Running examples in ‘geomorph-Ex.R’ failed
The error most likely occurred in:

> ### Name: morphol.disparity
> ### Title: Morphological disparity for one or more groups of specimens
> ### Aliases: morphol.disparity
> ### Keywords: analysis
> 
> ### ** Examples
> 
> data(plethodon)
> Y.gpa<-gpagen(plethodon$land, print.progress = FALSE)    #GPA-alignment
> gdf <- geomorph.data.frame(Y.gpa, species = plethodon$species, 
+ site = plethodon$site)
> 
> # Morphological disparity for entire data set
> morphol.disparity(coords ~ 1, groups = NULL, data = gdf, 
+ iter = 999, print.progress = FALSE)
No factor in formula or model terms from which to define groups.
Procrustes variance:
0.004923493 
[1] 0.004923493
> 
> # Morphological disparity for entire data set, accounting for allometry
> morphol.disparity(coords ~ Csize, groups= NULL, data = gdf, 
+ iter = 999, print.progress = FALSE)
No factor in formula or model terms from which to define groups.
Procrustes variance:
0.004663261 
[1] 0.004663261
> 
> # Morphological disparity without covariates, using overall mean
> morphol.disparity(coords ~ 1, groups= ~ species*site, data = gdf, 
+ iter = 999, print.progress = FALSE)

Call:
morphol.disparity(f1 = coords ~ 1, groups = ~species * site,  
    iter = 999, data = gdf, print.progress = FALSE) 



Randomized Residual Permutation Procedure Used
1000 Permutations

Procrustes variances for defined groups
  Jord.Allo   Jord.Symp  Teyah.Allo  Teyah.Symp 
0.003825239 0.005937274 0.003355766 0.006575694 


Pairwise absolute differences between variances
              Jord.Allo   Jord.Symp   Teyah.Allo  Teyah.Symp
Jord.Allo  0.0000000000 0.002112035 0.0004694738 0.002750455
Jord.Symp  0.0021120348 0.000000000 0.0025815087 0.000638420
Teyah.Allo 0.0004694738 0.002581509 0.0000000000 0.003219929
Teyah.Symp 0.0027504548 0.000638420 0.0032199286 0.000000000


P-Values
           Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
Jord.Allo      1.000     0.023      0.613      0.002
Jord.Symp      0.023     1.000      0.008      0.522
Teyah.Allo     0.613     0.008      1.000      0.001
Teyah.Symp     0.002     0.522      0.001      1.000


> 
> # Morphological partial disparities for overal mean
> morphol.disparity(coords ~ 1, groups= ~ species*site, partial = TRUE, 
+ data = gdf, iter = 999, print.progress = FALSE)

Call:
morphol.disparity(f1 = coords ~ 1, groups = ~species * site,  
    partial = TRUE, iter = 999, data = gdf, print.progress = FALSE) 



Randomized Residual Permutation Procedure Used
1000 Permutations

Procrustes variances for defined groups; partial variances (disparities) were calculated.
   Jord.Allo    Jord.Symp   Teyah.Allo   Teyah.Symp 
0.0009808306 0.0015223780 0.0008604527 0.0016860754 

Proportion of total disparity for each group:
 Jord.Allo  Jord.Symp Teyah.Allo Teyah.Symp 
 0.1942340  0.3014767  0.1703956  0.3338937 


Pairwise absolute differences between variances
              Jord.Allo    Jord.Symp   Teyah.Allo   Teyah.Symp
Jord.Allo  0.0000000000 0.0005415474 0.0001203779 0.0007052448
Jord.Symp  0.0005415474 0.0000000000 0.0006619253 0.0001636974
Teyah.Allo 0.0001203779 0.0006619253 0.0000000000 0.0008256227
Teyah.Symp 0.0007052448 0.0001636974 0.0008256227 0.0000000000


P-Values
           Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
Jord.Allo      1.000     0.023      0.613      0.002
Jord.Symp      0.023     1.000      0.008      0.522
Teyah.Allo     0.613     0.008      1.000      0.001
Teyah.Symp     0.002     0.522      0.001      1.000


> 
> # Morphological disparity without covariates, using group means
> morphol.disparity(coords ~ species*site, groups= ~species*site, 
+ data = gdf, iter = 999, print.progress = FALSE)

Call:
morphol.disparity(f1 = coords ~ species * site, groups = ~species *  
    site, iter = 999, data = gdf, print.progress = FALSE) 



Randomized Residual Permutation Procedure Used
1000 Permutations

Procrustes variances for defined groups
  Jord.Allo   Jord.Symp  Teyah.Allo  Teyah.Symp 
0.001933408 0.001790153 0.001732998 0.001785645 


Pairwise absolute differences between variances
              Jord.Allo    Jord.Symp   Teyah.Allo   Teyah.Symp
Jord.Allo  0.0000000000 1.432543e-04 2.004103e-04 1.477632e-04
Jord.Symp  0.0001432543 0.000000e+00 5.715598e-05 4.508825e-06
Teyah.Allo 0.0002004103 5.715598e-05 0.000000e+00 5.264716e-05
Teyah.Symp 0.0001477632 4.508825e-06 5.264716e-05 0.000000e+00


P-Values
           Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
Jord.Allo      1.000     0.684      0.538      0.676
Jord.Symp      0.684     1.000      0.872      0.989
Teyah.Allo     0.538     0.872      1.000      0.868
Teyah.Symp     0.676     0.989      0.868      1.000


> 
> # Morphological disparity of different groups than those 
> # described by the linear model
> morphol.disparity(coords ~ Csize + species*site, groups= ~ species, 
+ data = gdf, iter = 999, print.progress = FALSE)

Call:
morphol.disparity(f1 = coords ~ Csize + species * site, groups = ~species,  
    iter = 999, data = gdf, print.progress = FALSE) 



Randomized Residual Permutation Procedure Used
1000 Permutations

Procrustes variances for defined groups
       Jord       Teyah 
0.001847505 0.001590402 


Pairwise absolute differences between variances
              Jord        Teyah
Jord  0.0000000000 0.0002571036
Teyah 0.0002571036 0.0000000000


P-Values
       Jord Teyah
Jord  1.000 0.251
Teyah 0.251 1.000


> 
> # Extracting components
> MD <- morphol.disparity(coords ~ Csize + species*site, groups= ~ species, 
+ data = gdf, iter = 999, print.progress = FALSE)
> MD$Procrustes.var # just the Procrustes variances
       Jord       Teyah 
0.001847505 0.001590402 
> 
> 
> ### Morphol.disparity can be used with previously-defined 
> ### procD.lm or lm.rrpp class objects
> 
> data(plethspecies)
> Y.gpa<-gpagen(plethspecies$land)    #GPA-alignment

Performing GPA

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Making projections... Finished!
> gp.end<-factor(c(0,0,1,0,0,1,1,0,0))  #endangered species vs. rest
> names(gp.end)<-plethspecies$phy$tip
> 
> gdf <- geomorph.data.frame(Y.gpa, phy = plethspecies$phy, 
+ gp.end = gp.end)
Error in geomorph.data.frame(Y.gpa, phy = plethspecies$phy, gp.end = gp.end) : 
  Inputs have different numbers of observations
Execution halted