCopesRule, containing dated paleo-phylogenies for ammonite genera, ceratopsian species, and cervid species from Raia et al. 2015, along with ammonite trait data from same publication.
-Fixed error with missing ingroup constraint in createMrBayesTipDatingNexus reported by Melanie Hopkins, thanks!
-Released to CRAN as v3.0.0 after a long hiatus from new CRAN releases.