getSampleDCA {paleoAM}R Documentation

Get the Detrended correspondence Analysis (DCA) Score Value for A Single Sample

Description

For a single simulated assemblage sample, projects its location in DCA space defined by the original abundance data.

Usage

getSampleDCA(
  simSample,
  origAbundData,
  useTransformedRelAbundance = TRUE,
  projectIntoOrigDCA = TRUE,
  returnDCAforOrigAndSim = FALSE,
  whichAxes = 1,
  powerRootTransform = 1
)

Arguments

simSample

The assemblage data for a single sample (presumably from a simulation).

origAbundData

The original matrix of abundance data, to be used to project the simulated data into the same detrended correspondence analysis (DCA) space.

useTransformedRelAbundance

Should the DCA be analyzed

projectIntoOrigDCA

Should the new simulated data be projected in the DCA generated by analyzing the original data? This is TRUE by default, which is what most users will likely use, as it is the preferable way to consider how the new simulated data relates to the original data.

returnDCAforOrigAndSim

Should the DCA score values for both the new simulated data and the original abundance data be returned? Default is FALSE as projecting the new data into the original DCA space means the original data should never be meaningfully different the original score values.

whichAxes

Which dimensional score from the DCA should be used? By default this is 1. Unclear under what circumstances one would ever use a value other than 1, though, as detrending the correspondence analysis causes distortion along all scores other than the first axis of the ordination. Only the first score can be returned when projectIntoOrigDCA = TRUE.

powerRootTransform

The power-root transform to be used on the abundance data before applying the DCA. By default this is 1, which means the data is not transformed at all. Note that the power-root transform is only performed if useTransformedRelAbundance = TRUE.

Details

Detrended correspondence analysis (DCA) is a common method for producing an ordination of ecological data. It isn't the only such method.

Value

A vector, containing either a single value, the DCA score value of the simulated sample, when returnDCAforOrigAndSim = FALSE, or a vector of the DCA scores for the original data and

See Also

This function is ultimately just a wrapper for using decorana in package vegan.


[Package paleoAM version 1.0.1 Index]