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Hannah van Noort

2018-Jun-16 20:37 UTC

[R] Problems running a PGLS model with phylogenetic uncertainty

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 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.

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]]))
}

Thank you in advance for any help, it's much appreciated!

Kind regards,

Hannah van Noort

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David Winsemius

2018-Jun-17 05:27 UTC

head link

[R] Problems running a PGLS model with phylogenetic uncertainty

> On Jun 16, 2018, at 1:37 PM, Hannah van Noort <hannahvnoort at
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"> ?corPagelNo 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 at 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

Hannah van Noort

2018-Jun-17 17:19 UTC

head link

[R] Problems running a PGLS model with phylogenetic uncertainty

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 at comcast.net>:
>
> > On Jun 16, 2018, at 1:37 PM, Hannah van Noort <hannahvnoort at
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 at 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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David Winsemius

2018-Jun-17 20:51 UTC

head link

[R] Problems running a PGLS model with phylogenetic uncertainty

> On Jun 16, 2018, at 10:27 PM, David Winsemius <dwinsemius at
comcast.net> wrote:
> 
> 
>> On Jun 16, 2018, at 1:37 PM, Hannah van Noort <hannahvnoort at
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.
I didn't notice on first reading that your said you had attached a file
about "phylogenetic
tree information." There was only one file in the material passed to Rhelp
readers and htat was the .txt data file. Files ending in anything other than
".txt", ".ps", ".pdf", or ".png" will
get scrubbed by hte mail-server that mediated rhelp communication. So you can
fool your mail-client into thinking that a file is plain text by adding a
'.txt' extension and communication will be improved.

Since drafting this I see that you sent another message to both me and Rhelp.
I'm the only one who will get the `.nex` and `.R` files. They were scrubbed
by the mailserver. I've looked at the .R file and wil now follow my own
advice and append a .txt extension  and attach to this email. The 190KB
output.nex file is also basically a text file and I'm applying the same
treatment:


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 > 
> 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 at 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
> 
> ______________________________________________
> R-help at 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

R help - Jun 2018 - Problems running a PGLS model with phylogenetic uncertainty

[R] Problems running a PGLS model with phylogenetic uncertainty

[R] Problems running a PGLS model with phylogenetic uncertainty

[R] Problems running a PGLS model with phylogenetic uncertainty

[R] Problems running a PGLS model with phylogenetic uncertainty