add categoryCompare


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@64432 bc3139a8-67e5-0310-9ffc-ced21a209358
first version bump prior to creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
bumped version numbers after creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
removed anyTesting.R

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@64787 bc3139a8-67e5-0310-9ffc-ced21a209358
added readme for github page
tell .Rinstignore to ignore the markdown readme file
added relevant links to readme.md
added readme for github page

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68079 bc3139a8-67e5-0310-9ffc-ced21a209358
tell .Rinstignore to ignore the markdown readme file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68080 bc3139a8-67e5-0310-9ffc-ced21a209358
added relevant links to readme.md

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68081 bc3139a8-67e5-0310-9ffc-ced21a209358
switched the graph output

Based on interactions with Paul Shannon, decided the graph output should be a directed graph. Also went from 2 for loops creating an adjacency matrix to an sapply on a matrix of comparison indices. This should be quite a bit faster.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68082 bc3139a8-67e5-0310-9ffc-ced21a209358
Can successfully handle zero order graphs

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68083 bc3139a8-67e5-0310-9ffc-ced21a209358
single node graphs also handle well

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68084 bc3139a8-67e5-0310-9ffc-ced21a209358
Removed error in createGraph2 due to bad variable name.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68085 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of github.com:rmflight/categoryCompare
added the 'addEdge' method from graph

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@68131 bc3139a8-67e5-0310-9ffc-ced21a209358
The 'annotation' and 'annotation<-' generics have been moved from Biobase
(2.17.8) to BiocGenerics (0.3.2). All packages that 'setMethods' on these
generics import them from BiocGenerics.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@69535 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump all packages before creating 2.11 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
bump package versions after creating 2.11 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/categoryCompare@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
added ORCID to description