Splitting lme residual plot into separate boxplots - r

Question

Using the basic plot function (plot.intervals.lmList) from an lme model (called meef1), I produced a massive graph of boxplots. My vector v2andv3commoditycombined has 98 levels.
plot(meef1, v2andv3commoditycombined~resid(.))
I would like to separate by the grouping values of my variable v2andv3commoditycombined to either graph them separately, order them, or exclude some. I'm not sure if there is code to do this or if I have to extract information from the lme output. If that is the case, I'm not sure what to extract to create the boxplots as extracting the residuals returns only one value for each level. If this is impossible, any advice on how to space out the commodity names would be equally helpful.
Thank you.

Answer 1

For each level of v2andv3commoditycombined, what exactly would you like your Y axis and your X axis to be? Since you're splitting the plots by v2andv3commoditycombined, you obviously can't also use that as one of your axes.
Let's pretend you just want do the traditional residuals on the Y axis and fitted values on the X axis, in a separate plot for each of the 98 levels. You can change the code to do plot whatever it is you actually want to plot.
As per ?plot.lme, you would do something like this:
plot(meef1,resid(.,type='pearson',level=1)~fitted(.,level=1)|v2andv3commoditycombined);
Make sure you stretch out your plot window beforehand so that it's nice and big, otherwise you might get an error saying something about margins. The following might produce a better-looking plot:
plot(meef1,resid(.,type='pearson',level=1)~fitted(.,level=1)|v2andv3commoditycombined,pch='.',cex=1.5,abline=0);
Since it wasn't clear from your question I went ahead and assumed you're interested in the individual level residuals (i.e. how much each datapoint differs from the predicted value given its random variables), and that you have one level of nesting in your random formula. If you want population residuals (i.e. how much each datapoint differs from the average predicted value), change both instances of level to say level=0. If you have K levels of nesting, change them to level=K and good luck.
I also assumed you wanted standardized residuals (because you can use the convenient rule of thumb that absolute values greater than 3 are possible outliers, regardless of what scale the original data are on). If not, see ?residuals.lme for other valid options for the type argument.
Oh, and the name of your variables suggests that you're looking at some sort of financial time series. If so, have a look at ACF(meef1) to see if there is a lot of autocorrelation. If there is, you could remedy it by instead fitting a model where the response (Y) variable is diff(...) the original variable. If you're seeing really skewed residuals, you might consider log-transforming your response variable before taking the diff.