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Estimates rarefacted size of phenotypic spaces

Source: R/rarefact_space_size.R
rarefact_space_size.Rd

rarefact_space_size

Usage

rarefact_space_size(
  formula,
  data,
  n = NULL,
  replace = FALSE,
  seed = NULL,
  cores = 1,
  pb = TRUE,
  iterations = 30,
  ...
)

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.

n

Integer vector of length 1 indicating the number of samples to be use for rarefaction (i.e. how many samples per group will be gather at each iteration). Default is the minimum sample size across groups. Integer vector of length 1 indicating the number of samples to be use for rarefaction (i.e. how many samples per group will be gather at each iteration). Default is the minimum sample size across groups.

replace

Logical argument to control if sampling is done with replacement. Default is FALSE.

seed

Integer vector of length 1 setting the seed (see set.seed). If used results should be the same on different runs, so it makes them replicable.

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).

pb

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

iterations

Integer vector of length 1. Controls how the number of times the rarefaction routine is iterated. Default is 30.

...

Additional arguments to be passed to space_size.

Value

A data frame containing the mean, minimum, maximum and standard deviation of the size difference across iterations for each pair of groups.

Details

The function applies a rarefaction sub-sampling procedure for evaluating pairwise space size differences (internally using space_size). The size of a phenotypic space might change as a function of number of samples. Hence, ideally, spaces should be compared between groups of similar sample sizes. Rarefaction allows to compare groups of unbalanced sample sizes by randomly re-sampling observations using the same number samples across groups iteratively.

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

rarefact_space_similarity, space_size_difference

Author

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

Examples

{
# load data
data("example_space")

# get rarefacted MCP space size 
# (try with more iterations on your own data)
rarefact_space_size(
 formula = group ~ dimension_1 + dimension_2,
 data = example_space,
 method = "mcp")

# mst rarefacted
rarefact_space_size(
 formula = group ~ dimension_1 + dimension_2,
 data = example_space,
 method = "mst")
}
#>   group   n mean.size  min.size  max.size   sd.size
#> 1    G1 150  6.062202  6.062202  6.062202 0.0000000
#> 2    G2 150  8.000190  7.602379  8.377236 0.1661115
#> 3    G3 150 18.474301 17.351547 19.841210 0.6339556
#> 4    G4 150 11.619925 10.471626 12.544382 0.4116350
#> 5    G5 150 15.768072 15.034279 17.010687 0.5025562