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ChangeLog
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-------------------
Version: 0.7
Date: 2021-02-13
* Fix matrix object having more than one class in R 4.0.0. Clean up the rest of methods.
-------------------
Version: 0.6-9
Date: 2020-07-13
* Remove Bioconductor packages from the suggested list to fix the issue on macOS
-------------------
Version: 0.6-8
Date: 2020-06-22
* Fix matrix object having more than one class in R 4.0.0
-------------------
Version: 0.6-7
Date: 2020-05-07
* Fix CRAN issues:
* Replace all require() with requireNamespace()
* use namespace tags for kohonen:: and Mclust:: functions
* Add importFrom() to NAMESPACE file
-------------------
Version: 0.6-6
Date: 2014-03-24
* Declared 'biocLite' as a global variable in source code
-------------------
Version: 0.6-5
Date: 2014-03-21
* Moved 'clValid' vignette to folder 'vignettes'
* Moved 'methods' and 'class' from 'Depends' field to 'Imports'
field in DESCRIPTION file
-------------------
Version: 0.6-4
Date: 2011-10-17
* Added 'clValid.pdf' back to 'inst/doc'
-------------------
Version: 0.6-3
Date: 2011-10-17
* Removed unnecessary files from 'inst/doc'
* Changed license to LGPL-3
-------------------
Version: 0.6-2
Date: 2011-01-25
* Fixed bug in NAMESPACE file (removed call to .onLoad())
-------------------
Version: 0.6-1
Date: 2010-11-05
* Changed format for reading biological annotation files from
Excel 2003/2007 to comma separated
* Split R code into four files: clValid-Classes.R,
clValid-Methods.R, clValid-internal.R, clValid-functions.R
-------------------
Version: 0.6
Date: 2009-11-17
* matchGO : Made change to identify annotated probes with
category="all" argument.
* clValid : Missing values are now allowed in clValid(). For the
correlation metric the use="pairwise.complete.obs" option is used,
while the na.rm=TRUE option is used when calculating means for the
AD and ADM measures.
* annotationListToMatrix : Added new function to convert annotation
lists to TRUE/FALSE logical matrices: columns = functional
classes, rows = genes
* readAnnotationFile : Added function to read biological
annotation file from Excel spreadsheet
* getRanksWeights : Added function to obtain ranks and weights
for rank aggregation from clValid object
* BSI, BHI : Changed functions to work with TRUE/FALSES matrices
from annotateListToMatrix (thanks to Rainer Machne for suggestion)
* sota : History of diversities for ancestor nodes are now stored.
* sota : Moved break for maxDiversity with unrest.growth==FALSE to
occur at same point as break for maxCycles (thanks to Rainer
Machne)
* clValid : Added argument 'verbose' to track pecentage completion
of cluster validation
* clValid : Now attempts automatic download and installation of
Bioconductor annotation packages if not currently installed
* clValid-class : Added slot 'labels' to contain the
character vector giving the item (gene) labels.
* clValid, BHI, BSI : Updated to use package GO.db instead of
defunct GO package. Also, added argument 'dropEvidence' to select
type of GO evidence used.
* Packages RankAggreg and RODBC added to list of recommended
packages
* Packages kohonen and mclust changed from required to recommended
list of packages
* Packages GO and moe430 removed from list of recommend packages,
added packages GO.db and moe430a.db
* Vignette updated to include example of rank aggregation using
package RankAggreg, and also illustrates usage of 'dropEvidence'
argument and reading in biological annotation files using
Excel
-------------------
Version: 0.5-7
Date: 2008-07-28
* Added latex style file and made minor changes to clValid-class.Rd
-------------------
Version: 0.5-6
Date: 2008-01-27
* sota, sota.print, sota.plot : Fixed these to print and plot properly
when actual number of clusters is fewer than requested number
(i.e. some clusters are not populated)
* Added fixes to catch cases where fewer than requested number of
clusters is returned by clustering method. A warning message is
given when this occurs.
-------------------
Version: 0.5-4
Date: 2007-12-14
* The default titles for plotting the validation measures were
changed to "Internal validation", "Stability validation", and
"Biological validation" for internal, stability, and biological
validation, respectively.
* The functions for calculating each validation measure: dunn,
connectivity, BHI, BSI, stability; and the internal function
matchGO are all exported now. Users can call these directly if
they have an external clustering algorithm they want to evaluate,
or if they just have a dissimilarity matrix (though the original
data matrix is still required for the stability measures APN,
AD, ADM, and BSI).
* clValid : Now accepts data frames w/integer data
* clValid : Attempts to automatically install Bioconductor
metadata packages if they are not currently available
* clValid : A new argument 'maxitems' was added to limit the
number of clustered items. If R is being used interactively and
'maxitems' is exceeded, the user is prompted about whether to
continue. If R is not being used interactively the function exits
with an error message.
* clValid : Accepts ExpressionSet objects rather than the now
defunct exprSet objects