HuismanOlffFresco or HOF models are a series of five nested species response models which define skewed, symmetric, plateau, monotone and flat responses along ecological gradients.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  ## 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, ...)

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 
freq.limit 
Lowest frequency of species analysed. 
level 
Probability for model selection (1P). 
test 
Test for model selection. Alternatives are 
type 
the type of residuals which should be returned (see

species 
Names of the species displayed in graphs. 
x, object 
An object from 
newdata 
Vector of gradient values for prediction. 
resp 
Fitted response models. 
model 
Specific HOF model used, if not selected automatically. 
... 
Other parameters 
Not yet written.
Function fitted
returns the fitted values for the used
grad
, and predict
for any values in newdata
.
Function HOF.fit
returns an object of class "HOF"
which
contains the fitting results and other useful information.
These functions are at their alpha stage: proceed with caution.
Jari Oksanen
Huisman, J., Olff, H. & Fresco, L.F.M. (1993). A hierarchical set of models for species response analysis. Journal of Vegetation Science 4, 3746.
Oksanen, J. & Minchin, P.R. (2002). Continum theory revisited: what shape are species responses along ecological gradients? Ecological Modelling 157, 119129.
plotGrad
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