Question: Where has the R Ape 'chronogram' function gone (Non-Parametric Rate Smoothing)?
0
gravatar for BlastedBadger
2 days ago by
Thule
BlastedBadger50 wrote:

Hi,

I want to use several methods to estimate the age of nodes in a phylogeny. I plan on using Ape's chronos function that relies on a penalized likelihood method (Sanderson 2002), but I also would like to test the NPRS method (Non Parametric Rate Smoothing, Sanderson 1997). I read some tutorial where they say it's in the chronogram function, but I see no such function in Ape v4.1. Where is it? Was it removed?

ADD COMMENTlink modified 2 days ago • written 2 days ago by BlastedBadger50
2

This page may help: http://grokbase.com/t/r/r-sig-phylo/112as2y3m8/replacement-for-chronogram

ADD REPLYlink written 2 days ago by cpad01121.0k
1
gravatar for BlastedBadger
2 days ago by
Thule
BlastedBadger50 wrote:

From Ape's log, chronogram has indeed been deprecated.

CHANGES IN APE VERSION 2.5-2

DEPRECATED & DEFUNCT

o evolve.phylo() and plot.ancestral() have been removed.

o chronogram(), ratogram(), and NPRS.criterion() have been removed.

But as mentionned in this page (thanks @cpad0112), using the parameter lambda=0 in chronos is similar to applying the NPRS.

ADD COMMENTlink written 2 days ago by BlastedBadger50
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