Hi, I’m writing with an issue using the chronos function in ape:
I have a rooted supertree of 186 taxa (genetic & linguistic data), and am trying to time-calibrate with a set of divergence dates (genetic & linguistic; available for about 1/3 of nodes). I’m using chronos and calling agemin and agemax from a table of dates: tree.dated <- chronos(tree, calibration = makeChronosCalib(tree, node=dat$node, age.min=dat$agemin, age.max=dat$agemax)) I have the following error: Setting initial dates... Fitting in progress... get a first set of estimates Error in nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) : gradient function must return a numeric vector of length 161 In addition: Warning message: In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) : NA/NaN function evaluation I have had a brief look at the chronos function, and cannot determine where the error is generated. The error message is slightly different if I alter the substitution model, and seems to trip up at a different point. I’m not sure if it begins in setting “ini.rate” as this appears to be where the error appears for model = “discrete”. I have tried updating ape, altering my set of dates to a few nodes, removing the date for the root, listing node numbers and ages rather than calling it from the table, and reading my tree with read.nexus and in parenthetic format in case the tree object was problematic. I’ve noticed that the vector length the gradient function must generate varies depending on the number of known node ages provided - but I can’t figure out much more than that. I was hoping someone had some suggestion on how I can deal with this error - essentially where the source of the error might be so I can adjust my input accordingly! Or, alternatively if anyone has a suggestion for different ways to time-calibrate the tree (other than chronos). Thank you! Best, Riana _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
