Transformation and Median for avgdist

[Microbiology]

I addressed issue #242 and #243 by adding an option to transform the count data and calculate median instead of mean. 😄

The updates pass my R command checks.

[jarioksa]

Seems to work like intended. Some minor comments:

• it may be safe to use meanfun <- match.fun(meanfun) before using the meanfun function.
• the function takes now extra arguments (...), but these are ignored. You could use them in output <- apply(afunc, 1:2, meanfun, ...) to allow meanfun with extra arguments, such as trim in mean().
• the use of return is not necessary and we do not have it in vegan unless necessary (i.e., when exiting the function before reaching the end).

[Microbiology]

Thanks for the feedback! :)

I made the suggested revisions and updated the pull request.

[jarioksa]

Fine! Merging now. Thanks for your work!

[jarioksa]

@Microbiology : I made some maintenance tweaks to avgdist and commited them to master as 8a0e3f0. Please check these.

There are several commits, and the commit message are intended to be so verbose that you can judge the reasoning behind the changes. Please check chose if you disagree with the changes.

[Microbiology]

These look great, thanks @jarioksa! :)