calibrate: 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 dsvord
calibrate(dsvord,site,dims=1:ncol(dsvord$points),
family='gaussian',gamma=1,keep.models=FALSE)
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.
Arguments
dsvord
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
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.
See Also
predict for the complementary function that fits GAM models
for species