However Anneke, the error that you first get is not our catch of the names
not matching, but is instead coming from somewhere within, but where I
cannot immediately tell. Perhaps send me the traceback.
Also note that name.check() only works with data in a 2d matrix and not a
3d array.
Emma
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Emma Sherratt, PhD.
Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L112 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au
Twitter: @DrEmSherratt
Caecilians are legless amphibians...
* __
(\ .-. .-. /_")
\\_//^\\_//^\\_//
`"` `"` `"`*
learn more about them here: www.emmasherratt.com/caecilians
On 11 June 2015 at 22:39, Emma Sherratt <emma.sherr...@gmail.com> wrote:
> Anneke,
>
> You are using match() incorrectly. See below:
>
> > library(geomorph)
> Loading required package: rgl
> > data(plethspecies)
> > Y.gpa<-gpagen(plethspecies$land)
> > physignal(plethspecies$phy,Y.gpa$coords,method="Kmult",iter=99)
> $phy.signal
> [,1]
> [1,] 0.9572538
>
> $pvalue
> [,1]
> [1,] 0.03
>
> > match(plethspecies$phy, Y.gpa$coords) # doesn't work
> [1] NA NA NA NA
> > match(plethspecies$phy$tip.label, dimnames(Y.gpa$coords)[[3]]) # works
> [1] 7 1 8 3 9 5 4 2 6
>
> By specifying $tip.label and dimnames() you will be able to see the
> problem with your dataset. It's likely to be a trailing space or _.
>
> Emma
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Emma Sherratt, PhD.
>
> Lecturer in Zoology,
> Zoology Division, School of Environmental and Rural Science,
> Room L112 Bldg C02,
> University of New England,
> Armidale, NSW, Australia, 2351
> Tel: +61 2 6773 5041
> email: emma.sherr...@une.edu.au
> Twitter: @DrEmSherratt
>
> Caecilians are legless amphibians...
>
> * __
> (\ .-. .-. /_")
> \\_//^\\_//^\\_//
> `"` `"` `"`*
>
> learn more about them here: www.emmasherratt.com/caecilians
>
>
>
>
> On 11 June 2015 at 18:29, Anneke van Heteren <a.h.vanhete...@gmail.com>
> wrote:
>
>> Dear friends and colleagues
>>
>>
>>
>> I am trying to run physignal in geomorph (R), but I am running into a
>> problem I do not understand. Here is the code I am using and the error
>> message:
>>
>> > physignal(ursid_phyl, Regr_res_av, iter=99)
>>
>> Error in match.names(clabs, names(xi)) :
>>
>> names do not match previous names
>>
>>
>>
>> However:
>>
>> > name.check(ursid_phyl,Regr_res_av)
>>
>> [1] "OK"
>>
>>
>>
>> But:
>>
>> > match(ursid_phyl,Regr_res_av)
>>
>> [1] NA NA NA NA
>>
>> > match(Regr_res_av,ursid_phyl)
>>
>> [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
>>
>> [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
>>
>>
>>
>> This suggested to me that physignal might need the columns to carry the
>> same names rather than the rows (as my phylogeny is list of 4 and I have 15
>> landmarks=45 variables), but when I transposed my data, I get a different
>> error message:
>>
>> > trans_regr_res_av <-t(Regr_res_av)
>>
>> > physignal(ursid_phyl, trans_regr_res_av, iter=99)
>>
>> Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) :
>>
>> Number of taxa in data matrix and tree are not not equal.
>>
>>
>>
>> I do not know what I could try next to calculate physignal. Any help
>> would be appreciated. This is the phylogeny that I am using:
>>
>>
>>
>> (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3);
>>
>>
>> Thanks in advance.
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Anneke van Heteren
>>
>>
>>
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>>
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>>
>
>
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