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 <dwinsem...@comcast.net>:
>
> > On Jun 16, 2018, at 1:37 PM, Hannah van Noort <hannahvno...@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@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
>
>
>
>
>
>
"Maxgrowthrate" "Forrang" "Weight_av"
Diomedea_exulans 0.6600 1500.0000 8.6500
Diomedea_epomophora 0.9200 1250.0000 9.0000
Thalassarche_chrysostoma 1.8400 250.0000 3.3250
Thalassarche_melanophrys 2.1700 470.0000 3.5700
Phoebetria_palpebatra 1.8400 1350.0000 2.9500
Macronectes_giganteus 1.7300 200.0000 4.5650
Fulmarus_glacialis 5.0800 500.0000 0.6150
Procellaria_aequinoctialis 1.8000 7000.0000 1.3350
Puffinus_tenuirostris 2.2400 50.0000 0.5850
Puffinus_puffinus 2.8600 450.0000 0.4200
Oceanites_oceanicus 8.0000 250.0000 0.0350
Oceanodroma_leucorhoa 3.5600 615.0000 0.0450
Phaethon_rubricauda 2.2400 200.0000 0.6700
Pelecanus_occidentalis 3.6000 20.0000 3.4500
Fregata_magnificens 0.9000 500.0000 1.4750
Morus_bassanus 3.0000 300.0000 3.0000
Sula_dactylatra 1.7000 50.0000 1.9900
Sula_leucogaster 2.0000 40.0000 1.3500
Sula_sula 1.7000 40.0000 1.1500
Phalacrocorax_carbo 3.6500 7.0000 2.7500
Phalacrocorax_aristotelis 3.1100 9.0000 1.7700
Larus_dominicanus 2.0000 10.0000 1.0250
Larus_occidentalis 2.5000 75.0000 1.1000
Larus_argentatus 3.2000 21.0000 1.1350
Rissa_tridactyla 5.0000 36.0000 0.4000
Sterna_bergii 3.0000 40.0000 0.3600
Sterna_sandvicensis 4.5000 20.0000 0.2200
Sterna_dougallii 6.4000 25.0000 0.1250
Sterna_hirundo 6.2000 15.2000 0.1350
Sterna_paradisaea 5.9000 20.0000 0.1180
Sterna_fuscata 2.2000 500.0000 0.2000
Anous_stolidus 3.6000 180.0000 0.1725
Anous_minutus 5.0000 10.0000 0.1210
Cepphus_columba 4.0000 7.0000 0.5000
Cepphus_grylle 2.9000 4.0000 0.4700
Uria_lomvia 1.0500 170.0000 1.1000
Alca_torda 3.1000 12.0000 0.7200
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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