Predict species abundances in an ordination
This function fits a Generalized Additive Model (GAM) for each species in a data.frame against an ordination.
## S3 method for class 'dsvord'
predict(object,comm,minocc=5,dims=1:ncol(object$points),
family='nb',gamma=1,keep.models=FALSE,...)object |
an object of class dsvord |
comm |
a community matrix or data.frame with samples as rows and species as columns |
minocc |
the minimum number of occurrences to model a species |
dims |
which specific dimensions to include |
family |
the error distribution specifier for the GAM function; can be 'nb' for negative binomial, 'poisson' for the Poisson distribution, or 'binomial' for presence/absence data |
gamma |
the gamma parameter to control fitting GAM models |
keep.models |
a switch to control saving the individual GAM models |
... |
ancillary arguments to function predict |
The predict function sequentially and independently fits a GAM model of each species distribution as a function of ordination coordinates, using the family and gamma specifiers supplied in the function call, or their defaults. The function fits two or three dimensional models; if the length of dims is greater than three the dimensions are truncated to the first three chosen.
A list object with vector elements aic, dev.expl, adj.rsq, and matrix fitted. Optionally, if keep.models is TRUE, a list with all of the GAM models fitted. list element aic gives the model AICs for each species, dev.expl gives the deviance explained, adj.rsq gives the adjusted r-Squared, and fitted gives the expected abundance of each species in each sample unit.
calibrate for the complementary function that fits GAM models for environment variables
data(bryceveg) dis.man <- dist(bryceveg,method="manhattan") demo.nmds <- nmds(dis.man,k=4) ## Not run: res <- predict(demo.nmds,bryceveg,minocc=10)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.