Wednesday, August 8, 2012

Some fixes in the functions from yesterday

This morning I fixed some bugs a couple of the new functions to phytools that I posted about yesterday: specifically fancyTree(...,type="traitgram3d") and phylomorphospace3d. I also made one minor change to anc.ML, my function for ancestral character estimation using maximum likelihood.

The most important updates were all to the function fancyTree. First, there was a problem in the way that I was passing optional arguments to and within the function using ... (dot-dot-dot or three dots). If one has a set of optional arguments, and you just want to pass them directly to another function that is going to be call internally, then this can be done using ... as a stand-in for these arguments. For instance:

foo<-function(x,y,...) plot(x,y,...)

will pass the optional arguments in ... directly to plot (which is a generic function with many optional arguments).

In my case, though, I wanted to gather optional arguments depending on a method (to be called internally), work with the arguments, and then send them to another function. I accomplished this (I believe correctly) using hasArg and list(...). This basically works as follows:

  if(hasArg(X)) X<-list(...)$X # get phenotypic data if provided
  else stop("no phenotypic data provided")
  if(!hasArg(A)){ # if ancestral states not provided
    ... # estimate ancestral states
  } else A<-list(...)$A # otherwise get them
  ... # do some other stuff
  phylomorphospace3d(tree,X,A,control=control) # plot

This seems to work, although it was somewhat difficult to find out online if this is the current best practice for optional arguments. Maybe a reader of the blog knows better!

As evidenced by the pseudocode above, fancyTree(...,type="traitgram3d") now accepts user supplied ancestral character states for internal nodes. We might have these, for instance, by simulation.

Finally, I also made some minor updates to phylomorphopsace3d (changing how the tip spheres are scaled) and anc.ML (adjusting the bound for optim(...,method="L-BFGS-B").

In addition to uploading these new function versions to the phytools page, I have also built a new package version (v 0.1-87) which can be downloaded here.

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