# Process object with raw data previously generated and saved in rda format (see vulpes21x29.raw.R)
# for the foxes ("Vulpes vulpes") specimens and perform Procrustes alignments with
# Morpho.
# 1. Convert to class matrix
V.mat <- as.matrix( vulpes21x29.raw[ , 2:dim( vulpes21x29.raw )[2] ] )
# 2. Add row names and save object to be used in examples in the package
row.names( V.mat ) <- vulpes21x29.raw[ , 1 ]
V.mat.unal <- V.mat
devtools::use_data( V.mat.unal )
# 3. Run matrix2array to generate an object of
# class array readable by Morpho and then save it as rda object
V.arr <- matrix2array( X = V.mat, coords = 3 )
V.arr.unal <- V.arr
devtools::use_data( V.arr.unal )
# 4. We have the 21 foxes specimens in object "V.arr".
# So now we remove the common fox "Vulpes_1" in C.PS from V.arr and
# align it to the mean shape of C.PS so the "Vulpes vulpes" have
# the same orientation than the rest of carnivores
# Save the procSym object
V.arr.nov1 <- V.arr[,,-1]
V.PS.nov1 <- Morpho::align2procSym( x = C.PS, newdata = V.arr.nov1 )
dimnames( V.PS.nov1 ) <- dimnames( V.arr.nov1 )
devtools::use_data( V.PS.nov1 )
# 5. Get the vulpes (Vulpes_1) from C.PS and add it to V.PS array
V.PS <- array( dim = c( 29, 3, 21 ) )
dimnames( V.PS ) <- list( paste( "lmk", seq( 1:29 ), sep="" ),
c( "x", "y", "z" ),
c( "Vulpes_1",
dimnames( V.PS.nov1 )[[3]] ) )
V.PS[,,1] <- C.PS$rotated[,,13] # Vulpes_1
V.PS[,,2:21] <- V.PS.nov1
# 6. Save alignment with 21 foxes (Vulpes vulpes) in rda format (class matrix)
V <- array2matrix( X = V.PS, coords = 3 )
devtools::use_data( V )
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