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
To unsubscribe from this group and stop receiving emails from it, send an
email to morphmet+unsubscr...@morphometrics.org.
--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
To unsubscribe from this group and stop receiving emails from it, send an email
to morphmet+unsubscr...@morphometrics.org.
