Refactor R code so that non-user functions have dot prefix

[poonlab]

Refactor R code so that non-user functions have dot prefix

[MathiasRenaud]

All occurrences of non-user function in solveODE.R (get.times) were updated to have dot prefix. As for removing these functions from the package metadata, does that involve removing from NAMESPACE?

[ArtPoon]

Yes. Please check whether anything gets broken by re-installing the package with `R CMD INSTALL pkg` and running the unit test suite.

…

On May 10, 2017, at 3:52 PM, MathiasRenaud ***@***.***> wrote: All occurrences of non-user function in solveODE.R (get.times) were updated to have dot prefix. As for removing these functions from the package metadata, does that involve removing from NAMESPACE? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[MathiasRenaud]

After making the changes, I ran the test suite and got the error: ERROR in test.get.times: Error in func() : could not find function ".get.times". So I added the line export(.get.times) back to NAMESPACE and ran the test suite again with no issues.

[gtng92]

Did the same for .export(.to.newick) export(.preprocess.tree) and export(rescale.tree). Test suite works (save for nLTT)

[ArtPoon]

Right, I forgot that to run the unit tests we have to expose those functions in namespace.

…

Sent from my iPhone

On May 10, 2017, at 5:20 PM, gtng92 ***@***.***> wrote: Did the same for .export(.to.newick) export(.preprocess.tree) and export(rescale.tree). Test suite works (save for nLTT) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[ArtPoon]

We'll leave the . non-user functions in namespace for unit testing but not add these functions to documentation with the implicit understanding that these are not meant to be directly called by the user.

[ArtPoon]

Close issue when prefixes have been added on current set of functions.