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

2018-12-12 Thread John S Denton
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 function returning pLL of -1E100

2018-12-12 Thread John S Denton
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] simulate a packed morphospace of landmark coordinates?

2019-06-19 Thread John S Denton
I'm trying to simulate different degrees of morphospace packing of geometric morphometric coordinates ("packing" defined, for the purposes of this exploration, as closely-abutting regions having minimal overlap with other species in the space), using a tree and an empirical input covariance