negBinMod: negBinMod

In RAD: Fit RAD models to biological data

Description

negBinMod fits a negative bionomial model to data. Use to fit Total Abundance (Ni)

Usage

negBinMod(NB.form, data, est.var=TRUE, scale.covar=FALSE , trace=TRUE)

Arguments

NB.form	an object of class "formula" (or one that can be coerced to that class):a symbolic description of the model to be fitted. An offset in the form offset(log(area sampled)) should be included in the model formula to adjust for differences in area sampled between sites.
data	a data frame containing the all variables in the formula including the offset and the response. Each row should be a different site.
scale.covar	Should the model matrix be scaled (TRUE/FALSE)? Useful if models do not converge. Setting this to TRUE will save the column means and sd for later prediction.
est.var	estimate the variance-covariance matrix using newton-raphson
trace	print model trace

Details

negBinMod used glm.nb (MASS) to get initial parameters & then uses nlminb to fit model. Allows calculation of se for overdispersion parameter. Output is otherwise identical to glm.nb

Value

coef	coefficents
vcov	variance-covariance matrix
logl	log-likelihood
AIC	AIC
residuals	model residuals, calculated using PIT
fitted	fitted values
mean.X	column means for model matrix if scale.covar is TRUE
sd.X	column sds for model matrix if scale.covar is TRUE
formula	model formula

Authors

Piers Dunstan and Scott Foster

Examples

N.form <- N~1  + depth + O2_AV + temp_AV + offset(log(area))
model.N <- negBinMod(N.form,data=fish.data,est.var=TRUE,scale.covar =FALSE)
plot(model.N$fitted,model.N$residuals)
abline(h=0)

RAD documentation built on May 2, 2019, 9:36 a.m.