bump versions prior to creating BioC 2.13 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
bump version after release branch has been created

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore@81690 bc3139a8-67e5-0310-9ffc-ced21a209358
rename inst/doc to vignettes and bump version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore@82430 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge commit '4e6bb11244483d655f118ab769c992d08228b6a7' into trunk
merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore@83026 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge commit '29290ff3debbb81ffb681f204899dacdef4b1ea5' into trunk
merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore@83027 bc3139a8-67e5-0310-9ffc-ced21a209358
Added transformation='linearize-with-PnG-scaling' as a new read.FCS transformation option in order to facilitate Gating-ML 2.0 compliance. This option does linearization and also divides values by gain ( values) for parameters stored on linear scale.
Minor fix for decimal $PnG values; also added some comment.
Fixed the evaluation of the Compensated Parameter, the code there was wrong and went probably unnoticed for some time. The wrong code is
t(solve(spillMat)[parameter,]%*%t(df[,cols]))
The same issue existed in the compensate method (see flowFrame-accessors.R) and it has been fixed by "phd" long time ago. The new code is
tmp <- (df[,cols] %*% solve(spillMat))
colnames(tmp) <- cols
tmp[,parameter]
That is the same as tmp <- t(solve(t(spillMat))%*%t(df[,cols]))
which is essentially what the compensate method is doing.
Changed the implementation of the Gating-ML 2.0 ASinH transformation calculation.
The previous 'direct' implementation seems to work just fine for me; however,
Wayne Moore suggested, that this calculation may be more stable:
(it is giving the same results based on my tests)
Merge branch 'FCS-PnG-based-scaling-support' of github.com:jspidlen/flowCore into test
fix conflicts
Merge branch 'better-asinh-implementation' of github.com:jspidlen/flowCore into test
Moved hyperlog license notice in order to avoid R CMD build/check warning.
Merge branch 'move-hyperlog-notice' of github.com:jspidlen/flowCore into test
Merge commit '476fa6f2f2fe3cb0ce9bf54691f79263172d1f29' into trunk