calibrate: Calculate fitted environmental attributes in an ordination

In labdsv: Ordination and Multivariate Analysis for Ecology

Calculate fitted environmental attributes in an ordination

Description

Fits a Generalized Additive Model (GAM) for each environmental variable in a data.frame against an ordination.

Usage

## S3 method for class 'dsvord'
calibrate(ord,site,dims=1:ncol(ord$points),
           family='gaussian',gamma=1,keep.models=FALSE,...)

Arguments

ord	an ordination object of class dsvord
site	a matrix or data.frame with sample units as rows and environmental variables as columns
dims	the specific dimensions of the ordination to consider
family	the error distribution specifier for the GAM function
gamma	the gamma parameter to control fitting GAM models
keep.models	a switch to control saving the individual GAM models
...	arguments to pass

Details

The calibrate function sequentially and independently fits a GAM model for each environmental variable as a function of ordination coordinates, using the family and gamma specifiers supplied in the function call, or their defaults. The model fits two or three dimensional models; if the length of dims is greater than three the dimensions are truncated to the first three chosen.

Value

A list object with vector elements aic, dev.expl, adj.rsq, and fitted value matrix. Optionally, if keep.models is TRUE, a list with all of the GAM models fitted. List element aic gives the model AICs for each variable, dev.expl gives the deviance explained, adj.rsq gives the adjusted r-Squared, and fitted gives the expected value of each variable in each sample unit.

Author(s)

David W. Roberts [e-mail]

See Also

predict for the complementary function that fits GAM models for species

Examples

data(bryceveg)
dis.man <- dist(bryceveg,method="manhattan")
demo.nmds <- nmds(dis.man,k=4)
## Not run: res <- calibrate(demo.nmds,brycesite[,c(2,4,7,12)],minocc=10)

labdsv documentation built on April 10, 2023, 5:08 p.m.