nichelap: Overlap of Two Species Responses along a Gradient.

In gravy: Gradient Analysis of Vegetation

Description

Functions estimates the amount of overlap of two fitted species responses along a single gradient.

Usage

## S3 method for class 'HOF'
nichelap(sp1, sp2, test = "BIC", ...)
## S3 method for class 'HOF.frame'
nichelap(df, test = "BIC", ...)
## S3 method for class 'nichelap.HOF.frame'
as.matrix(x, ...)

Arguments

sp1, sp2	Fitted response models for two species.
df	Fitted responses for a data frame of several species.
test	The test used to select the HOF model.
x	The result of nichelap for a data frame of several species.
...	Other arguments passed to functions.

Details

The function finds the niche overlap as an overlap of fitted response curves (Lawesson & Oksanen 2002). The input can either consist of fitted responses for two species, or of responses fitted to several species in a data frame. If the input is a frame of several fitted responses, overlaps will be found for each pair of species.

For each pair of species, the function will return a vector with total areas for each species, the total area of the overlap, the proportion of overlap from the total covered jointly by two species, and the proportion of each species covered by the other species. The total area is defined so that the the maximum response height and total gradient range is unity. Consequently, the reported areas are proportions of the maximum attainable area (species occurs at its attainable maximum over the whole gradient range). Function as.matrix returns the last two entries in a matrix similar to Lawesson & Oksanen (2002), table 4.

The functions are based on the standard R\ function integrate.

Value

Function returns a vector of niche statistic for each pair of species. For a response frame, these vectors are each an item in a list.

Note

At the moment, the function knows only HOF models.

Author(s)

Jari Oksanen

References

Lawesson, J.E. & Oksanen, J. (2002). Niche characteristics of Danish woody species as derived from coenoclines. Journal of Vegetation Science 13, 279–290.

See Also

integrate, HOF.

Examples

data(mtf01)
data(mtf.alt)
attach(mtf.alt)
mods <- HOF(mtf01, Altitude, M=1)
lap <- nichelap(mods)
lap
mat <- as.matrix(lap)
mat
# Similar formatting as in Lawesson & Oksanen (2002)
round(100*mat)

gravy documentation built on May 2, 2019, 4:46 p.m.