indval: IndVal scores based on relative abundance across, and...

In TITAN2: Threshold Indicator Taxa Analysis

IndVal scores based on relative abundance across, and occurrence frequency within, groups

Description

Calculates indicator value scores using the original method of Dufrene and Legendre (1997) for all taxa in a site-by-taxon matrix split into two groups along an environmental gradient. A modified version (indvals) calculates indicator value scores using a modification of Dufrene and Legendre (1997), whereby relative abundance is computed as total relative abundance across groups rather than as mean relative abundance.

Usage

indval(grp, spp, allscores = FALSE)

indvals(grp, spp, allscores = FALSE)

Arguments

grp	A binary vector (0,1) indicating group membership for partitioning of rows in 'spp' according to a ranks of an environmental variable.
spp	A site-by-taxon matrix of taxa counts at each sampling location.
allscores	A logical indicating whether the list of scores returned by the function should be truncated. The default is to return just the largest IndVal (of two, one for each side of the partition) and on which side of the partition the score occurs. If allscores is TRUE, IndVals on both sides of the partition, as well as their relative abundances are also returned.

Details

The modified version of the original IndVal method was developed to address potential for bias in change point identification for highly skewed samples. This and the function 'indvalps' are run when the argument 'ivTot' in the original TITAN function call is set to TRUE. The function 'indval' is expected to be used more frequently, and 'indvals' is provided largely for comparative purposes.

Value

A 2-column matrix with the same nrow as the matrix 'spp'. The first column consists of a 1 (left) or 2 (right) for each taxon indicating on which group produced the largest IndVal score, and the second column contains the actual IndVal score.

Author(s)

M. Baker and R. King

References

Dufrene, M. and P. Legendre. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs 67:345-366.

See Also

indvalp(), indvalps(), getivz()

TITAN2 documentation built on Nov. 15, 2023, 1:09 a.m.