[R] Problems running a PGLS model with phylogenetic uncertainty

[Hannah van Noort]

Hi again,

My apologies for the incomplete script last time. Hereby the updated
dataset, phylogenetic tree information and R-script. This time the errors I
mentioned should pop up.
Once again thank you in advance for any help/tips.

Kind regards,

Hannah van Noort

2018-06-17 7:27 GMT+02:00 David Winsemius <dwinsemius using comcast.net>:

>
> > On Jun 16, 2018, at 1:37 PM, Hannah van Noort <hannahvnoort using gmail.com>
> 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 with different Lambda values) and for other
> La
> > mbda values I run into "error in eigen(val) : infinite or missing values
> in
> > 'X' ". I've tried several optimizers and removing some outlier values but
> > the same errors keep on popping up.. Does anyone know how to solve this
> > problem?
> > Below a part of my script with the specific dependent and independent
> varia
> > bles and I've also attached files with the relevant data and phylogenetic
> > tree information.
>
> d <- read.table("~/Seabirddat_growth.txt", head=TRUE)
> library(AICmodavg)
> Error in library(AICmodavg) : there is no package called ‘AICmodavg’
> library(AICcmodavg)
> >
> > Cand.models = list()
> > niter = 100
> > for (i in 1:niter) {
> >  Cand.models[[i]] = gls(Maxgrowthrate ~ log.Forrang+log.Weight_av),
>
> A syntax error is thrown here -------------------------------------^
> #removed paren
> > data =
> > d, method= "ML", na.action=na.omit
>
> And here ---------------------------^
> >                         correlation = corPagel(value=0.4, trees[[i]]))
>
> And after fixing these errors I get the error that `gls` is not found
> (even after adding `library(AICcmodavg)`
>
>  could not find function "gls"
> > ?corPagel
> No documentation for ‘corPagel’ in specified packages and libraries:
> you could try ‘??corPagel’
> > ??gls
> > library(nlme)
>
> Attaching package: ‘nlme’
>
> The following object is masked from ‘package:dplyr’:
>
>     collapse
>
> > Cand.models = list()
> > niter = 100
> > for (i in 1:niter) {
> +  Cand.models[[i]] = gls(Maxgrowthrate ~ log.Forrang+log.Weight_av, data =
> + d, method= "ML", na.action=na.omit,
> +                         correlation = corPagel(value=0.4, trees[[i]]) )
> + }
> Error in corPagel(value = 0.4, trees[[i]]) :
>   could not find function "corPagel"
> > ??corPagel
> > library(ape)
>
> Attaching package: ‘ape’
>
> The following object is masked from ‘package:Hmisc’:
>
>     zoom
>
> > Cand.models = list()
> > niter = 100
> > for (i in 1:niter) {
> +  Cand.models[[i]] = gls(Maxgrowthrate ~ log.Forrang+log.Weight_av, data =
> + d, method= "ML", na.action=na.omit,
> +                         correlation = corPagel(value=0.4, trees[[i]]) )
> + }
> Error in corPagel(value = 0.4, trees[[i]]) :
>   object "phy" is not of class "phylo"
>
>
>
> Perhaps you have yet another unnamed package with a corPagel that doesn't
> require a second argument of class "phylo"? I've reached "the end of my
> rope".
>
>
>
>
> > }
> >
> > Thank you in advance for any help, it's much appreciated!
>
> Please submit code that will run in a clean session. Close R. Do not save
> anything except your history. Delete or rename your `.Rdata` file and
> staart a fresh session. then include everything needed to get the behavior
> you are reporting.
>
> >
> > Kind regards,
> >
> > Hannah van Noort
> > <Seabirddat_growth.txt>______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
>

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