Aligning the original and mirrored versions of each specimen and calculating Procrustes distance

Once all specimens have been aligned together and the semilandmarks slid:

The coordinates should be saved in gpaspecimens_slid_coords

- pull out the original and mirrored coordinates for each specimen

the files are in this order:
 [1] "morton1103ply_flipped.nts"       "morton1103ply.nts"            
 [3] "morton1188ply_flipped.nts"       "morton1188ply.nts"            
 [5] "morton1192ply_flipped.nts"       "morton1192ply.nts"            
 [7] "morton1306ply_flipped.nts"       "morton1306ply.nts"            
 [9] "morton1306plyerror_flipped.nts"  "morton1306plyerror.nts"      
[11] "morton1306plyerror2_flipped.nts" "morton1306plyerror2.nts"      
[13] "morton1319ply_flipped.nts"       "morton1319ply.nts"            
[15] "morton1329ply_flipped.nts"       "morton1329ply.nts"            
[17] "morton1486ply_flipped.nts"       "morton1486ply.nts"            
[19] "morton1973ply_flipped.nts"       "morton1973ply.nts"            
[21] "morton25ply_flipped.nts"         "morton25ply.nts"              
[23] "morton413ply_flipped.nts"        "morton413ply.nts"            
[25] "morton422ply_flipped.nts"        "morton422ply.nts"            
[27] "morton432ply_flipped.nts"        "morton432ply.nts"            
[29] "morton434ply_flipped.nts"        "morton434ply.nts"            
[31] "morton451ply_flipped.nts"        "morton451ply.nts"            
[33] "morton51ply_flipped.nts"         "morton51ply.nts"              
[35] "morton547ply_flipped.nts"        "morton547ply.nts"            
[37] "morton631ply_flipped.nts"        "morton631ply.nts"            
[39] "morton645ply_flipped.nts"        "morton645ply.nts"            
[41] "morton646ply_flipped.nts"        "morton646ply.nts"            
[43] "morton762ply_flipped.nts"        "morton762ply.nts"            
[45] "morton772ply_flipped.nts"        "morton772ply.nts"            
[47] "morton778ply_flipped.nts"        "morton778ply.nts"            
[49] "morton787ply_flipped.nts"        "morton787ply.nts"            
[51] "morton808ply_flipped.nts"        "morton808ply.nts"            
[53] "morton901ply_flipped.nts"        "morton901ply.nts"            
[55] "morton902ply_flipped.nts"        "morton902ply.nts"            
[57] "morton913ply_flipped.nts"        "morton913ply.nts"            
[59] "morton913plyerror_flipped.nts"   "morton913plyerror.nts"        
[61] "morton913plyerror2_flipped.nts"  "morton913plyerror2.nts"      
[63] "morton915ply_flipped.nts"        "morton915ply.nts"


morton1103slid <- gpaspecimens_slid_coords[,,1:2]
morton1188slid <- gpaspecimens_slid_coords[,,3:4]
morton1192slid <- gpaspecimens_slid_coords[,,5:6]
morton1306slid <- gpaspecimens_slid_coords[,,7:8]
morton1306errorslid <- gpaspecimens_slid_coords[,,9:10]
morton1306error2slid <- gpaspecimens_slid_coords[,,11:12]
morton1319slid <- gpaspecimens_slid_coords[,,13:14]
morton1329slid <- gpaspecimens_slid_coords[,,15:16]
morton1486slid <- gpaspecimens_slid_coords[,,17:18]
morton1973slid <- gpaspecimens_slid_coords[,,19:20]
morton25slid <- gpaspecimens_slid_coords[,,21:22]
morton413slid <- gpaspecimens_slid_coords[,,23:24]
morton422slid <- gpaspecimens_slid_coords[,,25:26]
morton432slid <- gpaspecimens_slid_coords[,,27:28]
morton434slid <- gpaspecimens_slid_coords[,,29:30]
morton451slid <- gpaspecimens_slid_coords[,,31:32]
morton51slid <- gpaspecimens_slid_coords[,,33:34]
morton547slid <- gpaspecimens_slid_coords[,,35:36]
morton631slid <- gpaspecimens_slid_coords[,,37:38]
morton645slid <- gpaspecimens_slid_coords[,,39:40]

morton646slid <- gpaspecimens_slid_coords[,,41:42]

morton762slid <- gpaspecimens_slid_coords[,,43:44]

morton772slid <- gpaspecimens_slid_coords[,,45:46]

morton778slid <- gpaspecimens_slid_coords[,,47:48]

morton787slid <- gpaspecimens_slid_coords[,,49:50]

morton808slid <- gpaspecimens_slid_coords[,,51:52]

morton901slid <- gpaspecimens_slid_coords[,,53:54]

morton902slid <- gpaspecimens_slid_coords[,,55:56]

morton913slid <- gpaspecimens_slid_coords[,,57:58]
morton913errorslid <- gpaspecimens_slid_coords[,,59:60]

morton913error2slid <- gpaspecimens_slid_coords[,,61:62]
morton915slid <- gpaspecimens_slid_coords[,,63:64]


- Procrustes align each pair (do not slide the semi-landmarks, they are fixed now)

morton1103aligned <- gpagen(morton1103slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1188aligned <- gpagen(morton1188slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1192aligned <- gpagen(morton1192slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1306aligned <- gpagen(morton1306slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1306erroraligned <- gpagen(morton1306errorslid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1306error2aligned <- gpagen(morton1306error2slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1319aligned <- gpagen(morton1319slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1329aligned <- gpagen(morton1329slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1486aligned <- gpagen(morton1486slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton1973aligned <- gpagen(morton1973slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton25aligned <- gpagen(morton25slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton413aligned <- gpagen(morton413slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton422aligned <- gpagen(morton422slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton432aligned <- gpagen(morton432slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton434aligned <- gpagen(morton434slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton451aligned <- gpagen(morton451slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton51aligned <- gpagen(morton51slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton547aligned <- gpagen(morton547slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton631aligned <- gpagen(morton631slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton645aligned <- gpagen(morton645slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton646aligned <- gpagen(morton646slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton762aligned <- gpagen(morton762slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton772aligned <- gpagen(morton772slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton778aligned <- gpagen(morton778slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton787aligned <- gpagen(morton787slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton808aligned <- gpagen(morton808slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton901aligned <- gpagen(morton901slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton902aligned <- gpagen(morton902slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton913aligned <- gpagen(morton913slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton913erroraligned <- gpagen(morton913errorslid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton913error2aligned <- gpagen(morton913error2slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)
morton915aligned <- gpagen(morton915slid, Proj = TRUE,PrinAxes = TRUE, ShowPlot = TRUE)

- pull out the coordinates into a separate variable

morton1103alignedproc <- morton1103aligned$coords
morton1188alignedproc <- morton1188aligned$coords
morton1192alignedproc <- morton1192aligned$coords
morton1306alignedproc <- morton1306aligned$coords
morton1306erroralignedproc <- morton1306erroraligned$coords
morton1306error2alignedproc <- morton1306error2aligned$coords
morton1319alignedproc <- morton1319aligned$coords
morton1329alignedproc <- morton1329aligned$coords
morton1486alignedproc <- morton1486aligned$coords
morton1973alignedproc <- morton1973aligned$coords
morton25alignedproc <- morton25aligned$coords
morton413alignedproc <- morton413aligned$coords
morton422alignedproc <- morton422aligned$coords
morton432alignedproc <- morton432aligned$coords
morton434alignedproc <- morton434aligned$coords
morton451alignedproc <- morton451aligned$coords
morton51alignedproc <- morton51aligned$coords
morton547alignedproc <- morton547aligned$coords
morton631alignedproc <- morton631aligned$coords
morton645alignedproc <- morton645aligned$coords
morton646alignedproc <- morton646aligned$coords
morton762alignedproc <- morton762aligned$coords
morton772alignedproc <- morton772aligned$coords
morton778alignedproc <- morton778aligned$coords
morton787alignedproc <- morton787aligned$coords
morton808alignedproc <- morton808aligned$coords
morton901alignedproc <- morton901aligned$coords
morton902alignedproc <- morton902aligned$coords
morton913alignedproc <- morton913aligned$coords
morton913erroralignedproc <- morton913erroraligned$coords
morton913error2alignedproc <- morton913error2aligned$coords
morton915alignedproc <- morton915aligned$coords

-calculate the Procrustes Distance (Overall asymmetry value)


ProcDistAll <- rep(NA,28)

ProcDistAll[[1]] <- sqrt(sum((morton1103alignedproc[,,1]-morton1103alignedproc[,,2])^2))
ProcDistAll[[2]] <- sqrt(sum((morton1188alignedproc[,,1]-morton1188alignedproc[,,2])^2))
ProcDistAll[[3]] <- sqrt(sum((morton1192alignedproc[,,1]-morton1192alignedproc[,,2])^2))
ProcDistAll[[4]] <- sqrt(sum((morton1306alignedproc[,,1]-morton1306alignedproc[,,2])^2))
ProcDistAll[[5]] <- sqrt(sum((morton1319alignedproc[,,1]-morton1319alignedproc[,,2])^2))
ProcDistAll[[6]] <- sqrt(sum((morton1329alignedproc[,,1]-morton1329alignedproc[,,2])^2))
ProcDistAll[[7]] <- sqrt(sum((morton1486alignedproc[,,1]-morton1486alignedproc[,,2])^2))
ProcDistAll[[8]] <- sqrt(sum((morton1973alignedproc[,,1]-morton1973alignedproc[,,2])^2))
ProcDistAll[[9]] <- sqrt(sum((morton25alignedproc[,,1]-morton25alignedproc[,,2])^2))
ProcDistAll[[10]] <- sqrt(sum((morton413alignedproc[,,1]-morton413alignedproc[,,2])^2))
ProcDistAll[[11]] <- sqrt(sum((morton422alignedproc[,,1]-morton422alignedproc[,,2])^2))
ProcDistAll[[12]] <- sqrt(sum((morton432alignedproc[,,1]-morton432alignedproc[,,2])^2))
ProcDistAll[[13]] <- sqrt(sum((morton434alignedproc[,,1]-morton434alignedproc[,,2])^2))
ProcDistAll[[14]] <- sqrt(sum((morton451alignedproc[,,1]-morton451alignedproc[,,2])^2))
ProcDistAll[[15]] <- sqrt(sum((morton51alignedproc[,,1]-morton51alignedproc[,,2])^2))
ProcDistAll[[16]] <- sqrt(sum((morton547alignedproc[,,1]-morton547alignedproc[,,2])^2))
ProcDistAll[[17]] <- sqrt(sum((morton631alignedproc[,,1]-morton631alignedproc[,,2])^2))
ProcDistAll[[18]] <- sqrt(sum((morton645alignedproc[,,1]-morton645alignedproc[,,2])^2))
ProcDistAll[[19]] <- sqrt(sum((morton646alignedproc[,,1]-morton646alignedproc[,,2])^2))
ProcDistAll[[20]] <- sqrt(sum((morton762alignedproc[,,1]-morton762alignedproc[,,2])^2))
ProcDistAll[[21]] <- sqrt(sum((morton772alignedproc[,,1]-morton772alignedproc[,,2])^2))
ProcDistAll[[22]] <- sqrt(sum((morton778alignedproc[,,1]-morton778alignedproc[,,2])^2))
ProcDistAll[[23]] <- sqrt(sum((morton787alignedproc[,,1]-morton787alignedproc[,,2])^2))
ProcDistAll[[24]] <- sqrt(sum((morton808alignedproc[,,1]-morton808alignedproc[,,2])^2))
ProcDistAll[[25]] <- sqrt(sum((morton901alignedproc[,,1]-morton901alignedproc[,,2])^2))
ProcDistAll[[26]] <- sqrt(sum((morton902alignedproc[,,1]-morton902alignedproc[,,2])^2))
ProcDistAll[[27]] <- sqrt(sum((morton913alignedproc[,,1]-morton913alignedproc[,,2])^2))
ProcDistAll[[28]] <- sqrt(sum((morton915alignedproc[,,1]-morton915alignedproc[,,2])^2))


ProcDist_males <- ProcDistAll[c(2, 4, 5, 7, 8, 10, 12, 13, 18, 20, 21, 24, 25, 28)]
ProcDist_females <- ProcDistAll[c(1, 3, 6, 9, 11, 14, 15, 16, 17, 19, 22, 23, 26, 27)]


**ignore the variables that have the word error in them, they were for a test of the landmark placement error that was an incorrect method and not used in the analysis**