Fix bug that meant non-linear path factors weren't stored in output of
splatSimulatePaths

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@125902 bc3139a8-67e5-0310-9ffc-ced21a209358

Hopefully fixes error when building on windows

* Fix to match Bioconductor version of scDD
* Add logo to repository

* Bump R version to 3.4
* Add row, col names to matrices

* Add locfit to NAMESPACE
* Add return values to logistic, showPP documentation
* Delete commented mergeParams function
* Switch to aes_string in compareSCESets
* Add examples to getParam, setParam
* Adjust line lengths
* Adjust indentation

The last SCESets was been added multiple times
instead of adding each one onces.

Fixes #4

Zero means was causing NAs in counts

Some parameters weren't being passed from SCESet method to matrix
method