Hi,

I'm using Geomorph to analyze a 3D landmark dataset. I'm having a number of 
issues both in subsetting my array and visualizing these data after 
Procrustes analysis. I'm working with a set of 28 specimens and 61 3D 
landmarks. Below is a sample of my .dta file from Landmark Editor.

####
trial.coords <- readland.nts('pseudoxy_project3.dta')

1 28L 183 0 Dim=3

C_infralineatus_AMNH165799
D_quadralineatus_AMNH153343
D_quadralineatus_AMNH153345
D_quadralineatus_AMNH160061
..........
-9.8451595e+000  -2.8541670e+000  -2.8408973e+000
-1.0106355e+001  -5.0837624e-001  -1.3406076e+000
-8.7275896e+000  -2.4869413e+000  -1.2266474e+000
-7.3323584e+000  -3.3111162e+000  -3.0307722e+000
..........

I then make classifiers for later grouping and subsetting based on species 
(please see below). I can neither subset the data or properly visualize the 
resulting PCA plot. I get can error regarding the class of my array 
dimnames.  Instead of a PCA plot of the designated axes organized by 
species, I get two 3D plots of PC1 (positive and negative loadings) with no 
labeling or legend. Below is some of my simple code. I'm new to Geomorph, 
so any help or advice would be greatly appreciated. If need be, I can send 
a reduced dataset to help with troubleshooting.

####
pseudoxy.gpa <- gpagen(trial.coords, ProcD = TRUE, Proj = TRUE, 
print.progress = TRUE) 

# PCA
categories.qpa <- strsplit(dimnames(pseudoxy.gpa$coords)[[3]], "_")  
# unlist into matrix format
classifiers.qpa <- matrix(unlist(categories.qpa), ncol=3, byrow=T) 
# add the specimen ID to the first column of the table 
classifiers.qpa <- cbind(dimnames(pseudoxy.gpa$coords)[[3]], 
classifiers.qpa) 
# rename the column headings
colnames(classifiers.qpa) <- c("FullID", "Genus", "Species", "ID")
# converts to data frame so can index using $
classifiers.qpa <- as.data.frame(classifiers.qpa)   

gp <- as.factor(paste(classifiers.qpa$Genus, classifiers.qpa$Species)) # 
create grouping variable
sub.gpa <- coords.subset(A = pseudoxy.gpa$coords, group = gp)
# I get the following error
Error in dimnames(specimens)[[3]] <- names : 'dimnames' must be a list 
#trying to coerce dimnames to a list does not help

pseudoxy.PCA <- plotTangentSpace(pseudoxy.gpa$coords, groups = gp, label = 
TRUE, legend = TRUE, axis1 = 1, axis2 = 2, warpgrids = TRUE)

# See attachment for confusing plot.

Thanks in advance,

Skip


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