geomorph (version 3.2.1)

combine.subsets: Combine separate landmark configurations

Description

Combine separate landmark configurations (subsets) into one landmark set

Usage

combine.subsets(..., gpa = TRUE, CS.sets = NULL)

Arguments

...

Class gpagen objects, Procrustes shape variables from class gpagen objects, or original landmarks. As many data sets as desired can be supplied, separated by commas. Additionally, arguments passed onto gpagen can be provided, but these arguments will be passed onto all GPAs performed. Therefore, it is recommended that GPA is performed first with gpagen, to maintain flexibility. Naming subsets is a good idea, as landmark names in the combined data set will take the subset name as a precursor.

gpa

A logical argument to indicate if either (1) GPA should be performed (if original landmarks are provided) or (2) gpagen objects are provided. If TRUE, this function will check to see if the input is an object of class gpagen, and if not, perform GPA. If FALSE, landmarks will be unchanged. (One would choose gpa = FALSE if inputting aligned coordinates and centroid size, separately. There might be little reason to do this, unless one wishes to intentionally not scale configurations.)

CS.sets

A list, array, or matrix of centroid sizes to use for scaling. The default is NULL and should be left so if gpa = TRUE. If gpa = FALSE and CS.set is null, all centroid sizes become 1.0, meaning no scaling of configurations by relative size is performed. If gpa = FALSE and CS.set is provided, scaling by relative size is performed according to the data input (One could weight configurations via this method.). If the CS.set input is a matrix, it is assumed that rows are specimens and columns correspond to the different landmark sets. Lists or arrays should be in the same order as the landmark sets.

Value

An object of class combined.set is a list containing the following

cords

An [p x k x n] array of scaled, concatenated landmark coordinates.

CS

A matrix of columns representing original centroid sizes of subsets, either input or found via GPA.

GPA

If gpa = TRUE, the gpagen results for each subset.

gpa.coords.by.set

A list of the coordinates following GPA for each subset.

adj.coords.by.set

A list of the coordinates of each subset, after rescaling.

points.by.set

A vector of the number of landmarks in each subset.

Details

This function combines landmark configurations (either landmarks requiring GPA or Procrustes shape variables following GPA) to create a different morphological data set. This might be of interest, for example, if one has landmarks digitized on separate images collected from the same organisms. (In the examples below, configurations for heads and tails of larval salamanders were collected separately from images taken on the same individuals.) An attempt is made to scale configurations by their relative centroid sizes, following the procedure in Davis et al. (2016); i.e., landmark coordinates are multiplied by CSi/(CSi + CSj + ...) before combining them, so that resulting combinations of landmarks are scaled to unit centroid size. This is only possible if GPA is performed on landmarks (gpa = TRUE) or centroid sizes are provided as an argument. Objects of class gpagen can be used rather than original landmarks (recommended, especially if curves or surface sliding semilandmarks are used, as different arguments cannot be passed onto onto separate GPAs via this function).

The procedure of Davis et al. (2016) is an extension of the "separate subsets" method of Adams (1999) for articulated structures.

References

Davis, M.A., M.R. Douglas, M.L. Collyer, & M.E. Douglas, M. E. 2016. Deconstructing a species-complex: geometric morphometric and molecular analyses define species in the Western Rattlesnake (Crotalus viridis). PloS one, 11(1), e0146166.

Adams, D. C. 1999. Methods for shape analysis of landmark data from articulated structures. Evolutionary Ecology Research. 1:959-970.

Examples

# NOT RUN {
data(larvalMorph) 
head.gpa <- gpagen(larvalMorph$headcoords, curves = larvalMorph$head.sliders)
tail.gpa <- gpagen(larvalMorph$tailcoords, curves = larvalMorph$tail.sliders)
comb.lm <- combine.subsets(head = head.gpa, tail = tail.gpa, gpa = TRUE)
summary(comb.lm)
# Plot first specimen and color code landmarks 
# (configurations are actual relative size)
comb.lm$coords[,,1]
plot(comb.lm$coords[,,1], pch = 21, bg = c(rep(1,26), rep(2,64)), asp = 1)

# choose to override scaling by relative size 
comb.lm <- combine.subsets(head = head.gpa$coords, 
tail = tail.gpa$coords, gpa = FALSE, CS.sets = NULL)
summary(comb.lm)
plot(comb.lm$coords[,,1], pch = 21, bg = c(rep(1,26), rep(2,64)), asp = 1)
# }