**Bluecology blog**, and kindly contributed to R-bloggers)

# Checking residual distributions for non-normal GLMs

## Quantile-quantile plots

If you are fitting a linear regression with Gaussian (normally

distributed) errors, then one of the standard checks is to make sure the

residuals are approximately normally distributed.

It is a good idea to do these checks for non-normal GLMs too, to make

sure your residuals approximate the model’s assumption.

Here I explain how to create quantile-quantile plots for non-normal

data, using an example of fitting a GLM using Student-t distributed

errors. Such models can be appropriate when the residuals are

overdispersed.

First let’s create some data. We will make a linear predictor (ie the

true regression line) `eta`

and then simulate some data by adding

residuals. We will simulate two data-sets that have the same linear

predictor, but the first will have normally distributed errors and the

second will have t distributed errors:

```
n <- 100
phi <- 0.85
mu <- 0.5
set.seed(23)
x <- rnorm(n)
eta <- mu + phi * x
nu <- 2.5
tau <- 3
y_tdist <- eta + (rt(n, df=nu)/sqrt(tau))
y_normdist <- eta + rnorm(n, sd = 1/sqrt(tau))
plot(x, y_tdist)
points(x, y_normdist, col = "red", pch = 16, cex = 0.8)
legend("topleft", legend = c("t-distributed errors", "normally distributed errors"), pch = c(1,16), col = c("black", "red"))
```

Notice how the t-distributed data are more spread out. The `df`

parameter, here named `nu=2.5`

controls how dispersed the data are.

Lower values will give data that are more dispersed, large values

approach a normal distribution.

Now let’s fit a Gaussian glm (just a linear regression really) to both

these data-sets

```
m1_norm <- glm(y_normdist ~ x)
m1_t <- glm(y_tdist ~ x)
```

We should check whether the two models meet the normal assumption, using

the standard ‘qq’ (quantile-quantile) plot:

```
par(mfrow = c(1,2))
plot(m1_norm, 2)
plot(m1_t, 2)
```

These plots compare the theoretical quantiles to the actual quantiles of

the residuals. If the points fall on the straight line then the

theoretical and realised are very similar, and the assumption is met.

Clearly this is not the case for the second model, which is

overdispersed.

We know it is overdispersed because the theoretical quantiles are much

smaller than the actual at the tails (notice how the ends down then up).

The p-values (or CIs if you use them) for `m1_t`

are therefore likely

biased and too narrow, leading potentially to type I errors (us saying

that x affects y, which in fact it does not). In this case we know we

haven’t made a type I error, because we made up the data. However, if

you were using real data you wouldn’t be so sure.

## Doing our own quantile-quantile plot

To better understand the QQ plot it helps to generate it yourself,

rather than using R’s automatic checks.

First we calculate the model residuals (in `plot(m1_t)`

R did this

internally):

```
m1_t_resid <- y_tdist - predict(m1_t)
```

Then we can plot the quantiles for the residuals against theoretical

quantiles generated using `qnorm`

. Below we also plot the original QQ

plot from above, so you can see that our version is the same as R’s

automatic one:

```
par(mfrow = c(1,2))
qqplot(qnorm(ppoints(n), sd = 1), m1_t_resid)
qqline(m1_t_resid, lty = 2)
plot(m1_t,2)
```

I added the `qqline`

for comparative purposes. It just puts a line

through the 25th and 75th quantiles.

## QQ plot for a non-normal GLM

Now we have learned how to write our own custom for a QQ plot, we can

use it to check other types of non-normal data.

Here we will fit a GLM to the `y_tdist data`

using student-t distributed

errors. I do this using the Bayesian package `INLA`

.

```
library(INLA)
data <- list(y=y_tdist, x = x)
mod_tdist <- inla(y ~ x, family="T", data=data,
control.predictor = list(compute = TRUE),
control.family =
list(
hyper =
list(prec = list(prior="loggamma",param=c(1,0.5)),
dof = list(prior="loggamma",param=c(1,0.5))
)
)
)
```

The `family ="T"`

command tells INLA to use the t-distribution, rather

than the Normal distribution. Note also I have specified the priors

using the `control.family`

command. This is best practice. We need a

prior for the precision (1/variance) and a prior for the `dof`

(=

degrees of freedom, which has to be >2 in INLA).

It is sometimes help to visualise the priors, so we can check too see

they look sensible. Here we visualise the prior for the `dof`

, (which in

INLA has a min value of 2):

```
xgamma <- seq(0.01, 10, length.out = 100)
plot(xgamma+2, dgamma(xgamma, 1, 0.5), type = 'l', xlab = "Quantile", ylab = "Density")
```

We don’t really expect values much greater than 10, so this prior makes

sense. If we used an old-school prior that was flat in 2-1000 we might

get issues with model fitting.

Now enough about priors. Let’s look at the estimated coefficients:

```
mod_tdist$summary.fixed
## mean sd 0.025quant 0.5quant 0.975quant mode
## (Intercept) 0.5324814 0.07927198 0.3773399 0.5321649 0.6891779 0.5315490
## x 0.7229362 0.08301006 0.5565746 0.7239544 0.8835630 0.7259817
## kld
## (Intercept) 3.067485e-12
## x 6.557565e-12
```

Good the CIs contain our true values, and the mean is close to our true

value too.

What about the hyper-parameters (the precision and DF)? We need to get

INLA to run some more calucations to get accurate estimates of these:

```
h_tdist <- inla.hyperpar(mod_tdist)
h_tdist$summary.hyperpar[,3:5]
## 0.025quant 0.5quant 0.975quant
## precision for the student-t observations 0.2663364 0.6293265 1.163440
## degrees of freedom for student-t 2.2404966 2.7396391 4.459057
```

The estimate for the DF might be a ways off the mark. That is ok, we

expect that, you need lots of really good data to get accurate estimates

of hyper-parameters.

Now, let’s use our skills in creating QQ plots to make QQ plot using

theoretical quantiles from the t distribution.

First step is to extract INLA’s predictions of the data, so we can

calculate residuals

```
preds <- mod_tdist$summary.fitted.values
resids <- y_tdist - preds[,4]
```

Next step is to extract the marginal estimates of the DF and precision

to use when generating our QQ plot (the quantiles will change with the

DF):

```
tau_est <- h_tdist$summary.hyperpar[1,4]
nu_est <- h_tdist$summary.hyperpar[2,4]
```

Now we can use `qt()`

to generate theoretical quantiles and the

residuals for our realised quantiles:

```
qqplot(qt(ppoints(n), df = nu_est), resids * sqrt(tau_est),
xlab = "Theoretical quantile", ylab = "residuals")
qqline(resids * sqrt(tau_est), lty = 2)
```

Note that I multiply the residuals by the sqrt of the precision

estimate. This is how INLA fits a t-distributed

GLM.

I do the same for the `qqline`

.

Our residuals are now falling much closer to the line. The model is

doing a much better job of fitting the data. You could also calculate

the WAIC for this model and a Gaussian one, to compare the fits. The

t-distributed GLM should have a lower WAIC (better fit).

We can now be confident that our CIs are accurate.

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