[MORPHMET] physignal in geomorph

2015-06-11 Thread Anneke van Heteren
 

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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Re: [MORPHMET] physignal in geomorph

2015-06-11 Thread Emma Sherratt
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.


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Re: [MORPHMET] physignal in geomorph

2015-06-11 Thread Emma Sherratt
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.