v1.3.23 first commit. Added tests for transform-apply bug

Tests will catch the obvious case. Needed added tests to catch edge
cases, for instance, when there is only one sample or one OTU, does it
still behave as expected? Should probably also add support/warnings
when user-provided functions do not return a vector with the same
number of elements as ntaxa(physeq).
Once this is in place, need to re-run `R CMD check phyloseq`
v1.3.23 better fix for transform_sample_counts, and most tests
v1.3.23 passes all tests, and new examples added to doc
Merge pull request #187 from joey711/transform-apply-fix

v1.3.23 Fixed bug for specific orientation in transform_sample_counts, tests/doc added

Fixes:
https://github.com/joey711/phyloseq/issues/186