Friday, June 27, 2014

Updates to phylomorphospace3d & locate.yeti; new version of phytools

I just posted a new version of phytools. This can be downloaded from the phytools page & installed from source; however I have also submitted this version (phytools 0.4-20) to CRAN, so hopefully it will be accepted by the CRAN gatekeepers and spread out onto all the CRAN mirrors within a few days.

Some important updates in this version relative to the latest minor version include:

1. An update to locate.yeti to permit the use of a set of edge constraints to search for the ML position of the leaf to be added to the tree.

2. An update to phylomorphospace3d so that it now checks internally to see if the package rgl has been installed, and then loads it if available. This permits me to change phytools relationship with rgl from Depends to Suggests, which is designed to allow users to install & load phytools on systems where rgl cannot be installed.

This version of phytools also has a wide range of other new functions & updates relative to the last CRAN version, for instance:

1. A new version of contMap that permits some trait values for tip taxa to be missing from the dataset.

2. A new function, plotTree.wBars, that permits users to plot square or circular phylograms with bars instead of tip labels (e.g., 1, 2, 3).

3. A new function, setMap, to set the color-ramp for an object of class "contMap" or "densityMap"..

4. Some other useful updates to contMap and densityMap.

5. A new version of fancyTree that fixes a small bug for type = "scattergram".

6. The aforementioned new function (locate.yeti) for locating the position of a cryptic or recently extinct taxon on an ultrametric phylogeny using continuous character data.

7. An S3 generic method rep for objects of class "phylo" and "multiPhylo" (here).

8. A new option in phylomorphospace3d to color internal edges.

Finally, 9. New options for node placement in square phylograms plotted with plotSimmap and plotTree.

That's it!

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