Re: [R] glm cannot find valid starting values

From: Dan Bebber <danbebber_at_forestecology.co.uk>
Date: Fri 21 Jul 2006 - 23:22:36 EST

Brian Ripley wrote:

>
> BTW, your example cannot be pasted in as 'sdat' self-references.  It could
> be fixed, but I gave up at that point.
>

Oh dear, I'm very sorry. I forgot to run rm(list=ls(all=TRUE)) before testing.
The corrected code is:

#Data:

S <- c(0, 0, 0, 0, 28, 0, 1, 7, 0, 0, 39, 2, 0, 0, 40, 0, 0, 0, 0,
0, 0, 15, 0, 0, 3, 0, 0, 0, 2, 0, 3, 0, 30, 0, 20, 0, 1, 0, 0,
1, 21, 0, 0, 4, 14, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 3, 0,
2, 5, 0, 0, 0, 0, 0, 0, 0, 25, 0, 5, 0, 0, 0, 1, 0, 1, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 1, 10, 0, 0, 0, 0, 0, 9, 1, 1, 1, 1, 0, 0, 3,
0, 27, 7, 0, 0, 0, 0, 0, 1, 1, 4, 2, 1, 2, 4, 1, 4, 6, 12, 4,
6, 3, 4, 0, 4, 0, 6, 1, 3, 1, 4, 4, 1, 1, 2, 1, 6, 1, 0, 0, 1,
0, 1, 0, 0, 6, 0, 0, 0, 0, 2, 2, 3, 1, 6, 2, 2, 1, 1, 4, 4, 3,
3, 7, 1, 3, 5, 6, 4, 0, 1, 4, 2, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0,
1, 0, 4, 0, 0, 1, 0, 2, 0, 0, 1, 2, 0, 4, 0, 2, 0, 3, 0, 2, 2,
0, 4, 0, 2, 0, 1, 2, 3, 0, 0, 0, 0, 3, 1, 0, 0, 0, 3, 2, 1, 2,
1, 1, 2, 0, 0, 3, 3, 1, 0, 1, 1, 2, 0, 1, 0, 1, 0, 1, 3, 2, 0,
0, 2, 1, 0, 1, 0, 0, 0, 0, 0, 0, 4, 2, 4, 0, 2, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 3, 2, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 4, 1, 0, 0, 1) M <- 620+c(0,cumsum(S[-328]))
sdat <- data.frame(S,M)
#S is the number of N individuals that irreversibly change state in a time
#interval t. The data provided are a subset of the full data set.
#M is the cumulative sum of individuals that have changed state up to t-1.
#Assume that the rate of state change is constant (S ~ kM), but the
#distribution of S is clustered.
#N can be estimated by fitting:
qpglm <- glm(S ~ M, family = quasipoisson(link = identity), sdat) summary(qpglm)
N.est <- -coef(qpglm)[1]/coef(qpglm)[2]
N.est
#i.e. x-intercept is minus intercept/slope
#To estimate confidence limits on N.est, fit models without intercept to
#N.est - M + x, where x is an integer. The model will have the lowest
deviance
#when x = 0.
x <- 0
Mdif <- N.est - M + x
qpglm2 <- glm(S ~ -1 + Mdif, family = quasipoisson(link = identity), sdat) summary(qpglm2)
#Use analysis of deviance to estimate confidence limits on N.est:
disp <- summary(qpglm)$dispersion
dfres <- df.residual(qpglm)
dev.res <- deviance(qpglm)
#From MASS4, p. 210, assume that changes in deviance scaled by
#dispersion as |x| increases have an F distribution
dev.crit <- dev.res+qf(0.95,1,dfres)*disp dev.crit
#values of x for which the deviance = dev.crit give approximate 95%
confidence limits
#on N.est.
#The error occurs when x <= -91.7:
x <- -91.7
sdat$Mdif <- N.est - sdat$M + x
strt <- coef(glm(S ~ -1 + I(Mdif+1), family = quasipoisson(link = identity), sdat))
qpglm2 <- glm(S ~ -1 + Mdif, family = quasipoisson(link = identity), start=strt, sdat)

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