combineBlocks: Combine and scale blocks of shape configuration data

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

Combine and scale blocks of shape configuration data

Description

Combines two or more blocks of shape configuration data into a block list. Scales all data blocks using the normalised centroid size method from Profico et al. (2019) (and further described by Collyer et al. 2020). Such scaling occurs by default but is optional and can be prevented. A superblock is produced by column-wise concatenation of the individual blocks.

Usage

combineBlocks(blocks, cent.scale = TRUE)

Arguments

blocks	vector of 'block' object names produced by the dodecBlock, formatBlock, readPts or readGPSA functions. e.g. blocks = c(block1, block2, block3)
cent.scale	a logical value indicating if the blocks should be scaled using the normalised centroid size method adapted from geomorph::combine.subsets. Default value TRUE.

Details

The block data is scaled using the normalised centroid size method from Profico et al. (2019) and Collyer et al. (2020) if cent.scale = TRUE. Dimensions of the blocks are retained for downstream analyses. combineBlocks adapts the normalised centroid size method from the combine.subsets function in the geomorph package (Adams and Ot?rola-Castillo 2013).

Value

a 'blockList' object, used for downstream analyses, that contains the data blocks and a superblock formed from the column-wise concatenation of all data blocks. The list contains the elements:

block.list	a list containing the data blocks and a concatenated superblockblock
p	number of points in the configurations of each data block
k	number of dimensions that the points in each configuration has
n	number of configurations included in each data block

References

Adams DC, Ot?rola-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

Collyer ML, Davis MA, Adams DC. 2020. Making heads or tails of combined landmark configurations in geometric morphometric data. Evolutionary Biology 47: 193-205 https://doi.org/10.1007/s11692-020-09503-z

Profico A, Piras P, Buzi C, Del Bove A, Melchionna M, Senczuk G, Varano V, Veneziano A, Raia P, Manzi G. 2019. Seeing the wood through the trees. Combining shape information from different landmark configurations. Hystrix, the Italian Journal of Mammalogy, 30: 157-165 https://doi.org/10.4404/hystrix-00206-2019

Examples

block1 <- dodecBlock()
block2 <- dodecBlock()
block.list <- combineBlocks(blocks = c(block1, block2))

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