RAD (version 0.3)

truncMod: truncMod

Description

truncMod fits a truncated negative bionomial model to data. Use to fit Species Richness (S\_i)

Usage

truncMod(trunc.form, trunc.pts, data, dist = 'NB', scale.covar=FALSE, est.var = TRUE, trace = TRUE)

Arguments

trunc.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.

trunc.pts

A vector of truncation points of model. Must be of length equal to the numbers of rows(sites) of data. Set to N for fitting truncated species richness

data

a data frame containing the variables in the formula including the offset and the response. Each row should be a different site.

dist

one of either NB (negative binomial) or poission

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

Value

coef

coefficents

vcov

variance-covariance matrix

logl

log-likelihood

AIC

AIC

residuals

model residuals, calculated using PIT

fitted

fitted values

sds

dfdf

sums

model sums

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

Details

truncMod used glm.nb (MASS) or glm to get initial parameters for untruncated likelihoood & then uses nlminb to fit truncated model. Allows calculation of se for overdispersion parameter.

Examples

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