Fits Huisman-Olff-Fresco (HOF) Response Models for Species along an Ecological Gradient.

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

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## 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

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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