Create an Average Coordinate Shape for a Set of Endocasts

To calculate the average coordinates of all of the endocasts:

Files you need:
gpaspecimens_slid_coords - from aligning all of the specimens' original and mirrored endocasts and sliding the semi-landmarks:
First separate out the coordinates that go to the original and flipped endocasts:

- if you look here you can see the order my endocasts are in for the gpaspecimens_slid_coords file, so I need to extract every even set of coordinates for the original endocasts and every odd set for the flipped.

-created a variable of odd numbers using seq(from #, to #, by #) so from 1 to 60, every 2:

x = seq(1,60,2)

y = seq(2,60,2)

because I had some duplicate endocasts for error testing I actually want:

x1 = seq(1,8,2)
x2 = seq(13,60,2)

y1 = seq(2,8,2)
y2 = seq(14,60,2)

Then I pull out the coordinates for the original and flipped endocasts:

gpaspecimens_slid_coords_original <- gpaspecimens_slid_coords[,,y]
gpaspecimens_slid_coords_flipped <- gpaspecimens_slid_coords[,,x]

or for me:
gpaspecimens_slid_coords_original <- gpaspecimens_slid_coords[,,c(y1,y2)]
gpaspecimens_slid_coords_flipped <- gpaspecimens_slid_coords[,,c(x1,x2)]

now you have 2 3D arrays with just the original and just the flipped coordinates after gpa alignment and semi-landmark sliding.

To create the average landmark coordinates for a set of specimens:

you will need the mshape() function from geomorph:

library(geomorph)
mean_original_shape <- mshape(gpaspecimens_slid_coords_original)
mean_flipped_shape <- mshape(gpaspecimens_slid_coords_flipped)


You can also find the specimen closest to the average shape:

using geomorph:

findMeanSpec(gpaspecimens_slid_coords)  - from all endocasts, both original and flipped
or
findMeanSpec(gpaspecimens_slid_coords_original) - just original
findMeanSpec(gpaspecimens_slid_coords_flipped) - just flipped

it will output the name of the specimen and the specimen number (where it appears in the array)