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Bioconductor Changlog.
Thu, 21 May 2009
flowClust
small fix to hist() method for subsetting when the object is one-dimensional
flowClust
adding a summarizeFilter method in order to collect the information from the filterResult
flowClust
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowClust
bumping flowClust version to 2.0.4
minor updates to documentation files
a fix to Map.Rd
flowClust
initialization using random partitioning
flowClust
Changed biocViews entry of Statistics to Bioinformatics.
flowClust
modified .ellipse() to get rid of the precision problem arisen due to the large difference in the lengths of the two axes of an ellipse
flowClust
small fix: rectify the problem of not transforming the mu estimates in getEstimates() and the plotting methods when lambda is 1.
flowClust
fixed Rd 2 parser warnings
flowClust
Using pkg-config in configuration to make it easier to build against the GSL library.
flowClust
bulk update; version 2.0
flowClust
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowClust
fixed access to parameters slot which has changed in flowCore
flowClust
fixed access to parameters slot which has changed in flowCore
some changes to cope with recent redefinition of "parameterFilter" class in flowCore (the "parameters" slot now takes a "parameters" object (which is a list) instead of a character vector; changed tmixFilter function and %in% method accordingly)
flowClust
when K takes a vector of values, hier clustering needs to be applied only once since the classification tree is the same for all values of K
flowClust
Major update: enable K to take a vector of values, and include the option of running short EMs for random initializations
- add classes flowClustList and tmixFilterResultList
- define all the utility and plotting methods for these two classes
- include the criterion replacement method
- add optional arguments criterion, B.init, tol.init to flowClust()
- update all man pages and the vignette
- bump version to 1.7.0
NOTE: there is a mysterious bug found when defining the tmixFilterResultList class. The data part cannot be assessed directly by typing the object name; it has to be assessed through the .Data slot. Tracked down to find that it may be related to the multipleFilterResult or AssayData class it extends.
flowClust
Major update: enable K to take a vector of values, and include the option of running short EMs for random initializations
- add classes flowClustList and tmixFilterResultList
- define all the utility and plotting methods for these two classes
- include the criterion replacement method
- add optional arguments criterion, B.init, tol.init to flowClust()
- update all man pages and the vignette
- bump version to 1.7.0
NOTE: there is a mysterious bug found when defining the tmixFilterResultList class. The data part cannot be assessed directly by typing the object name; it has to be assessed through the .Data slot. Tracked down to find that it may be related to the multipleFilterResult or AssayData class it extends.
flowClust
minor changes to split and tmixFilter man pages
added criterion function;
made changes to man pages and vignette according to Florian's suggestions about the split/Subset method (dropped the select argument, deprecated the split argument);
dropped select argument also for Subset (with signature data.frame/matrix)
flowClust
added criterion function;
made changes to man pages and vignette according to Florian's suggestions about the split/Subset method (dropped the select argument, deprecated the split argument);
dropped select argument also for Subset (with signature data.frame/matrix)
flowClust
fixed (back) the problem of deallocation of PrecisionTmp
flowClust
add criterion()
bumped version number
flowClust
code beautification and fixes for flowCore integration
flowClust
some more updates:
in C code, update YTrans when estimating lambda in M-step instead of in update_z_u() -- just increase efficiency, shouldn't bring changes to outputs
update hist method
minor changes to README, vignette, etc.
flowClust
option for gaussian mixture model
make existing methods adapt to gaussian mixture model
fix minor bugs in density plots
update man pages to reflect recent additions/changes
update getEstimates; includes an approximate variance estimate
flowClust
update getEstimates(); includes an approximate variance estimate
flowClust
update README instructions for Windows users; move README to inst directory
flowClust
update README instructions for Windows users
minor change to Makevars.win
flowClust
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowClust
Changed unprintable character to '.
flowClust
modified namespace - not to import the curv2filter, curv1filter and quadGate classes from flowCore for compatibility with previous versions of flowCore
modified namespace - import only relevant classes and methods instead of the whole namespace from flowCore
flowClust
minor changes in flowClust.c (esp. up_data_z_weight) and BoxCox.C to increase computational efficiency;
compute output covariance matrix (sigma) in C
flowClust
setMethods.R - put back default value in the replacement function
namespace - quotation marks removed
flowClust.c - comment out R_init_flowClust
setMethods.R - remove default value in the replacement function
all for testing only
flowClust
Adds the flowClust package to bioconductor.