HVordination: CALCULATE ORDINATION FOR HYPERVOLUME COMPUTATION

In CeresBarros/ToolsCB: Ceres's Useful R Functions

CALCULATE ORDINATION FOR HYPERVOLUME COMPUTATION

Description

Calculates an ordination across two datasets prior to calculating two hypervolumes (one from each dataset)

Usage

HVordination(
  datatable,
  HVidvar,
  init.vars = NULL,
  ordination = "PCA",
  noAxes = NULL,
  plotOrdi = TRUE,
  outputs.dir = NULL,
  file.suffix = NULL,
  saveOrdi = FALSE,
  saveOrdiSumm = TRUE
)

Arguments

datatable	is a data.table contained the raw data for the two hypervolumes
HVidvar	the name or number of the column (in HVdata1/2) containing the ID of each hypervolume.
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.
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.
noAxes	determines the number of axes/columns to use for hypervolume calculation
plotOrdi	activates/desactivates plotting for ordinations - plots are saved to PDFs not plotted interactively
outputs.dir	is the directory to store results
file.suffix	is a character string used as a suffix in file names
saveOrdi	activates/deactivates saving ordination object
saveOrdiSumm	activates/deactivates saving ordination summary outputs

Value

a list of points used to build hypervolumes and final number of axes.

CeresBarros/ToolsCB documentation built on Aug. 23, 2024, 4:22 p.m.