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Estimates pairwise size differences of phenotypic spaces

Source: R/space_size_difference.R
space_size_difference.Rd

space_size_difference

Usage

space_size_difference(
  formula,
  data,
  cores = 1,
  method = "mcp",
  pb = TRUE,
  outliers = 0.95,
  ...
)

Arguments

formula

an object of class "formula" (or one that can be coerced to that class).Must follow the form group ~ dim1 + dim2 where dim1 and dim2 are the dimensions of the phenotype space and group refers to the group labels.

data

Data frame containing columns for the dimensions of the phenotypic space (numeric) and a categorical or factor column with group labels.

cores

Numeric vector of length 1. Controls whether parallel computing is applied by specifying the number of cores to be used. Default is 1 (i.e. no parallel computing).

method

Character vector of length 1. Controls the method to be used for quantifying space size. Three metrics are available:

  • mcp: minimum convex polygon area using the function mcp. The minimum sample size (per group) must be 2 observations.

  • density: kernel density area using the function kernelUD. The minimum sample size (per group) must be 6 observations.

  • mst: minimum spanning tree using the function spantree. The minimum sample size (per group) must be 5 observations. This method is expected to be more robust to the influence of outliers.

pb

Logical argument to control if progress bar is shown. Default is TRUE.

outliers

Numeric vector of length 1. A value between 0 and 1 controlling the proportion of outlier observations to be excluded. Outliers are determined as those farthest away from the sub-space centroid.

...

Additional arguments to be passed to space_size for customizing space size calculation.

Value

A data frame containing the space size difference for each pair of groups.

Details

The function estimates the pairwise size difference in phenotypic space as a simple subtraction between the sizes of two spaces. As such it can be seen as an additional metric of similarity complementing those found in space_similarity.

References

Araya-Salas, M, & K. Odom. 2022, PhenotypeSpace: an R package to quantify and compare phenotypic trait spaces R package version 0.1.0.

See also

space_size, space_similarity, rarefact_space_size_difference

Author

Marcelo Araya-Salas marcelo.araya@ucr.ac.cr)

Examples

{
# load data
data("example_space")

# MCP size (try with more iterations on your own data)
mcp_size <- space_size_difference(
 formula = group ~ dimension_1 + dimension_2,
 data = example_space,
 method = "mcp")

# MST size
mcp_size <- space_size_difference(
 formula = group ~ dimension_1 + dimension_2,
 data = example_space,
 method = "mst")
}