HOF: Fits Huisman-Olff-Fresco (HOF) Response Models for Species...

In gravy: Gradient Analysis of Vegetation

Description

Huisman-Olff-Fresco or HOF models are a series of five nested species response models which define skewed, symmetric, plateau, monotone and flat responses along ecological gradients.

Usage

## Default S3 method:
HOF(spec, grad, M, y.name, family = binomial, ...)
## S3 method for class 'data.frame'
HOF(veg, grad, M, freq.limit = 10, ...)
## S3 method for class 'HOF'
plot(x, ...)
## S3 method for class 'HOF.frame'
plot(x, level = 0.95, test ="F", species, ...) 
## S3 method for class 'HOF'
fitted(object, model, ...)
## S3 method for class 'HOF'
residuals(object, type = c("deviance", "working",
  "response", "pearson"), model, ...)
## S3 method for class 'HOF'
predict(object, newdata, model, ...)
## S3 method for class 'HOF'
GaussPara(resp, model, ...)

Arguments

spec	Species data vector.
veg	Vegetation data frame.
grad	Gradient data vector.
M	Maximum attainable value in the HOF model, similar to binomial denominator.
y.name	Name of the species (stupid, but I used this in loops).
family	Error distribution. Alternatives are binomial, poisson and gaussian.
freq.limit	Lowest frequency of species analysed.
level	Probability for model selection (1-P).
test	Test for model selection. Alternatives are "F", "Chisq", "AIC", "AICc" and "BIC".
type	the type of residuals which should be returned (see residuals.glm).
species	Names of the species displayed in graphs.
x, object	An object from HOF(spec, ...).
newdata	Vector of gradient values for prediction.
resp	Fitted response models.
model	Specific HOF model used, if not selected automatically.
...	Other parameters

Details

Not yet written.

Function fitted returns the fitted values for the used grad, and predict for any values in newdata.

Value

Function HOF.fit returns an object of class "HOF" which contains the fitting results and other useful information.

Note

These functions are at their alpha stage: proceed with caution.

Author(s)

Jari Oksanen

References

Huisman, J., Olff, H. & Fresco, L.F.M. (1993). A hierarchical set of models for species response analysis. Journal of Vegetation Science 4, 37-46.

Oksanen, J. & Minchin, P.R. (2002). Continum theory revisited: what shape are species responses along ecological gradients? Ecological Modelling 157, 119-129.

See Also

plotGrad

Examples

data(mtf01)
data(mtf.alt)
attach(mtf01)
attach(mtf.alt)
mod <- HOF(BAUERUBI,Altitude, M=1)
mod
plot(mod)
mod <- HOF(mtf01, Altitude, 1)
plot(mod)
mod

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