getivz {TITAN2}

Performs calculation of IndVal z scores from observed and permuted values

Description

A wrapper function that calls 'indval' or 'indvals' to obtain observed IndVal scores and 'permiv' to generate permuted values, then calculates z scores and associated p-values.

Usage

getivz(
  clss,
  spp,
  ivTot = ivTot,
  nPerm = nPerm,
  numClass = numClass,
  imax = imax,
  messaging = FALSE
)

Arguments

clss

A matrix of binary (0,1) group membership based on partitions of sampling sites ranked along an environmental gradient.

spp

A site-by-taxon matrix of taxa counts at each sampling location.

ivTot

A logical indicating whether IndVal scores should be calculated using total relative abundance or the mean relative abundace originally proposed by Dufrene and Legendre (1997).

nPerm

The number of permutations to be used by 'permiv'.

numClass

The number of classes used to partition samples along the enviorinmental gradient. The default is the total number of observations less two times the minimum split size ('minSplt').

imax

A logical indicating whether taxon-specific change points should be determined using IndVal maxima or z-score maxima (as in TITAN v1.0).

messaging

message user?

Details

This function calls two subfunctions to first calculate IndVals and their associated direction (i.e., a decreasing taxon, group 1, is associated with the left side of any partition, whereas an increasing taxon, group 2, is associated with the right) and second to develop permuted values for each candidate partition. Output includes the indicator direction (1 or 2), z scores, IndVal scores, and associated p value (obtained by the fraction of times an observed IndVal is greater than those obtained from numPerm randomizations of equivalent group sizes). For more detail regarding the relative benefits and potential drawbacks of using imax=T or imax=F, see Baker and King (2013).

Value

A matrix containing four submatrices (the first from [1:numTxa,], the second from [(numTxa+1):(2*numTxa),], etc.), the first two of which include indicator direction and z scores.

Group Membership

A vector for every taxon showing decreasing (1) or increasing (2) group membership at each value of 'envcls'

z scores

A vector for every taxon showing IndVal z scores at each value of 'envcls'

IndVals

A vector for every taxon showing IndVal scores at each value of 'envcls'

p values

A vector for every taxon showing IndVal p values at each value of 'envcls'

Author(s)

M. Baker and R. King

References

Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37.

Baker ME and RS King. 2013. Of TITAN and straw men: an appeal for greater understanding of community data. Freshwater Science 32(2):489-506.

See Also

indval(), indvals(), indvalp(), indvalps(), permiv(), ivzsums()