readPts.Rd
Reads, collates and transforms landmark configurations from multiple specimens. readPts
expects a directory containing two or more files with .pts extensions (i.e. landmark configurations exported from the Landmark Editor, Wiley et al. 2005).
readPts(dirpath, landmarkRM = c(), gpa = TRUE)
dirpath | the directory path where two or more landmark configurations with .pts extensions will be found. |
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landmarkRM | a vector of landmarks to be excluded from the data block. |
gpa | a logical value indicating whether generalized Procrustes analyses should be performed. Default is |
a 'block' class object, used for downstream analyses. The list contains the elements:
collation of landmark configurations without Procrustes transformation
landmark configurations after Procrustes transformation organised into a 3D array
landmark configurations after Procrustes transformation organised into a 2D matrix
centroid sizes of landmark configurations without Procrustes transformation
number of landmarks that each configuration within the data block has
number of dimensions that each landmark within the data block has
number of landmark configurations included in the data block
matrix for correctly calculating position of curve semilandmarks (see geomorph::gpagen
for more detail)
vector passed for defining positions of semilandmarks on surfaces (see geomorph::gpagen
for more detail)
readPts
reads landmark configurations from .pts files into the R environment, organises the configurations into a single array, and performs generalized Procrustes analysis on the array if required. Several objects are calculated for downstream analyses including centroid sizes for each landmark configuration.
readPts
is a wrapper function for the read.pts
and cSize
functions from the Morpho
package (Schlager 2017), and the gpagen
, two.d.array
and arrayspecs
functions from the geomorph
package (Adams and Otárola-Castillo 2013).
Landmarks are identified by their sequence within the configuration, which is an important consideration when excluding landmarks from the data block. For example, landmarkRM = c(1,3)
would remove the first and third landmarks from all configurations once they were read into the R environment, and thus the data block would not include landmark 1 and landmark 3. The landmarkRM
term might be used for analyses that want to test the sensitivity of dataset covariation on one or more landmarks.
Adams DC, Otárola-Castillo E. 2013. geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution 4:393–399 https://doi.org/10.1111/2041-210X.12035
Schlager S. 2017. Morpho and Rvcg–shape analysis in R. In Zheng G, Li S, Székely (eds.) Statistical shape and deformation analysis. Academic Press, London. Pp. 217–256.
Wiley DF, Amenta N, Alcantara DA, Ghosh D, Kil YJ, Delson E, Harcourt-Smith W, Rohlf FJ, St. John K, Hamann B. 2005. Evolutionary morphing. Proceedings of the IEEE Visualization 2005 (VIS’05), 431–438.
if (FALSE) { # Example 1 # For this example to work a directory (/...) containing .pts files must first be prepared. dirpath <- "/..." block1 <- readPts(dirpath) block1@p block1@k block1@n # Example 2 # Exclude the first and third landmarks from the data block block2 <- readPts(dirpath, landmarkRM = c(1, 3)) block2@p block2@k block2@n }