Our original intent was that PythonEmbedInR would differ from PythonInR only in that it would have a private/embedded copy of Python (rather than "connecting" to an already installed copy). However there are a number of changes we've made that we feel should also be in PythonInR. Examples:
Don't convert to primitive those classes that extend primitive.
Convert Python int/long to 'numeric'
This issue covers 'catching up' for current changes. Going forward we should submit pull requests as we make changes to our package.