dodecBlock.Rd
Generates a block of n dodecahedra where the vertices of each dodecahedron represent a landmark configuration with p = 20 points in k = 3 dimensions. The data block is transformed using generalized Procrustes analysis.
dodecBlock( n = 10, dist_x = NULL, dist_y = NULL, dist_z = NULL, theta_x = NULL, theta_y = NULL, theta_z = NULL, size = NULL, noise = NULL, vertex_shift = NULL, plot = FALSE )
n | the number of configurations to generate for the data block. Default is 10. Must be 2 or greater. |
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dist_x, dist_y, dist_z | optional integer or vector to specify a distance along the stated axis (i.e. |
theta_x, theta_y, theta_z | optional integer or vector to specify an angle for rotating the configuration about its origin in the stated axis (i.e. |
size | optional integer or vector for scaling the configurations. If no value is specified then configurations will not be scaled relative to one another. If a single integer is supplied (e.g. |
noise | optional integer for introducing noise to the configurations. If no value is specified then |
vertex_shift | optional integer or vector to specify a distance along the z axis for translating the first vertex in each configuration. This argument can be used to introduce variation into the data block. If no value is specified then vertex 1 in each configuration will not be translated. If a single integer is supplied (e.g. |
plot | a logical value indicating whether the configurations should be plotted. Default is FALSE. |
a 'blockList' object of n dodecahedra, used for downstream analyses. The list contains the elements:
configurations without Procrustes transformation
configurations after Procrustes transformation organised into a 3D array
configurations after Procrustes transformation organised into a 2D matrix
centroid sizes of the configurations
number of points in the configurations of each data block
number of dimensions that the points in each configuration has
number of configurations included in each data block
dodecBlock
builds a data block of configurations that have been transformed using generalized Procrustes analysis. The resulting data block is a three dimensional array with n = 2 or greater configurations, with each configuration represented by p = 20 points that have k = 3 dimensions. Several objects are calculated for downstream analyses including centroid sizes for each configuration.
formatBlock
uses the cSize
function from the Morpho
package (Schlager 2017), and the gpagen
, two.d.array
and arrayspecs
functions from the geomorph
package (Adams and Ot?rola-Castillo 2013).
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
Schlager S. 2017. Morpho and Rvcg-shape analysis in R. In Zheng G, Li S, Sz?kely (eds.) Statistical shape and deformation analysis. Academic Press, London. Pp. 217-256.
# Example 1: Generate a block with ten configurations block <- dodecBlock() # Example 2: Generate a block with five configurations. # Rotate the configurations and translate the first vertex in each configuration. # Plot the result. block2 <- dodecBlock(n = 5, theta_z = seq(from = 0, to = 270, by = 60), vertex_shift = 0:4, plot = TRUE)