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
>
>
>
>
> --
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