mgcv (version 1.1-8)

gam.neg.bin: GAMs with the negative binomial distribution

Description

The gam modelling function is designed to be able to use the negative.binomial and neg.bin families from the MASS library, with or without a known $\theta$ parameter. A value for theta must always be passed to these families, but if $\theta$ is to be estimated then the passed value is treated as a starting value for estimation.

If the scale argument passed to gam is positive, then it is used as the scale parameter theta is treated as a fixed known parameter and any smoothing parameters are chosen by UBRE. If scale is not positive then $\theta$ is estimated. The method of estimation is to choose $\hat \theta$ so that the GCV (Pearson) estimate of the scale parameter is one (since the scale parameter is one for the negative binomial).

$\theta$ estimation is nested within the IRLS loop used for GAM fitting. After each call to fit an iteratively weighted additive model to the IRLS pseudodata, the $\theta$ estimate is updated. This is done by conditioning on all components of the current GCV/Pearson estimator of the scale parameter except $\theta$ and then searching for the $\hat \theta$ which equates this conditional estimator to one. The search is a simple bisection search after an initial crude line search to bracket one. The search will terminate at the upper boundary of the search region is a Poisson fit would have yielded an estimated scale parameter <1. search="" limits="" can="" be="" set="" in="" gam.control.

Note that neg.bin only allows a log link, while negative.binomial also allows "sqrt" and "identity". In addition the negative.binomial family results in a more informative gam summary.

Examples

library(MASS) # required for negative binomial families
set.seed(3)
n<-400
x0 <- runif(n, 0, 1)
x1 <- runif(n, 0, 1)
x2 <- runif(n, 0, 1)
x3 <- runif(n, 0, 1)
pi <- asin(1) * 2
f <- 2 * sin(pi * x0)
f <- f + exp(2 * x1) - 3.75887
f <- f + 0.2 * x2^11 * (10 * (1 - x2))^6 + 10 * (10 * x2)^3 * (1 - x2)^10 - 1.396
g<-exp(f/5)
# negative binomial data  
y<-rnbinom(g,size=3,mu=g)
# unknown theta ...
b<-gam(y~s(x0)+s(x1)+s(x2)+s(x3),family=negative.binomial(1))
plot(b,pages=1)
print(b)
b<-gam(y~s(x0)+s(x1)+s(x2)+s(x3),family=neg.bin(1)) # unknown theta
plot(b,pages=1)
print(b)
# known theta example ...
b<-gam(y~s(x0)+s(x1)+s(x2)+s(x3),family=negative.binomial(3),scale=1)
plot(b,pages=1)
print(b)
# Now use "sqrt" link available in negative.binomial (but not neg.bin)
set.seed(1)
f<-f-min(f);g<-f^2
y<-rnbinom(g,size=3,mu=g)
b<-gam(y~s(x0)+s(x1)+s(x2)+s(x3),family=negative.binomial(1,link="sqrt")) 
plot(b,pages=1)
print(b)