obs.summ: Summarizes results from TITAN's analaysis of observed data

In dkahle/TITAN2: Threshold Indicator Taxa Analysis

Summarizes results from TITAN's analaysis of observed data

Description

This function populates the first seven columns of the 'sppmax' output table with results summarized for each taxon from the output of 'getivz'.

Usage

obs.summ(ivzScores, taxa, srtEnv, minSplt = minSplt, imax = imax)

Arguments

ivzScores	The product of the 'getivz' function. A data matrix comprised of four submatrices including group membership, z scores, IndVals, and p values.
taxa	A site by taxon matrix with counts observed at each sampling location.
srtEnv	A sorted version of the environmental gradient.
minSplt	The minimum split size used to determine partitions along the environmental gradient. The defualt is to use the argument from the original TITAN function call.
imax	A logical indicating whether taxon-specific change points should be determined using IndVal maxima or z-score maxima (as in TITAN v1.0).

Details

The items summarized for each taxon include (1) the env value at the IndVal maximum, (2) the env value at the z-score maximum, (3) the taxon's occurrence frequency, (4) group membership (decreaser or increaser), (5) the observed IndVal score, (6) the probability that the taxon's IndVal score could be generated by random chance, (7) the z score. As the values 3-7 are computed for every taxon at each candidate change point, values for the table are determined by the maximum (IndVal or z score) indicated by the value of 'imax'. For further detail regarding the advantages and disadvantages of using imax=T or imax=F, see Baker and King (2013).

Value

The function output consists of a list of three objects:

obs1

a logical indicating decreasing taxa

obs2

a logical indicating increasing taxa

sppmax

a partially completed summary output table for all taxa

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

getivz(), titan()

dkahle/TITAN2 documentation built on Nov. 15, 2023, 2:49 p.m.