Tuesday, March 8, 2011

Significant updates: phylomorphospace()

I just made a few significant updates to my function to create the phylomorphospace() plots of Sidlauskas (2008). This new version can be downloaded from my R phylogenetics page (direct link to code here).

First, I removed the requirement that the user provide a matrix of the estimated states at internal nodes of the tree. Now, if this is left out the function will simply use the {ape} function ace() to estimate these values using maximum likelihood.

Second, I liked the appearance of Luke's ecomorph plot a lot, so I decided to make a slightly modified version of this design the default for the function. This means that internal nodes are small filled circles, and terminal nodes are larger filled circles (although I did not use the same size disparity as in Luke's plot - see below). In addition, plotting tip labels is now optional and can be turned off by setting label=FALSE.

Finally, third, I added some basic error checking to make the function less buggy.

Feedback welcome!

[Click on image for a higher quality version.]

3 comments:

  1. That first update was buggy, but I just fixed it (I hope).

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  2. Mauricio Torres-MejiaAugust 17, 2011 at 5:01 PM

    Hey Liam, I used your phylomorphospace function with the function world of the package maps to plot a phylogeny in the world map. Longitude and latitude were used as x and y variables. The location of the ancestral nodes maybe is not correct, but the map is useful to show the spatial distribution of tips. Thanks for making your function available!

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  3. Very cool. If you would like to share this (at any point), I would like to post it on the blog.

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