readGPSA: Read pseudolandmarks into a data block

In aharmer/morphoBlocks: Constructing a Multiple-Part Morphospace Using a Multiple-Block Method

Read pseudolandmarks into a data block

Description

Reads and organises pseudolandmarks from Generalized Procrustes Surface Analysis (GPSA; Pomidor et al. 2015) into a data block. readGPSA expects a directory containing a single .dat file containing homologised points for one block of pseudolandmark configurations.

Usage

readGPSA(dirpath)

Arguments

dirpath

the directory path where a file containing homologised pseudolandmark points will be found. The homologised points file will have a .dat extension and must be produced using the Generalized Procrustes Surface Analysis software tool (Pomidor et al. 2015).

Details

readGPSA reads a matrix of pseudolandmark configurations from a .dat file into the R environment and organises the configurations into an array. Several objects are calculated for downstream analyses including centroid sizes for each pseudolandmark configuration. Note that centroid sizes are not calculated for the original meshes processed using GPSA, but are instead calculated for the homologised pseudolandmark points from each of those meshes after processing with GPSA. readGPSA is a wrapper function for the fread function from the data.table package (Dowle and Srinivasan 2020), the cSize function from the Morpho package (Schlager 2017), and the arrayspecs function from the geomorph package (Adams and Otárola-Castillo 2013).

Value

a 'block' class object, used for downstream analyses. The list contains the elements:

raw	collation of pseudolandmark configurations organised as a 2D matrix
gpa.3D	pseudolandmark configurations organised into a 3D array
gpa.2D	duplication of raw. The duplication occurs so that the object structure is consistent with the structure produced by closely-related functions (e.g. readPts)
centroid	centroid sizes of pseudolandmark configurations
p	number of pseudolandmarks that each configuration within the data block has
k	number of dimensions that each pseudolandmark within the data block has
n	number of pseudolandmark configurations included in the data block

References

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

Dowle M, Srinivasan A. 2020. data.table: Extension of 'data.frame'. R package version 1.13.4. https://CRAN.R-project.org/package=data.table

Pomidor BJ, Makedonska J, Slice DE. 2016. A landmark-free method for three-dimensional shape analysis. PLoS One 11: e0150368 https://doi.org/10.1371/journal.pone.0150368

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.

Examples

## Not run: 
# For this example to work a directory (/...) containing .dat file must first be prepared.
dirpath <- "/..."
block1 <- readGPSA(dirpath)
block1@p
block1@k
block1@n

## End(Not run)

aharmer/morphoBlocks documentation built on Nov. 21, 2022, 5:45 p.m.