fidelity: Calculate Fidelity Values

In vegsoup: Classes and Methods for Phytosociology

Description

Method fidelity calculates fidelity values for objects inheriting 'VegsoupPartition' and returns an extended object of class VegsoupPartitionFidelity. Function fidelity is based on the implementation of function strassoc in indicspecies and offers all it's methods plus some more (see ‘Details’).

Functions Phi and Indval calculates the phi and Indval statistics according to phi in package optpart, respectively, indval of package labdsv. Function FisherTest is a slightly faster alternative to fidelity(obj, method = "fisher"). Phi and Indval are also faster implementations compared to fidelity without option fast = TRUE. All three methods do not return an 'VegsoupPartitionFidelity' object, but the requested statistic as a "data.frame"! Take sqrt(Indval(x)) to obtain comparable results with fidelity(x, method = "IndVal.g").

Usage

## S4 method for signature 'VegsoupPartition'
fidelity(obj, method = "r.g", group = NULL, nboot = 0, alpha = 0.05, c = 1,
		 alternative = "greater", fast = FALSE, verbose = TRUE, ...)

## S4 method for signature 'VegsoupPartition'
FisherTest(obj, alternative = "greater")

## S4 method for signature 'VegsoupPartitionFidelity'
FisherTest(obj)

## S4 method for signature 'VegsoupPartition'
Phi(obj)

## S4 method for signature 'VegsoupPartition'
Indval(obj, ...)

## S4 method for signature 'VegsoupPartitionFidelity'
getStat(obj)

Arguments

obj	'VegsoupPartition' object.
method	indicator measure.
group	grouping variable.
nboot	number of boot straps, defaults to.
alpha	significance.
c	Forgot what that this is?
fast	accelerate computations using package parallel.
verbose	display computation status bar.
alternative	alternative hypothesis. For fidelity takes effect only for method = "Fisher"
...	For fidelity additional arguments for method = "fisher.s" and for Indval arguments passed to indval.

Details

Methods currently implemented for method fidelity include the following:

• r: phi (point-biserial correlation coefficient)

• r.g: phi, group equalised

• cos: cosine (Ochiai index)

• cos.g: cosine (Ochiai index), group equalised

• r.ind: phi individual based

• r.ind.g: phi individual based, group equalised

• s.ind: square root of Indval A times Indval B

• s.ind.g: square root of Indval A.g * Indval B, group equalised

• IndVal.g: Indval, group equalised

• IndVal: Indval

• A.g: Indval A, group equalised

• A: Indval A

• B: Indval B

• u.hyp: Bruelheide's corrected u value (Bruelheide 2000)

• u.binB: Bruelheide's corrected u value uBinB (Bruelheide 2000)

• u.binA: Bruelheide's corrected u value uBinA (Bruelheide 2000)

• g: G statistic

• chi: chi-square statistic with Yates correction

• Fisher: Fisher test (Chytry et al. 2002)

• CR: Willner's constancy ratio (Willner 2006)

• TCR: Willner's total cover ratio (Willner 2006)

Value

For fidelity an object of class 'VegsoupPartitionFidelity'.

For FisherTest and Phi a 'matrix' of values with species as rows and partitions as columns. Note, for class VegsoupPartitionFidelity FisherTest just extracts what was already calculated.

Note

Calculations can be computationally intensive – be patient.

Author(s)

Roland Kaiser, based on code from Miquel De Cáceres Ainsa taken from function strassoc in package indicspecies.

References

Willner, W., Tichy, L., and Chytry, M. (2009). Effects of different fidelity measures and contexts on the determination of diagnostic species. Journal of Vegetation Science, 20(1):130-137.

Willner, W. (2006). The association concept revisited. Phytocoenologia, 36(1):67-76.

Tichy, L. and M. Chytry. 2006. Statistical determination of diagnostic species for site groups of unequal size. Journal of Vegetation Science 17:809-818.

Chytry, M., Tichy, L., Holt, J., and Botta-Dukat, Z. (2002). Determination of diagnostic species with statistical fidelity measures. Journal of Vegetation Science, 13(1):79-90.

De Cáceres, M., Font, X., and Oliva, F. (2008). Assessing species diagnostic value in large data sets: A comparison between phi-coefficient and ochiai index. Journal of Vegetation Science, 19(6):779-788.

De Cáceres, M. and Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12):3566-3574.

De Cáceres, M., Legendre, P., and Moretti, M. (2010). Improving indicator species analysis by combining groups of sites. Oikos, 119(10):1674-1684.

Bruelheide, H. (2000). A new measure of fidelity and its application to defining species groups. Journal of Vegetation Science, 11(2):167-178.

See Also

VegsoupPartitionFidelity

Examples

require(vegsoup)

data(windsfeld)

x <- VegsoupPartition(windsfeld, k = 2)
f <- fidelity(x)

head(getStat(f))

hist(f)

vegsoup documentation built on Feb. 24, 2021, 3 a.m.