Re: [R-sig-phylo] ape chronos function returning pLL of -1E100

S Denton Sent: Wednesday, December 12, 2018 1:20:20 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] ape chronos function returning pLL of -1E100 I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with branch lengths derived from a RAxML analysis. I'm using 4

Re: [R-sig-phylo] ape chronos function returning pLL of -1E100

nodes with conflicting ages, and R does not give errors about the formatting of the calibration table. ~John From: R-sig-phylo on behalf of John S Denton Sent: Wednesday, December 12, 2018 1:20:20 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] ape

[R-sig-phylo] ape chronos function returning pLL of -1E100

I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with branch lengths derived from a RAxML analysis. I'm using 4 outgroup calibrations. When I run the analysis using t.og <- chronos(tree, lambda = 1, model = "relaxed", quiet = FALSE, calibration = dd.out) I

Re: [R-sig-phylo] ape chronos error

Following Riana's query, it appeared that the tree she used had no branch lengths. chronos() now check for the presence of branch lengths and returns an explicit error message. Best, Emmanuel Le 16/12/2016 à 18:20, Emmanuel Paradis a écrit : Hi Riana, It's difficult to answer your

Re: [R-sig-phylo] ape chronos error

Hi Riana, It's difficult to answer your question. Can you send some sample data to reproduce this error? Best, Emmanuel Le 15/12/2016 à 22:58, Riana Rishad Minocher a écrit : Hi, I’m writing with an issue using the chronos function in ape: I have a rooted supertree of 186 taxa (genetic &

[R-sig-phylo] ape chronos error

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

Re: [R-sig-phylo] ape: chronos

Hi Daniel, Thank you for your report. It's not very clear how or why the penalized likelihood becomes NA (maybe a log of a negative number is calculated somewhere). chronos() is still under progress and I take good note of your fix. Best, Emmanuel Le 05/09/2016 à 10:27, Daniel Lang a

[R-sig-phylo] ape: chronos

Hi, I hope I did not overlook ape's bug tracker - which would be the most appropriate place to post the following: I ran into this error while dating a tree using apes' chronos function (discrete model): Error in if (new.ploglik - current.ploglik > 1e-06 && i <= dual.iter.max) { : missing