calcDivProf: Calculate a diversity profile

In chemodiv: Analysing Chemodiversity of Phytochemical Data

Calculate a diversity profile

Description

Function to calculate a diversity profile, i.e. calculate Hill diversity or Functional Hill Diversity for a range of q values.

Usage

calcDivProf(
  sampleData,
  compDisMat = NULL,
  type = "HillDiv",
  qMin = 0,
  qMax = 3,
  step = 0.1
)

Arguments

sampleData	Data frame with the relative concentration of each compound (column) in every sample (row).
compDisMat	Compound distance matrix, as calculated by compDis. Has to be supplied for calculations of Functional Hill diversity.
type	Type of Hill Diversity to calculate for the diversity profile. "HillDiv" or "FuncHillDiv".
qMin	Minimum value of q.
qMax	Maximum value of q.
step	Increment by which q will be calculated between qMin and qMax.

Details

The function calculates a diversity profile for each sample in sampleData. A diversity profile is a calculation of Hill Diversity or Functional Hill Diversity for a range of different values of q. This function performs the calculations, while chemoDivPlot can be used to conveniently create the diversity profile plot, where Hill Diversity is plotted as a function of q within the chosen range. The shape of the diversity profile curve reflects the evenness of compound proportions in the sample. For a perfectly even sample the curve is flat. The more uneven the compound proportions are, the more steep is the decline of the curve. A common range, used as default, of q values is between qMin = 0 and qMax = 3, as diversity should change little beyond qMax = 3. See calcDiv for further details on q.

Value

List with a diversity profile data frame with samples as rows and the Hill diversity or Functional Hill diversity for different q values as columns; and values for type, qMin, qMax and step.

References

Chao A, Chiu C-H, Jost L. 2014. Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers. Annual Review of Ecology, Evolution, and Systematics 45: 297-324.

Examples

data(minimalSampData)
data(minimalCompDis)
calcDivProf(sampleData = minimalSampData)
calcDivProf(sampleData = minimalSampData, compDisMat = minimalCompDis,
type = "FuncHillDiv")

data(alpinaCompData)
data(alpinaCompDis)
calcDivProf(sampleData = alpinaSampData, compDisMat = alpinaCompDis,
type = "FuncHillDiv", qMin = 1, qMax = 2, step = 0.2)

chemodiv documentation built on Aug. 18, 2023, 1:08 a.m.