Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.
This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.
This list is also available as an RSS feed (devel branch), and RSS feed (release branch)
Version bump
Bug fixed: CopyNumberPlots requires additional parameter
version bump to 1.1.1
specify experimenthub version and remove R version
update vignette with bioc url
remove archr2MAE and update link
version bump
remove commented codes
fix vignette for windows
Fixed unit test error due to update in gene annotations
1.1.3
Utest fix
bumped the package version v0.99.10
0.99.3
Update viableIDs.rda for release 3.18
Add files via upload
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Merge branch 'master' into devel
cite issue in news entry
fix stupid generated - close #25
new gh devel version
Add files via upload
versbump
.createAnnotation.R updated for epicV2. fixes adjustedDasen
epicv2clean rox manual
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Merge remote-tracking branch 'origin/master'
Update DESCRIPTION
Update Hclustering.R
Update corr_heatmap.R
Update README.md
Update DESCRIPTION
Update README.md
Update DESCRIPTION
Add files via upload
Delete man directory
bumped the package version v0.99.9
version bump
small bug fix
updates: - documentation update about output values - output variable/names parameter added to many functions - validity checks for spatialCoords are added to related functions - for loops are gone.
fix: remove eval=FALSE & bump version
bumped the package version v0.99.8
bump version to trigger build
update the version of scvi-tools in use, along with pandas, matplotlib, scanpy and numpy (but keep pandas < 2.0.0)
remove .o files
revised according to the review comments
feat: additional tests
bumped the package version v0.99.7
- In extremeGradientBoostingPredictInterface, expand the test data set to one-hot encoding format before subsetting it by selected features from training.
edgeR 3.99 - Lizhong Chen's updates to glmQLFit() including changes to C code.
feat: further improvements
add bfc argument, use temp location for testing
update gitignore file
com
increase version number
re-conf
resolve conflict
pull upstream to sync
version bumo
version bump
add more example
version bump
feat: readme update
edited vignette
edit some examples
feat: fixes
version bump
changes path
man files
edit like
edited path
Versio bump to trigger build
edit test input
edit the test set
bugfix Signed-off-by: Zongli Xu <xuz@lxd-02010942.niehs.nih.gov>
feat: minor update
Merge pull request #111 from rcastelo/new_api New API for GSVA based on method-specific parameter objects
Improving consistency in the documentation of help pages and vignette in the new API
Merge pull request #110 from axelklenk/new_api migrate vignette to new API; work around eSet/annotation() problem
migrate vignette to new API; work around eSet/annotation() problem
Merge pull request #109 from axelklenk/new_api add slots and constructor arguments for 'annotation', 'minSize', and …
add slots and constructor arguments for 'annotation', 'minSize', and 'maxSize' to parameter objects; remove the latter two from gsva()
Merge pull request #108 from axelklenk/new_api Add argument 'assay' to parameter objects to make example(gsva) work.
Add argument 'assay' to parameter objects to make example(gsva) work.
Fixed documentation and other stuff
Merge pull request #107 from axelklenk/new_api add code and docs for deprecation of old interface; add docs for new …
add code and docs for deprecation of old interface; add docs for new interface; eliminate argument parallel.sz; fix .gitignore
Merge pull request #106 from axelklenk/new_api New API -- now including man/*.Rd files
no idea what git is doing to me here...
fix .gitignore to have man/*.Rd files properly tracked.
fix .gitignore to have man/*.Rd files properly tracked.
Merge pull request #105 from axelklenk/new_api New API implementation as discussed
Merge branch 'dev_new_api' into new_api
New API first version, more documentation and unit tests to be added; existing code using the 'old' API should continue work.
Merge pull request #104 from axelklenk/new_api Restore original generic and signature for gsva(); add show methods for parameter objects
Merge branch 'dev_new_api' into new_api
add show methods for parameter classes.
restore previous gsva generic and method signatures
Merge pull request #103 from axelklenk/new_api New api
Merge branch 'dev_new_api' into new_api
Initial implementation of New API for all methods and gene set containers and almost all data containers. (TODO: continue refactoring, document and test.)
add class unions for new_api next step
Merge branch 'dev_new_api' into new_api
add regression test based on the vignette and an output file for comparison generated by the released version
add an experimental regression test based on the vignette -- work in progress!
add rnorm() and rpois() to NAMESPACE imports and save 'stats::' when using them to generate test data
Merge pull request #102 from axelklenk/new_api New api update
add unit tests for dispatch on unnamed arguments.
two minor modifications to make the remaining WARNING and NOTE disappear.
document new gsva methods to get rid of check warnings.
add unit tests for dispatch by param objects; rename param objects to comply to upper camel case convention.
add matrix/list methods for zscore, ssgsea, gsva; modify to use param for internal dispatch and parameters. Testgit add R/gsvaNewAPI.R
add 'param' argument (as missing) to all 'gsva' S4 methods to silence warnings during check. add roxygen2 documentation for newAPI methods.
add S4 method for dispatching on PLAGE parameter object
add automated generation of test input data
add simple unit tests for method-specific parameter objects and their constructors
fix --as-cran NOTE on using title case in the package title :-)
merge in a couple of unrelated fixes from devel
fix bug in gsvaParam contructor (add match.arg for kcdf, duh); sync slots and parameters documentation for gsvaParam class and constructor
Merge pull request #98 from rcastelo/96-gsva-method-parameter-class-and-constructor fix oversight in gsvaParam definition causing a Check error
fix oversight in gsvaParam definition causing a Check error
Merge pull request #97 from rcastelo/96-gsva-method-parameter-class-and-constructor 96 gsva method parameter class and constructor
Merge branch '96-gsva-method-parameter-class-and-constructor' of github.com:rcastelo/GSVA into 96-gsva-method-parameter-class-and-constructor
add gsvaParam class and constructor with argument names and documentation as before; switch from camel case to underscore names for getters (ssgseaParam and gsvaParam); and don't forget to update NAMESPACE
add gsvaParam class and constructor with argument names and documentation as before; switch from camel case to underscore names for getters (ssgseaParam and gsvaParam)
Merge pull request #95 from rcastelo/85-ssgsea-method-parameter-class-and-constructor 85 ssgsea method parameter class and constructor
... and don't forget various updates to .gitignore
finalize ssGSEA; remove allGenerics.R and, on second thoughts, make ssgseaParam getters *functions* instead of methods
Merge pull request #94 from rcastelo/devel new_api sync to devel, 2nd attempt
move constructors from allClasses.R to method-specific R files; add class definition, constructor and two get methods for ssGSEA to fix #85; add generics for get methods to new file allGenerics.R
Merge pull request #84 from rcastelo/78-plage-method-parameter-class-and-constructor add PLAGE method parameter class and constructor; modify CITATION to …
add PLAGE method parameter class and constructor; modify CITATION to work with both latin1 and UTF-8 encodings
Merge pull request #83 from rcastelo/73-zscore-method-parameter-class-and-constructor 73 zscore method parameter class and constructor
Delete register_cmethods.o Had been added by accident.
Delete ks_test.o Had been added by accident.
Delete kernel_estimation.o Had been added by accident.
Delete GSVA.so Had beed added by accident.
Merge pull request #82 from rcastelo/devel merge in changes to devel
fix issue #73: add zscore method parameter class and constructor (and a virtual superclass)
bumped the package version 0.99.6
1.1.2
datasets Rd
version bump 1.41.4
add unit tests for keggCompounds
Add man page for keggCompounds function
Rename function for getting list of compounds from pathway
Fix indentation error
Add function for getting compound list from pathway
1.1.1 Merge remote-tracking branch 'upstream/devel' into devel # Conflicts: # DESCRIPTION
0.99.11
version bump 1.41.3
remove escaped #s in Rd file
remove test_KEGGREST_package.R file
version bump 1.41.2
add stop_for_status in .get.kegg.url
version bump 1.41.1
update NEWS
using httr always with default - rename function to .get.kegg.url
Merge pull request #22 from CogDisResLab/devel fix: correct the url parsing
fix: correct the url parsing
feat: updated test
tweak help
version bump and update news
update vignettes - exclude large data downloads from cache - add example data to internals for testing / vignette - better 0 results handling
bump version
results man page fix, resolves #85
Merge pull request #113 from Appsilon/dev Main <- Dev
Merge pull request #125 from Appsilon/anirban.bump-version Anirban.bump version
Merge pull request #121 from Appsilon/anirban.better-vignettes Anirban.better vignettes
bump version
Merge pull request #116 from Appsilon/e2e-tests E2e tests
fix: spellings
fix: broken links and library calls
Merge branch 'dev' of github.com:Appsilon/shiny.gosling into e2e-tests
feat: Simplifying script for running tests (#120) * feat: Simplifying script for running tests * chore: Adding optparse * Update tests/run_cypress_tests.sh Co-authored-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com> * fix: Adding folders * style: lintr * fix: Adding run_example_app helper script * fix: Moving e2e folder --------- Co-authored-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
fix: add ggbio to wordlist
fix: revert example changes
fix: add new words to wordlist and arrange them alphabetically
docs: improve and add vignette
docs: add and improve vignettes
docs: add vignette with explanation of multivec data
Merge pull request #118 from Appsilon/anirban.vcf-vignette Anirban.vcf vignette and examples
fix: reverse change of library to require
fix: remove BiocManager from description
fix: spellings
fix: spelling errors
fix: update wordlist
fix: circos vcf example
fix: add more description to VCF.Rmd
fix: add more descriptions
Update inst/examples/circosVcfData/app.R Co-authored-by: Federico Rivadeneira <federivadeneira@gmail.com>
fix: add and update descriptions
fix: change library to require
fix: Incrementing timeout for screesnhots
fix: Removing unused job
fix: Removing unused script
fix: Passing port as options
fix: specifying IP
fix: typo
fix: conf
fix: set ci timeout to 60m
try: pak version stable
fix: rename example
fix: rename example
fix: rename example
fix: examples
fix: replace Visualising with Visualizing
fix: typo
fix: set eval=FALSE for all vignettes
fix: update decription
fix: description
fix: add genomic packages
fix: circos spelling
fix: lints
fix: set run-app to eval=FALSE and add images of apps
feat: add circos plots and sessionInfo
fix: ci syntax
fix: ci
fix
feat: Ensuring that the script returns when a test fails
fix: Adding .lock file
feat: adding CI
fix: Updating README
fix: Removing hardcoded port
feat: Adding readme
feat: Adding port
chore: sorting
chore: reordering
fix: Removing
feat: Adding threshold at 5 percent
fix: Avoid appending
Merge pull request #117 from Appsilon/anirban.fix-delection-spelling fix: deletion spelling is wrong: delection
Merge branch 'dev' into anirban.fix-delection-spelling
fix: deletion spelling is wrong: delection
fix: adding paths
feat: adding script to run all of the tests
tests: Adding tests
tests: Adding sarsCov
feat: Adding template for code generating scripts
tests: Adding tests for ruleMarks
tests: Adding tests for lineChart
feat: adding multitrack
feat: Adding pointplot
feat: adding ideogram
feat: Adding script to create testfiles
feat: Adding circularVisualEncoding test
chore: empty line
feat: Adding snapshot tests for areachart
feat: Adding tests and scripts for barchart
feat: Adding R script for barchart example
fix: Specifying port
fix: Updating screenshots https://github.com/cypress-io/cypress/issues/3324#issuecomment-542414532
chore: Adding cypress/videos
fix: Updating script running tests
fix: removing commented code
fix: Revert accidentally pushed to dev
feat: Adding R scripts
feat: registering plugin
feat: Adding e2e test for circularLinearWithBrush example
feat: Adding scripts
feat: adding plugins
chore: adding cypress paths
chore: Adding cypress paths
Merge pull request #108 from Appsilon/vedha.milestone-1-changes Improving the usage of csv data and adding a way to use a GRanges object as source
Merge pull request #110 from Appsilon/anirban.examples fix: add bar chart, line chart, point plot and ideogram example
Merge pull request #112 from Appsilon/anirban.fix-lints fix: lints
fix: remove renv and proj files
fix: update doc
fix: lints and spellings;
fix: update documentation
fix: add documentation to genomicFieldsToConvert; remove deprecated code;
fix: rename app files to app.R
fix: lints
fix: add documentation for genomicFieldsToConvert
feat: add rule mark chart
feat: add area and text chart example
fix: add bar chart, line chart, point plot and ideogram example
fix: more lints
fix: lints
fix: lints
fix: indent
revert: use the older RoxygenNote
Merge pull request #109 from Appsilon/anirban.plot-csv fix: csv files copy to .gosling
fix: add mode = "wb" for win
add: method = "auto"
fix: set core.longpaths
fix: remove fread
fix: install R.utils
fix: add repo
fix: install data.table
try: fread
fix: add gzfile
fix: print path
fix: try normalizePath
fix: shorten file name for windows
fix: remove # nolint
fix: use link shortner
fix: update documentation
fix: add utils:: to read.csv
fix: add documentation for missing parameters in track_data_gr
fix: add documentation for new functions
fix: csv files copy to .gosling
chore: have a default example as NA so just calling run_example() would display examples
chore: remove unused package dependency and move GenomicRanges to suggests
feat: adding a vignette for using a GRanges object in gosling
chore: making the print.gosling invisible and making the print method consistent
chore: building document and fixing R CMD checks
feat: adding a data wrapper for csv and GenomicRanges object Changes: * The use_gosling now adds a static resource directory .gosling to save local data and serve them * The gosling component has a shiny and gosling class with a print.gosling function * fix some lint errors
Merge branch 'main' into dev
Merge pull request #107 from Appsilon/add-code-coverage-check ci: Add code coverage check to the CI.
ci: Add code coverage check to the CI.
Merge pull request #106 from Appsilon/update-appsilon-readme-section Update appsilon readme section
chore: Update WORDLIST.
chore: Update Appsilon section in the README.
Merge pull request #92 from Appsilon/fix.renderGosling fix: Using renderReact
style: lintr, spellcheck
docs: Updating
docs: Updating docs
Merge branch 'fix.renderGosling' of github.com:Appsilon/shiny.gosling into fix.renderGosling
fix: Removing unneeded folder
Merge branch 'dev' into fix.renderGosling
fix: Using renderReact
Merge pull request #85 from Appsilon/add-cross-domain-ga-tag chore: Add second GA tag.
fix: Fix quotation marks.
chore: Add second GA tag.
Moved the source repository to TojalLab Fixed issue when running with fixed signatures matrix Reduced the maxeval time in rare cases when there is no convergence
removed build/ folder
removed build/ folder
fix: fix issue #302 - Allow optional parameters (...) to avoid errors if `filterFourierTransformArtefacts` is combined with another peaks function.
Merge remote-tracking branch 'upstream/devel' into devel
Add doi for source paper.
doc: add orcid for henning too
doc: add orcid for k wright
fix: q2 only returned result of last iteration when using nruncv>1
fix: robustSvd use default l1 coef when all input data missing Can happen when data is small and norms become small. If so return zero.
bump x.y.z version to odd y after creation of RELEASE_3_10 branch
bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
fix: R2VX was based on unscaled residuals Gave wrong results if matrix scaled within PCA function.
bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
bumpversion: patch release with doc
doc: add ggplot example
chore: remove lint
chore: use rbuildignore
refactor: remove lint in package repo
chore: update output for new roxygen version
chore: ignore binaries
bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
replace BiocInstaller biocLite mentions with BiocManager
bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
bump x.y.z versions to odd y after creation of 3_5 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
bump x.y.z versions to even y prior to creation of 3_5 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
bump x.y.z versions to odd 'y' after creation of 3_4 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@122712 bc3139a8-67e5-0310-9ffc-ced21a209358
bump x.y.z versions to even 'y' prior to creation of 3_4 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
bump version after creating 3.3 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@117081 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump versions prior to creation of 3.3 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@117079 bc3139a8-67e5-0310-9ffc-ced21a209358
add example for ggplot From: Henning Redestig <henning.red@gmail.com> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@113107 bc3139a8-67e5-0310-9ffc-ced21a209358
not kept up-to-date anymore From: Henning Redestig <henning.red@gmail.com> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@112639 bc3139a8-67e5-0310-9ffc-ced21a209358
to try a git-svn commit
tons of changes from git git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@112623 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumped version number of all packages after creation of 3.2 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumped versions of all packages prior to creating 3.2 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@109589 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump versions in trunk after creation of 3.1 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@102594 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump versions prior to creating 3.1 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@102591 bc3139a8-67e5-0310-9ffc-ced21a209358
Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit. Commit information: Commit id: fcea96afcecf5f1c3613d343c2ada180d4a42659 add variable specific cross-validation Committed by: Henning Redestig Author Name: Henning Redestig Commit date: 2015-02-07 12:32:03 +0100 Author date: 2015-02-07 12:32:03 +0100 git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@99185 bc3139a8-67e5-0310-9ffc-ced21a209358
Commit made by the Bioconductor Git-SVN bridge. Consists of 4 commits. Commit information: Commit id: 08b7fc9456072ec456fa2dd1c02cc52443d4423c continued cleanup Committed by: Henning Redestig Author Name: Henning Redestig Commit date: 2014-11-20 00:06:27 +0100 Author date: 2014-11-20 00:06:27 +0100 Commit id: b59e61f4c08517259050bfb6c55125d3940bdbc4 Merge branch 'master' of https://github.com/hredestig/pcaMethods Conflicts: DESCRIPTION Committed by: Henning Redestig Author Name: Henning Redestig Commit date: 2014-11-17 22:11:59 +0100 Author date: 2014-11-17 22:11:59 +0100 Commit id: fdd14fbf6f8047ebc2dc295bb2614e56a8569d91 squash! cleanup action Committed by: Henning Redestig Author Name: Henning Redestig Commit date: 2014-11-17 22:09:25 +0100 Author date: 2014-11-17 22:09:25 +0100 Commit id: d29a57cde2c8d1bf6efcd1c5404033f0c597a155 cleanup action - stop using Makevars scripts as new Rcpp does not need them - get rid of R cmd check warnings Committed by: Henning Redestig Author Name: Henning Redestig Commit date: 2014-11-17 21:47:24 +0100 Author date: 2014-11-17 21:46:13 +0100 git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@96928 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumping versions after creating 3.0 release branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump package versions prior to creating the 3.0 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@95439 bc3139a8-67e5-0310-9ffc-ced21a209358
Second version bump after creating 2.14 release branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
First version bump prior to creating 2.14 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@88838 bc3139a8-67e5-0310-9ffc-ced21a209358
Commit made by the Bioconductor Git-SVN bridge. Consists of 3 commit(s). Commit information: Commit id: a6284fd51282c74c8156434ceee8688cf8f9d084 Commit message: add llsImpute and llsImputeAll to the all methods to make it work with kEstimate Committed by Henning RedestigCommit date: 2014-03-12T22:33:22+01:00 Commit id: cd00c5e11215bb49b0b35808476b8faa117360a2 Commit message: use na.rm=TRUE for weightedMedian for proper handling of missing values in robustPca Committed by Henning Redestig Commit date: 2014-03-12T22:34:33+01:00 Commit id: 3c515ce2ce739b2f931d314bc378eaff6174bee4 Commit message: bump versin Committed by Henning Redestig Commit date: 2014-03-24T22:11:48+01:00 From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@87810 bc3139a8-67e5-0310-9ffc-ced21a209358 </pre> </div> Package: pcaMethods
Commit: 91b14f7010ad8d21c5eb715c432de361ae8b8091
Author: s.arora <s.arora@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-04 22:12:21 +0000
Commit message:
modify to new biocViews to DESCRIPTION file git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@87035 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 9fb822772ef756fe3ff34f2e73549eded5feb8db
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-02-04 18:07:39 +0000
Commit message:
bumped version as all packages that depend on Rcpp must be rebuilt git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@86058 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 5339af4dd516227c2d29fd9ac41f3a4fceeba841
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-12-01 12:26:56 +0000
Commit message:
switch to ISNAN for c++ compatbility git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@83778 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 1e12da7d21c6b72f8e31815dbd46b4851ef78935
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-10-14 21:47:19 +0000
Commit message:
bump version after release branch has been created git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@81644 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 6227b7c294fadbf3ae4ec100836dde4590d0b4bc
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-10-14 21:29:21 +0000
Commit message:
bump versions prior to creating BioC 2.13 branch git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@81642 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: a356662523247289d14dd59ce9fef3db3654c8ce
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-04-03 22:06:11 +0000
Commit message:
Bump y in version x.y.z to odd number in devel git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@75270 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 01fe07daa6fa9c7bfdcb52e568cf56631435b046
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-04-03 21:32:27 +0000
Commit message:
bump y of x.y.z version number for BioC 2.12 release git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@75263 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 0943dd6dbafba79cb3b2455a1b83d6a87ff56d71
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2013-03-12 21:43:34 +0000
Commit message:
remove wrong warning about missing values in robustPca git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@74244 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: fd0500893ac0aa9c994d66ce02f869313f8b76df
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-10-01 22:43:56 +0000
Commit message:
bump package versions after creating 2.11 branch git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@70052 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 85a3e447d79a2ec403ef0379d2410b44b008aa18
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-10-01 22:16:24 +0000
Commit message:
Bump all packages before creating 2.11 branch. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@70050 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 7d4a347098004e884526adb1edf3c3f2e0787863
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-09-12 18:57:14 +0000
Commit message:
weightedMedian is moving out of aroma.light so switch dependency git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@69380 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 104edc34c9e3f63ac0cc431f7391b1a26be0107e
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-18 17:37:10 +0000
Commit message:
bug in docu git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67793 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 2c8f1eca9b2c21f850195f05df471059586e2e58
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-16 21:04:56 +0000
Commit message:
bug in progressbar for xval git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67696 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 4e991a5788968db030cfbf7d5a3ed6a9c5d842a6
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-10 05:32:59 +0000
Commit message:
summary function repaired git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67495 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: d6ac9a117f83aad56eec34b96c78499905bb097e
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-09 21:46:08 +0000
Commit message:
version info update git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67485 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 23b8806bd0add6b3b920bcda4b25cc9e7b9f7d70
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-09 21:40:36 +0000
Commit message:
now warns if user sets svd for data with missing values git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67484 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 6c4a5ea198e50c903b313f604c642c43070b4787
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-09 06:11:59 +0000
Commit message:
bad args for txtp git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67457 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 145fa2d036aa52af47a223bab3d687ba96389b23
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-07-08 21:37:48 +0000
Commit message:
handle data frames, convert ot data frames' git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67437 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 92c1f22d36fac5f45ac843d5f82a2c04fae72fee
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-06-18 21:54:56 +0000
Commit message:
bump version again git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66810 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: cfdf8f55d14fdcfbdf832aab566bdfd34b32a0bc
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-06-18 21:54:12 +0000
Commit message:
export scores.pcaRes to avoid breaking packages that also load the pls package and thereby mask the S4 method from pcaMethods git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66809 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 4c19a97f6dac5a2c05b8629d4ed5164ab569bcc1
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-06-16 09:59:06 +0000
Commit message:
and re-bump version git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66772 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: fbab93099ca4a5991f5f465de2ed0453afa2ad21
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-06-16 09:58:20 +0000
Commit message:
forgot to commit new file git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66771 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 48b81705fdda9bbd84e0e8b42d9579d3733ec77b
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-06-14 20:54:43 +0000
Commit message:
cleanup, and hopefully better organization of S3/S4 methods git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66741 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: ee5193b393c2bcfed58e0406639cb6d1ecaab346
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-30 22:15:56 +0000
Commit message:
bumped version numbers after creating 2.10 branch git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@64680 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 88836da15aded643266a3efb00583588f280b308
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-30 22:05:02 +0000
Commit message:
first version bump prior to creating 2.10 branch git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@64678 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: f920db61aab026143faa24c48d014bab07283083
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-09 22:58:23 +0000
Commit message:
import residuals from BiocGenerics git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@63704 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 1be2ecc40ac4593940c1fe14d6d997ecadffaa7d
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2012-03-05 19:53:55 +0000
Commit message:
added setGeneric(residuals) git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@63492 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: e80d2b2b8d0fa78d75b7588a51999be2da1218ce
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-10-31 23:12:28 +0000
Commit message:
version bump for start of 2.10 development cycle git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@59924 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 9f8e182c665c151c4814611dfbc17939a31e43b2
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-10-31 22:59:03 +0000
Commit message:
bumped package version numbers prior to creating 2.9 branch git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@59920 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 61fb07debed8877271ee9fc1d2845da4a85a4361
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-05-31 21:32:08 +0000
Commit message:
cope with new roxygen version git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@55927 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: a1fbb1de55450e6978b578fa139a20181468f7e2
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-05-31 20:10:54 +0000
Commit message:
error fix in dmodx function git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@55924 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: bf1519740ccbbfbd47d1f13293ff1e6bcde00967
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-04-13 22:36:43 +0000
Commit message:
Bumped version numbers again for new BioC 2.9 devel cycle. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@54802 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: da17ae02ca8053323a1a85d801a54fbdb8f5a69a
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-04-13 22:27:35 +0000
Commit message:
Bumped version numbers for BioC 2.8 release. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@54800 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: e377f8952733a3cbf2abcf686d9351e6f5a4b5a0
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2011-01-17 14:41:39 +0000
Commit message:
appears i forgot to bump version number git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@51949 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 58dd7d6b5738583029fc043b12d9686a499b7598
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-11-28 10:31:31 +0000
Commit message:
use NumericMatrix everywhere for consistency git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@51082 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 73ce94d31672b25fad800e5458be096db3476a0c
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-11-28 10:16:38 +0000
Commit message:
changes in Rcpp git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@51081 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: d7b81d8d8ed6aa94c9b439d3cb85d97b79dfc591
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-10-18 05:57:44 +0000
Commit message:
Bumped version numbers again for new BioC 2.8 devel cycle. ERRATA: Previous bump was for BioC 2.7 release (of course), not 2.6! git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@50295 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 24494e1bf6c01b70c20e023fa142f04e57af47a1
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-10-18 05:34:23 +0000
Commit message:
Bumped version numbers for BioC 2.6 release git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@50293 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: cd83287f496a023c74b97b7192c99243360f5e84
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-09-12 07:02:07 +0000
Commit message:
Rterm.exe changed location in R-2.12, better to use R.exe git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@49356 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 63682a6d0034a3e52c9dab21b70e9cef4992907e
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 18:45:15 +0000
Commit message:
Bumped version numbers for BioC 2.7 trunk git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@46405 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 93337ad711d95d2bebf7c09bf50e9c1f488901cb
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-04-22 18:21:23 +0000
Commit message:
Bumped version numbers for BioC 2.6 release git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@46401 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 09c0f85901c2dcd0de33bb16cecf5e35c0f15e4c
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-03-31 00:21:32 +0000
Commit message:
version bump git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@45604 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 01696ad4a190203c9331633d88bf17e591cd8d30
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-03-31 00:17:05 +0000
Commit message:
bug fix in pareto scaling which caused it to revert to uv scaling git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@45603 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 10225e7d039de4bf496599e2b5f0518f06467d08
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-02-28 13:10:23 +0000
Commit message:
added subset slot again for capius sake git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44926 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 75b55c4f43032692e10a09d5a4d834526d867968
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-02-28 12:13:10 +0000
Commit message:
fix subsetting problem git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44925 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 6498ae29f29e38d96e8b81472e82ca716e45d043
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-02-05 08:29:25 +0000
Commit message:
tjo git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44517 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 096f7d3368124935b2b20f49c1a25f404df337ae
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-02-04 04:04:30 +0000
Commit message:
added missing argument descriptions git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44483 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: c97c05a843965286b7f3f48dd4e6fde2f1a3c4ce
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-23 05:29:07 +0000
Commit message:
more documentation git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44188 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 303d40ab4fe10a6a53fbc8d9bc080c7a00dcb60c
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-23 05:25:39 +0000
Commit message:
migration to roxygen and improved pre-processing git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44187 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 1c46bfdac9e48275b176b59f18eab96c0b156939
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-08 01:42:37 +0000
Commit message:
just a reformat of the news file. Nicer for emacs users shouldn't matter for vim users. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43898 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 07ad4e6d5b69feb3c6e08b85d7485f6de7e1348f
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-05 08:40:36 +0000
Commit message:
bugfix in xval git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43850 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 50d0cb91f111a09246eb7aba6ffbad5302a39066
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-05 07:28:28 +0000
Commit message:
previous fix git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43849 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: ebeecf379652ee9a21918521b1e57600b779de78
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-05 07:15:37 +0000
Commit message:
bug in Krzanowski CV git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43848 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: edec6cf851cd49213ba6c96f95c7f06a43f236ab
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-05 06:07:19 +0000
Commit message:
new makevars scripts, previous didnt work because Rscript is not in path git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43847 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 435f1aac4fd8e99ec9a973df019ac56d19331eeb
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-05 05:31:13 +0000
Commit message:
Rscript not reachable on bioconductors test servers so trying env R instead git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43845 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 7ec0101936315185684586990566c1582eb9daae
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-04 01:42:36 +0000
Commit message:
cpp version of nipals delivers same results as R version now on iris and metaboliteData git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43819 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 19974019d478cc582bfe1348ef2e41cdb7635482
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2010-01-02 15:22:23 +0000
Commit message:
C++ version of nipalsPca still gives wrong R2 git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43813 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 1b6e3a6166b59408d167e3bd2f8e2b59c2851860
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-12-30 04:47:45 +0000
Commit message:
improved cv including cv for svd type pca git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43787 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 31d439d517d84ec61b61760c357d5d84d6a2706a
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-11-02 01:41:34 +0000
Commit message:
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42777 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 49c78f5f3c0631b6248d879ba11c1ec2827ac79b
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-11-02 01:41:09 +0000
Commit message:
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42776 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 947fea686e9d829e76752c781e1ef52c9462d74d
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-11-02 01:39:42 +0000
Commit message:
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42775 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: bba2c39cd171f887f625df5598bf20ff3e06df54
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-11-02 01:38:45 +0000
Commit message:
must be in inst git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42774 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 6c0defe77a0af5c0e5067d03c06c61ef3392d7cd
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-11-02 01:20:56 +0000
Commit message:
added citation git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42773 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: faac0a3552f6e6441b13c053348233703ba166ed
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-27 23:45:24 +0000
Commit message:
Package version bump for BioC 2.6 devel. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42686 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: be40d9c1339995fdea9e3e0de30cd7ead6629bc9
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-10-27 23:33:29 +0000
Commit message:
Package version bump for BioC 2.5 release. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42684 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 39731fea6ff210e6e8814f730b29542b66ef5a68
Author: c.wong <c.wong@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-09-29 23:44:36 +0000
Commit message:
Fixed Rd files with duplicatd name 'pcaRes' by changing the name tag of class.nlpcaNet.Rd to 'pcaNet', instead of 'pcaRes'. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42054 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 05aa5255374a14acdf411526e87f7637121d08f8
Author: n.gopalakrishnan <n.gopalakrishnan@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-09-24 20:03:23 +0000
Commit message:
Fixed man page warnings git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@41936 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: f7cc5099800bdba964b9dd8976e41cbf49291786
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-09-06 03:06:55 +0000
Commit message:
Reformatted the Licence information in DESCRIPTION files to bring them into compliance. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@41539 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 23a9cbc71fbc1549bc1a048f4180b83cca3e7238
Author: w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-07-09 02:37:27 +0000
Commit message:
added missing slots to class documentation git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@40572 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: c49acbb9a8de7ea77cf33d06447564b3b7d1bc85
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-20 23:44:07 +0000
Commit message:
Bumped pkg versions for BioC 2.5 devel line. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@39015 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: e2e010442fb47250ed7889a1931ea845df103490
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-04-20 23:24:12 +0000
Commit message:
Bumped pkg versions for BioC 2.4 release. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@39013 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 8b1f79ded2381e0c82ab54453adfde6592bfa929
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-03-19 22:07:09 +0000
Commit message:
Changed biocViews entry of Statistics to Bioinformatics. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@38070 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 61ea818026766c9a64732a326ce262d01a1f0551
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-03-11 11:09:32 +0000
Commit message:
added kevin's biplot function and some getter functions git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37906 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 037d27fd7cfc095ceb81346c1e614dbc2611abcc
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-23 10:37:28 +0000
Commit message:
bugfix git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37565 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 795fa028d29271a2780c6efe859d9c70ede2058d
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-23 05:12:30 +0000
Commit message:
added predict and residuals methods git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37564 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: d3576d34aa4e428cdcad48209f8bddf972b2407c
Author: c.wong <c.wong@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2009-02-06 18:54:46 +0000
Commit message:
fixed Rdversion 2 parser warnings git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37210 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 2455aa683924f6c3ae3a030867703839c900f801
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-29 07:56:51 +0000
Commit message:
Fixed warnings and notes git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34968 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 376fd7f82e593d4728329632a2556a4d6838e15e
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-27 05:55:03 +0000
Commit message:
mistake.. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34912 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 428e9357e3e0c16971c9ae5bd764fa920eedf135
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-27 05:50:42 +0000
Commit message:
Fixed slplot so that it accepts differnt arguments for the scores and loading plots and complains if sl and ll are of wrong size. Added a show method as that often is the default function and not print. Small bugfix in nipals pca. Nipals pca is however poorly tested and might change again soon. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34911 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 4958f209271f2359e1671524ea2bc506f63e9c2f
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-21 22:46:31 +0000
Commit message:
Bumping version numbers for BioC 2.4 devel. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34814 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: c6c217cdfafcb0cff00282904a617f64d224943e
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-10-21 22:32:58 +0000
Commit message:
Bumping version numbers for BioC 2.3 release. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34811 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: fd7c053d928e8c4dbb35b6644f4c62bbfd11e7fc
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-30 00:25:58 +0000
Commit message:
Updating the version number for the trunk post-BioC 2.2 release. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@31432 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: e0e6a4f5929b6ea86796266e478ccb8296d155df
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-04-29 23:50:18 +0000
Commit message:
Updating the version number for the BioC 2.2 release. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@31430 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 84b7c0b8d1ca5e9b12bc1bf559dcdd87099e20a7
Author: p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2008-02-27 23:36:54 +0000
Commit message:
Replaced usage of soon to be defunct class exprSet with ExpressionSet. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@30244 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 303168d85180d0535a4c58a753dcfd9f0adc8e99
Author: w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-10-08 10:33:45 +0000
Commit message:
Fixed tiny bug in the slplot function preventing the ellipse to be drawn git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27836 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: de59d20530a66052dcf60d6f9effdc05999c7062
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-10-03 01:16:39 +0000
Commit message:
2nd version bump: bumped y to y+1 in version number x.y.z for all packages in bioc_2.1.manifest (so now y is odd again in trunk). git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27716 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 76e5b19a0f3658d81bd93761e38edca7599dc394
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-10-03 00:41:09 +0000
Commit message:
1st version bump: bumped version number x.y.z of all packages in bioc_2.1.manifest (if y was odd: y<-y+1, if y was even: y<-y+2, in all cases z <- 0). git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27709 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 1571c1be378eb4990d226722b6962dc105c8e7a0
Author: mtmorgan@fhcrc.org <mtmorgan@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-09-25 18:26:10 +0000
Commit message:
Remove dependence on R without version specification git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27507 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: b9b8af5a8cbcf85fb9901f8582a25318376c9c16
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-06-15 06:46:22 +0000
Commit message:
Applied Kevin Wrights diff for faster nipals. Nipals PCA really should be re-written in C for further speed improvement git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@25394 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: a02542e0d0239e78145f2988686192fd99c477fa
Author: sethf <sethf@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-05-12 04:56:41 +0000
Commit message:
SaveImage is deprecated, using LazyLoad instead git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24616 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: e26bf31b453a7a3fcc9166d2327f1897d8d33699
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-24 18:31:42 +0000
Commit message:
Bumped again version number x.y.z for all packages in bioc_2.0.manifest (y<-y+1). git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24217 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: ae676d3080dca7019e76f88322318b1e29662869
Author: hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-24 18:21:48 +0000
Commit message:
BioC 2.0 release version bump: bumped version number x.y.z for all packages in bioc_2.0.manifest (if y was odd: y<-y+1, if y was even: y<-y+2, in all cases z <- 0). git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24214 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 26bb63c8af153b1d3f28dde3d592018f28a95354
Author: w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-20 08:09:12 +0000
Commit message:
svnImpute returned too many scores/loadings, this was fixed. And now we also assign correct row/column names to scores/loading matrices git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24065 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: f1d2ec5d8c429b0d135966f6d2e85bf3229e9901
Author: w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-19 02:19:08 +0000
Commit message:
nipals(center=T) was also accidentially sclaing the data, as we used scale(data, center=T). This has been fixed. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24012 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: c2ee00ec4a9fedd0b0ca810ab78291c1e8e58348
Author: w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-13 07:18:48 +0000
Commit message:
added .onLoad method, SaveImage in DESCRIPTION was set to true. Lets hope this will fix the check error on bioconductor git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23835 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 51a3e59aef6c59ba609cb603da9863b25086b503
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-10 07:16:02 +0000
Commit message:
little bug in vignette git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23724 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 66c31a7c547e4d247090c28976f0f51488877d26
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-10 07:11:53 +0000
Commit message:
added vingette discussing handling of data with outliers git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23723 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 8d0085346e700ca5cbf50b4602890846f7f8d768
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-10 02:40:52 +0000
Commit message:
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23717 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: c367d43e21231faaeca866dc4a035aba8bcd2f8b
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-04-10 02:40:23 +0000
Commit message:
added a svd method that is robust to outliers. Also a pca method based on this robust svd. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23716 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 8cf2bb8a582a9417403287377704e4b5c3289afc
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-27 17:03:46 +0000
Commit message:
'}' missing git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22857 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: cf432a2feda2b8ddfd291f1a49063a56f6851cdb
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-27 13:24:13 +0000
Commit message:
added docu for the asExprSet function git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22855 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 62aaa8303db3d2d78291be2d4e9fd2bcc9747803
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-25 17:35:41 +0000
Commit message:
changed number of components for kEstimate to 5 to speed vignette creation up a bit. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22820 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: a241126fcfee847548238e996f6a63897e20bd5a
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-25 16:44:45 +0000
Commit message:
New method to convert pcaRes to exprSet, pca() does no longer retrun an exprSet object if exprSet was given as input, use asExprSet instead. Fixed a bug in the missing value vignette git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22819 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: fd0e499254ea0334632a85013149dec03f6158de
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-23 14:32:39 +0000
Commit message:
added vignette on missing value estimation for those who only wants that git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22792 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 613ca4b0d018934a7f1073fd0fde40c838b6bb18
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-21 11:01:09 +0000
Commit message:
Removed ellipse dependance by adding a simple (unexported) function for computing Hotelling ellipses. Added a todo file with some random thoughts that occured to me whilst using pcaMethods. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22722 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: b494a22178b406163d914a949447acc9d1ae60b8
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-15 07:38:45 +0000
Commit message:
Documentation updates, fixed a latex bug that prevented the package from beeing build correctly git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22633 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 102e25bb13db53f85b4e0ba85958af5d10d05a9e
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-14 06:36:55 +0000
Commit message:
kEstimate was not implemented in the fastest way :) This has been fixed now. Also it is now possible to get the estimation error for each individual incomplete variable. This allows to easily see for wich variables missing value imputation makes senes, and from wich we should better keep our fingers off. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22623 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 47627b4ed275e3a3d77ed6e6f2b1fd4fd9280cf1
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-09 10:44:50 +0000
Commit message:
Forgot to do a cvs add :)) git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22500 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 04f0809d627f8fed03d78c11db39af082c040494
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-09 10:43:44 +0000
Commit message:
Added a new method called kEstimateFast. This also estimates the best number of components / similar genes for missing value estimation. In contrast to kEstimate no cross validation is performed. The method just used original - estimate for all complete observations. This is a more rough estimate than provided by kEstimate. Fixed a bug in kEstimate and nlpca. Documentation updates. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22499 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 66528bb732c2da2da8ff3d1617d3f5df54f24617
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-07 12:33:18 +0000
Commit message:
Bugfix in docu regarding kEstimate change git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22462 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: a8581983add70ab3b1a42b7ed801adf21f87de13
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-05 17:06:11 +0000
Commit message:
Upgraded (hopefully) plotPcs so it works with Sweave and gives prettier output by basing it on pairs() instead of the not so beatiful slplot() git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22431 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: b072dc100905d70504d17a946bab6e8804a8c12f
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-05 16:08:29 +0000
Commit message:
K-Estimate now supports NRMSEP and Q2 as error measure. Some documentation updates. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22429 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: df100043fb5311332315bf65a1d3adce0c3d4a2b
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-05 07:24:06 +0000
Commit message:
Tiny bugfixes and I bumped to 1.7.0 as this should be considered a devel version and not release. Lets stay on 1.7.Z until everything works as meant. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22423 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 58f7f6011e4135da09c0c38b7d5fd77b971f1bdd
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2007-02-02 14:52:59 +0000
Commit message:
Added support for Non-linear PCA and made corresponding additions to the documentations. Also added simulated example data for use with nlpca. Changed Q2 cross-validation to guarantee that no full column or row is ever deleted. This is done by deleting diagonals from the matrix instead of values with random indices. The drawback here is that no less than a full diagonal can be deleted so the possible folds are limited, but this should be of no practical importance. The screeplot function was removed and replaced with plotR2 as screeplot is a generic function from stats with a rigid definiton which can not be safely modified (npcs in argument vs nPcs e.g.). Removed exclamation marks from warnings, messaged. I find them obnoxious. Also, i changed the use of the word 'gene' as a row in an expression matrix is not a 'gene' but a _variable_ measuring the expression estimates of a gene. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22378 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 3a37959fe69aedefae5ecadc256dcbfe6ab24ca3
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2006-12-13 02:58:21 +0000
Commit message:
This is a major update of pcaMethods. A missing value estimation method called llsImpute was included to allow better rating and comparison of the obtained results. The method is based on the paper by Kim et al, Bioinformatics 2005, for details see the documentation. Together with this method the nniRes (nearest neighbour imputation) was introduced, serving as return object for missing value estimation based on nearest neighbour imputation. Further updates: ppca : The threshold was changed to 1e-5, this leads to much more stable results kEstimate : The interface changed slightly, maxPcs was replaced by evalPcs. Now the user may enter arbitrary arrays of integer numbers, e.g. c(2,5,6) or 1:5 or 4:10. pca : now includes method nni, a wrapper for llsImpute, similar to pca. A new print method for class nniRes was also included. Some documentation updates. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@21474 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: ee6231e13513ec3c0138f187d6b008bbc10a77c1
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2006-10-23 19:23:36 +0000
Commit message:
- changed threshold in ppca to 1e-5. This will lead to more stable results. - Added parameter skipInac to decide weather inaccurate vectors of the orthonormal base should be skipped or not. FALSE is the default value, this is the opposite behaviour than in the 1.9 version. However receiving results of lower dimension than expected often leads to errors. - Updated vignette, the syntax was not uniform, e.g. we were talking about - eigenvectors, loadings, PCs, etc. Now we refere to loadings throughout the whole document. - Added a picture explaining why pca does not define a density model. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@20786 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 5f0bf7d3d468d8d1446ba725a81e95b45002bbbd
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2006-10-18 16:11:52 +0000
Commit message:
Removed \cr from vingnette that caused errors during build git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@20649 bc3139a8-67e5-0310-9ffc-ced21a209358Package: pcaMethods
Commit: 57d4c8093dfe3b95e5a10cf8ce7eea1b436ac064
Author: stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2006-10-18 15:20:52 +0000
Commit message:
kEstimate now prints a warning when the method is used on complete matrices without the allGenes = TRUE option. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@20645 bc3139a8-67e5-0310-9ffc-ced21a209358
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