Re: [R] Problems running a PGLS model with phylogenetic uncertainty

2018-06-16 Thread David Winsemius
> On Jun 16, 2018, at 1:37 PM, Hannah van Noort wrote: > > Hi everyone, > > I'm having trouble running a PGLS model with the package "AICmodavg". Did you mean "AICmodavg"? > I > continuously get the error of false convergence with certain Lambda > values (even > when trying to run the model

[R] Problems running a PGLS model with phylogenetic uncertainty

2018-06-16 Thread Hannah van Noort
Hi everyone, I'm having trouble running a PGLS model with the package "AICmodavg". I continuously get the error of false convergence with certain Lambda values (even when trying to run the model with different Lambda values) and for other La mbda values I run into "error in eigen(val) : infinite o

Re: [R] specifying random effects covariance structure in nlme

2018-06-16 Thread Peter Dalgaard
I haven't played with this for a decade or so, but I believe you can do something with pdBlocked(). Possibly ask over on R-sig-ME as this quickly gets beyond the R-help level. (Also, you are aware that it is not about what you want to estimate, but whether you believe the correlations are nonze

Re: [R] mzR fails to install/compile (linuxes)

2018-06-16 Thread Martin Morgan
mzR is a Bioconductor package so you might have more luck contacting the maintainer on the Bioconductor support site https://support.bioconductor.org or on the 'bioc-devel' mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel or most directly by opening an issue on the maintainer

[R] specifying random effects covariance structure in nlme

2018-06-16 Thread Chris Stride
Hi I'm trying to fit a mixed effects exponential decay model, in which I have random effects for the initial value (init), the asymptote (asymp), and the rate (rate). The catch is that I'd also like to estimate the correlation between init and asymp, but not between init and rate, or asymp a

Re: [R] mzR fails to install/compile (linuxes)

2018-06-16 Thread Peter Dalgaard
This is almost certainly a Makefile error. Something (A) is relying on something (B) without stating the dependency explicitly in the Makefile. You can get away with that (sometimes) in a non-parallel make, because the sequence of compilations is such that B gets built before A. However, with a