communityPGLMM.plot.random.effects doesn't work well

[arives]

When you have a lot of matrices, all the plotting region is filled by the legend bar. I suggest going back to using image() [since I never found a way to remove the legend bar in lattice]. And I don't like color.

Also, I liked the name communityPGLMM.plot.re as shorter. In fact, we could even shorten communityPGLMM to comPGLMM. That might be a nice way to distinguish it form the version in pez. Right now, the new version is pretty different.

[daijiang]

Tony,
To suppress the legend bar, set colorkey = FALSE. The nice thing about lattice and ggplot2 is that it will be so much easier to combine and custom plots later... In terms of color, I think you can use col.regions argument to use your own color scheme.

I can change the function name to communityPGLMM.plot.re.

The main reason I still used communityPGLMM is to be able to be compatible with pez. If we decide to short the name, I would go further and use something like cPGLMM or just PGLMM.

[daijiang]

@arives now both communityPGLMM.plot.re and communityPGLMM.show.re available in phyr. plot.communityPGLMM will plot observed values, and optionally predicted values (predicted = FALSE by default).