Wednesday, October 7, 2015

A few minor fixes & updates

I made a few minor updates to phytools in the past couple of days.

First, I fixed a bug in plotSimmap (and, consequently, in any function that uses plotSimmap internally, such as plotTree). The bug seems to result when the edges of the tree are neither in "cladewise" nor in "pruningwise" order, and I have fixed it by substituting the more standard "postorder" edge order (for post-order tree traversal) for ape's related "pruningwise" order. The fix can be seen here.

Second, I updated the phytools function which collapses a user-specified subtree to a star (unsurprisingly) so that it now accepts trees without edge lengths. Details of this update can be seen here.

Finally, third, and perhaps most amusingly, I corrected the spelling of "neighber" to "neighbor" in a message printed to report the number of nearest-neighbor-interchanges required to find the best tree in the phytools function for unweighted least-squares phylogeny inference from a distance matrix,

That's it.


  1. ¿Es necesario reinstalar de nuevo phytools? Lo descargue en septiembre en el workshop que impartiste en México. Saludos

    1. Se va a depender en cual tipo de análisis que estás haciendo, pero si todo esta trabajando corectamente, probablemente puedes esperar por la siguiente versión de CRAN. ¡Gracias!