hypervolumes: CALCULATE AND COMPARE TWO HYPERVOLUMES
In CeresBarros/ToolsCB: Ceres's Useful R Functions

hypervolumes

R Documentation

CALCULATE AND COMPARE TWO HYPERVOLUMES

Description

Calculates two hypervolumes on two sets of "raw" data or on the factor scores of an ordination done on the entire dataset (across the two sets of data).

Usage

hypervolumes(
  HVdata1,
  HVdata2,
  HVidvar,
  ordination = "PCA",
  init.vars = NULL,
  noAxes = NULL,
  do.scale = FALSE,
  HVmethod = "box",
  freeBW = FALSE,
  bwHV1 = NULL,
  bwHV2 = NULL,
  no.runs = 1,
  plotOrdi = TRUE,
  plotHV = TRUE,
  saveOrdi = FALSE,
  saveOrdiSumm = TRUE,
  outputs.dir,
  file.suffix,
  verbose = TRUE,
  plotHVDots = NULL,
  ...
)

Arguments

`HVdata1`	the `data.table` (or a object that can be converted to `data.table`) from which the first hypervolume will be calculated
`HVdata2`	the `data.table` (or a object that can be converted to `data.table`) from which the second hypervolume will be calculated. `HVdata1` and `HVdata2` must have the same column names and ideally the same number of rows.
`HVidvar`	the name or number of the column (in `HVdata1/2`) containing the ID of each hypervolume.
`ordination`	determines whether hypervolumes will be calculated on the raw data ("none") of on ordination factor scores (one of "PCA", "HillSmith", "dudi.mix"). Defaults to using a PCA.
`init.vars`	is a vector with the variable indices (column numbers) to use. Defaults to NULL and all variables are used - ATTENTION the user should not have more than 8 variables unless using an ordination to reduce dimensionality. See Blonder et al 2014.
`noAxes`	determines the number of axes/columns to use for hypervolume calculation
`do.scale`	activates scaling prior to the ordination/calculation of HVs
`HVmethod`	determines the method used to calculate hypervolumes - passed to `hypervolume::hypervolume` method argument
`freeBW`	determines whether a bandwidth estimator will be used to calculate bandwith per variable. Only used if `HVmethod` is "box" or "gaussian".
`bwHV1`	determines the bandwidth value for first hypervolume. Only used if `freeBW` is FALSE. see `hypervolume::hypervolume` Only used if `HVmethod` is "box" or "gaussian".
`bwHV2`	determines the bandwidth value for second hypervolume. Only used if `freeBW` is FALSE. see `hypervolume::hypervolume` Only used if `HVmethod` is "box" or "gaussian".
`no.runs`	determines how many times the HV calculations and comparisons are repeated
`plotOrdi`	activates/desactivates plotting for ordinations - plots are saved to PDFs not plotted interactively
`plotHV`	activates/desactivates plotting for hypervolumes - plots are saved to PDFs not plotted interactively
`saveOrdi`	activates/deactivates saving ordination object
`saveOrdiSumm`	activates/deactivates saving ordination summary outputs
`outputs.dir`	is the directory to store results
`file.suffix`	is a character string used as a suffix in file names
`verbose`	is passed to `⁠hypervolume::*⁠` functions to control printing of diagnostic outputs
`plotHVDots`	a `list` of further arguments passed to `hypervolume:::plot.HypervolumeList`.
`...`	further arguments passed to `hypervolume::hypervolume`.