Stratified analysis error at Uppass

[gtgus...@gmail.com]

Hi Nick and others,

My BioGeoBEARS DEC and DEC+J will initiate for a time stratified analysis and run for some time, before stopping when the stratified marginal ancestral state estimation begins. The error I am given is the In (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA,  :  unused control arguments ignored. However, when looking through the google group I found this error associated with earlier BioGeoBEARS when sourcing was still be done. I've gone through and verified I have removed all early versions of BioGeoBEARS and that I am operating with the most up-to-date versions of rexpokit, cladoRcpp, and BioGeoBEARS (see screen shot below). 

As this is a return to BioGeoBEARS for me I was running data that perviously worked (analyzed around 2017/2018) and when I compare the r.data files the ones produced following the error are almost exactly half the size of the older successful runs. So the analysis is indeed being cutoff. 

Thanks for any help you can provide. 

I am running Rstudio Version 2024.12.1+563 (2024.12.1+563) on a iMac 3.7 GHz 6-Core Intel Core i5 with Mac OS 15.3.2 (24D81).

Grey

[gtgus...@gmail.com]

Here are my files

[Nick Matzke]

Hi -- if all you've got is "In (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA,  :  unused control arguments ignored." -- this is a warning, not an error.  It can be ignored. 

It is something about one of the external optimiser functions (optimx I think; BioGeoBEARS can choose one of several optimizers, which all are from external R packages), I've never taken the time to figure it out as it seems to run fine on defaults.

Re: the .Rdata files, if you mean the files saved by BioGeoBEARS script, these contain no information saving all the steps in the search, so the length of the search will not change the size of the .Rdata file.  It's possible that some change from an old to new version of BioGeoBEARS might do so, or perhaps just an update of R; the "save" function that produces .Rdata files is from R base.

If the length of your search has changed, you can do a longer search if you want, e.g. by setting $use_optimx = "GenSA".  Usually this makes no difference, the vast amount of most searches is spent optimizing the last few decimal points of the parameters, having no physical significance. On rare occasions or complex models with many parameters, it might make sense to do.

Cheers,

Nick

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[gtgus...@gmail.com]

Nice! Yes, the analyses do appear to have run correctly. Good to know about the differences in the .Rdata files. 

Thanks for your help and time. 

I really appreciate it. 

Grey