Past exam of the mathematics course of the University of Cambridge / 2024 / iii / Paper 218 / 1

Write $Y_i$ for the colony count and $d_i$ for the dose on plate $i$. The first fit is the Poisson regressionThus its log-likelihood isThe Poisson deviance relative to the saturated model iswhere a summand with $y_i=0$ uses $0\log 0=0$.

At dose zero the fitted expected value is $e^{{\hat{\beta }}_0}=e^{3.321995}\simeq 27.72$ eradicated colonies. Increasing dose by one unit multiplies the fitted mean by $e^{{\hat{\beta }}_1}=e^{0.0001901}\simeq 1.000190$; for example, an increase of $100$ units multiplies it by about $1.0192$. The positive fitted effect is small and its displayed two-sided $p$-value, $0.105$, gives little evidence against a zero dose coefficient.

For the Poisson variance function $V(\mu )=\mu$, the code computes the Pearson chi-squared statisticand the Pearson dispersion estimatorThe first quantity measures goodness of fit; the second estimates the dispersion parameter, which equals one in a correctly specified Poisson regression. A standard rough calculation substitutes the residual deviance for the Pearson statistic and givesIf the reported upper-tail probability $4.908651\times 10^{-11}$ is inverted numerically, the actual Pearson statistic used by the code is about $82.93$, giving $\hat{\varphi }\simeq 5.18$. Either calculation reveals severe overdispersion.

The Pearson goodness-of-fit test has null hypothesis that the independent counts follow the fitted Poisson regression, in particular $\mathrm{Var}(Y_i\mid d_i)={\mu }_i$, against the alternative that the model does not fit; in this setting the scientifically relevant direction is overdispersion, $\mathrm{Var}(Y_i\mid d_i)>{\mu }_i$. Under the null, $X_P^2$ is approximately chi-squared distribution with $16$ degrees of freedom. Its tiny $p$-value decisively rejects the Poisson variance assumption.

The negative binomial regression keeps the logarithmic mean model but allows $\mathrm{Var}(Y_i\mid d_i)={\mu }_i+{\mu }_i^2/\theta$. It improves the residual deviance from $75.806$ to $18.011$, close to its $16$ residual degrees of freedom, and lowers the Akaike information criterion from $172.34$ to $141.66$. Both comparisons strongly favour the negative-binomial fit, although its dose coefficient remains statistically insignificant.

The variance $\mu +{\mu }^2/\theta$ approaches the Poisson distribution variance $\mu$ when $\theta \to \infty$. Equivalently, with $\alpha =1/\theta \ge 0$, the Poisson model is the boundary value $\alpha =0$. The usual Wilks theorem for a likelihood-ratio test assumes that the null parameter is an interior point of a smooth parameter space, so comparing the statistic with an ordinary ${\chi }_1^2$ law is invalid here.

A valid parametric bootstrap proceeds as follows. First fit the null Poisson model and retain its fitted means ${\hat{\mu }}_i$. For each bootstrap repetition $b=1,\dots ,B$, independently simulateusing the original doses, refit both the Poisson and negative-binomial models to that simulated data, and calculateFor the observations calculate the analogous $T_{obs}$. The bootstrap $p$-valueuses the null distribution with its boundary and finite-sample fitting behaviour automatically reproduced. A large $B$ controls the Monte Carlo error of this estimate.