[Subgroup-commits] r64 - pkg/rsubgroup pkg/rsubgroup/R pkg/rsubgroup/inst/java pkg/rsubgroup/java pkg/rsubgroup/man pkg/rsubgroup/tests www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 24 10:15:57 CET 2020
Author: atzmueller
Date: 2020-02-24 10:15:57 +0100 (Mon, 24 Feb 2020)
New Revision: 64
Modified:
pkg/rsubgroup/DESCRIPTION
pkg/rsubgroup/NAMESPACE
pkg/rsubgroup/NEWS
pkg/rsubgroup/R/AAAonLoad.R
pkg/rsubgroup/R/classes.R
pkg/rsubgroup/R/subgroup.R
pkg/rsubgroup/inst/java/subgroup.jar
pkg/rsubgroup/java/readme-subgroup-jar.txt
pkg/rsubgroup/man/SDTaskConfig-class.Rd
pkg/rsubgroup/tests/test.R
www/index.php
Log:
Changes in version 0.8 (2019-05-23)
===================================
* Improvements
* included new SDTaskConfig#parfilter: Provides the minimal improvement
value for the postfilter (for min-improve-* filters), or the significance
level (P) for sig-improve-* filters.
* updated org.vikamine.kernel version
* package-internal: fixed Java requirements (string) in DESCRIPTION
* Bug fixes.
* fixed bug in automatic discretization used in rsubgroup VIKAMINE kernel
Modified: pkg/rsubgroup/DESCRIPTION
===================================================================
--- pkg/rsubgroup/DESCRIPTION 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/DESCRIPTION 2020-02-24 09:15:57 UTC (rev 64)
@@ -1,18 +1,18 @@
-Package: rsubgroup
-Type: Package
-Title: Subgroup Discovery and Analytics
-Version: 0.7
-Date: 2015-07-01
-Author: Martin Atzmueller
-Maintainer: Martin Atzmueller <martin at atzmueller.net>
-Description: A collection of efficient and effective tools and
- algorithms for subgroup discovery and analytics. The package
- integrates an R interface to the org.vikamine.kernel library
- of the VIKAMINE system (http://www.vikamine.org) implementing
- subgroup discovery, pattern mining and analytics in Java.
-Classification/ACM: G.4, H.2.8, I.5.1
-License: GPL (>= 3)
-Depends: R (>= 2.6.0), methods, rJava (>= 0.6-3), foreign (>= 0.8-40)
-SystemRequirements: Java (>= 6.0)
-Collate: 'AAAonLoad.R' 'randomSeed.R' 'classes.R' 'subgroup.R'
+Package: rsubgroup
+Type: Package
+Title: Subgroup Discovery and Analytics
+Version: 0.8
+Date: 2019-05-23
+Author: Martin Atzmueller
+Maintainer: Martin Atzmueller <martin at atzmueller.net>
+Description: A collection of efficient and effective tools and
+ algorithms for subgroup discovery and analytics. The package
+ integrates an R interface to the org.vikamine.kernel library
+ of the VIKAMINE system (http://www.vikamine.org) implementing
+ subgroup discovery, pattern mining and analytics in Java.
+Classification/ACM: G.4, H.2.8, I.5.1
+License: GPL (>= 3)
+Depends: R (>= 2.6.0), methods, rJava (>= 0.6-3), foreign (>= 0.8-40)
+SystemRequirements: Java (>= 8)
+Collate: 'AAAonLoad.R' 'randomSeed.R' 'classes.R' 'subgroup.R'
URL: http://www.rsubgroup.org
\ No newline at end of file
Modified: pkg/rsubgroup/NAMESPACE
===================================================================
--- pkg/rsubgroup/NAMESPACE 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/NAMESPACE 2020-02-24 09:15:57 UTC (rev 64)
@@ -1,5 +1,5 @@
-exportPattern("^[^\\.]")
-
-import(methods)
-import(rJava)
+exportPattern("^[^\\.]")
+
+import(methods)
+import(rJava)
importFrom(foreign, write.arff)
\ No newline at end of file
Modified: pkg/rsubgroup/NEWS
===================================================================
--- pkg/rsubgroup/NEWS 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/NEWS 2020-02-24 09:15:57 UTC (rev 64)
@@ -1,46 +1,58 @@
-rsubgroup NEWS
-
-For a detailed list of changes, see the svn commit history at
-svn://r-forge.r-project.org/svnroot/subgroup/
-
-Changes in version 0.7 (2015-07-xx)
-===================================
-* Improvements
- * document setting Java heap space before loading the rsubgroup library.
- * Improve error handling (exception signaling) when running subgroup discovery
- using an ARFF file directly.
- * SDTaskConfig now provides an option mintp, that allows to set the minimal
- true positives threshold to be contained in a subgroup, which is usually
- very effective for pruning.
- * The Pattern class now contains a list of selection expressions (selectors)
- for the subgroup, not only the description. Using the is.pattern.matching
- function, a match of a pattern and a data instance can be checked now.
- * In SDTaskConfig, postfilter can be a single filter or a vector of filters,
- that are then applied in order on the results. This allows e.g., the combination
- of minimal improvement filtering with weighted covering post-processing.
- * Implement/enable new quality function (Adjusted residuals, cf. Agresti 2007)
- ==> qf="ares"
- * For a binary target variable, the resulting patterns now also store the
- chi-squared value comparing subgroup and population w.r.t. the target in the
- parameters field.
- * ToDataFrame shows the chi-squared value for a binary target.
-
-* Bug fixes:
- * fix providing attributes=NULL (i.e., automatically include all attributes)
- into subgroup discovery
- * fix max-attribute-value bug in SGSelectorGenerator, causing the inclusion
- of two few selectors in subgroup discovery methods
-
-
-
-Changes in version 0.6 (2014-09-10)
-===================================
-* Improvements:
- * optimizations in the beam search algorithm
- * significant memory optimization (dataset storage, access)
- * ARFF: enable import of "empty" attributes, i.e., with an empty value domain
- (this can occur, for example, when importing columns with only 'NA' in R)
-
-* Bug fixes:
- * exclude target from subgroup attributes
+rsubgroup NEWS
+
+For a detailed list of changes, see the svn commit history at
+svn://r-forge.r-project.org/svnroot/subgroup/
+
+Changes in version 0.8 (2019-05-23)
+===================================
+* Improvements
+ * included new SDTaskConfig#parfilter: Provides the minimal improvement
+ value for the postfilter (for min-improve-* filters), or the significance
+ level (P) for sig-improve-* filters.
+ * updated org.vikamine.kernel version
+ * package-internal: fixed Java requirements (string) in DESCRIPTION
+
+* Bug fixes.
+ * fixed bug in automatic discretization used in rsubgroup VIKAMINE kernel
+
+Changes in version 0.7 (2015-07-01)
+===================================
+* Improvements
+ * document setting Java heap space before loading the rsubgroup library.
+ * Improve error handling (exception signaling) when running subgroup discovery
+ using an ARFF file directly.
+ * SDTaskConfig now provides an option mintp, that allows to set the minimal
+ true positives threshold to be contained in a subgroup, which is usually
+ very effective for pruning.
+ * The Pattern class now contains a list of selection expressions (selectors)
+ for the subgroup, not only the description. Using the is.pattern.matching
+ function, a match of a pattern and a data instance can be checked now.
+ * In SDTaskConfig, postfilter can be a single filter or a vector of filters,
+ that are then applied in order on the results. This allows e.g., the combination
+ of minimal improvement filtering with weighted covering post-processing.
+ * Implement/enable new quality function (Adjusted residuals, cf. Agresti 2007)
+ ==> qf="ares"
+ * For a binary target variable, the resulting patterns now also store the
+ chi-squared value comparing subgroup and population w.r.t. the target in the
+ parameters field.
+ * ToDataFrame shows the chi-squared value for a binary target.
+
+* Bug fixes:
+ * fix providing attributes=NULL (i.e., automatically include all attributes)
+ into subgroup discovery
+ * fix max-attribute-value bug in SGSelectorGenerator, causing the inclusion
+ of two few selectors in subgroup discovery methods
+
+
+
+Changes in version 0.6 (2014-09-10)
+===================================
+* Improvements:
+ * optimizations in the beam search algorithm
+ * significant memory optimization (dataset storage, access)
+ * ARFF: enable import of "empty" attributes, i.e., with an empty value domain
+ (this can occur, for example, when importing columns with only 'NA' in R)
+
+* Bug fixes:
+ * exclude target from subgroup attributes
* fix loading of ARFF file, for attributes/values with trailing spaces
\ No newline at end of file
Modified: pkg/rsubgroup/R/AAAonLoad.R
===================================================================
--- pkg/rsubgroup/R/AAAonLoad.R 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/R/AAAonLoad.R 2020-02-24 09:15:57 UTC (rev 64)
@@ -2,7 +2,7 @@
# rsubgroup package R classes
#
# This file is part of the rsubgroup package.
-# Copyright (C) 2011-2015 by Martin Atzmueller
+# Copyright (C) 2011-2019 by Martin Atzmueller
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
Modified: pkg/rsubgroup/R/classes.R
===================================================================
--- pkg/rsubgroup/R/classes.R 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/R/classes.R 2020-02-24 09:15:57 UTC (rev 64)
@@ -2,7 +2,7 @@
# rsubgroup package R classes
#
# This file is part of the rsubgroup package.
-# Copyright (C) 2011-2015 by Martin Atzmueller
+# Copyright (C) 2011-2019 by Martin Atzmueller
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -43,12 +43,13 @@
nodefaults = "logical",
relfilter = "logical",
postfilter = ".vectorOrCharacter",
- attributes = ".vectorOrNull"
+ attributes = ".vectorOrNull",
+ parfilter = "numeric"
),
prototype(qf="ps", method="sdmap", k = as.integer(20),
minqual = as.integer(0), minsize = as.integer(0), mintp = as.integer(0),
maxlen = as.integer(7), nodefaults = FALSE, relfilter = FALSE,
- postfilter = "", attributes = NULL)
+ postfilter = "", parfilter = 0.05, attributes = NULL)
)
SDTaskConfig <- function(...){
Modified: pkg/rsubgroup/R/subgroup.R
===================================================================
--- pkg/rsubgroup/R/subgroup.R 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/R/subgroup.R 2020-02-24 09:15:57 UTC (rev 64)
@@ -2,7 +2,7 @@
# rsubgroup package R classes
#
# This file is part of the rsubgroup package.
-# Copyright (C) 2011-2015 by Martin Atzmueller
+# Copyright (C) 2011-2019 by Martin Atzmueller
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -104,6 +104,9 @@
J(task, "setPostFilter", filter)
}
}
+ if (!is.na(config at parfilter)) {
+ J(task, "setPostFilterParameter", config at parfilter)
+ }
if (is.null(config at attributes)) {
attributesArrayObject <- .GetAllAttributesAsJArray(ontology = ontology)
J(task, "setAttributes", attributesArrayObject)
Modified: pkg/rsubgroup/inst/java/subgroup.jar
===================================================================
(Binary files differ)
Modified: pkg/rsubgroup/java/readme-subgroup-jar.txt
===================================================================
--- pkg/rsubgroup/java/readme-subgroup-jar.txt 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/java/readme-subgroup-jar.txt 2020-02-24 09:15:57 UTC (rev 64)
@@ -1,28 +1,28 @@
-The rsubgroup package contains the subgroup.jar file which provides
-the functionality of the core org.vikamine.kernel package of the VIKAMINE system
-for subgroup discovery and analytics.
-
-VIKAMINE is licensed under LGPL >= 2.1.
-Copyright (C) 2003-2008 by Martin Atzmueller, and contributors.
-Copyright (C) 2008-2015 by Martin Atzmueller, Florian Lemmerich, and contributors.
-
-The source code can be obtained at www.vikamine.org, and the SVN repository
-sourceforge.net/p/vikamine/code/HEAD/tree/trunk/ => org.vikamine.kernel
-
-Below, we include an excerpt from the org.vikamine.kernel README-COPYING.txt
-file:
-------------------------
-The org.vikamine.kernel package (this package), called the "software" from now on,
-is provided under the terms of the GNU Lesser General Public (LGPL) version 2.1
-(see file lgpl-license.txt) or (at your option) any later version.
-
-Thus, we require that a product containing any parts of this software
-announces that the software has been used.
-
-The latest version of the software can always be obtained on
- >>> http://www.vikamine.org <<<.
-
-This package utilizes the libraries:
-- Apache commons-math
-- jdom (jdom.org)
+The rsubgroup package contains the subgroup.jar file which provides
+the functionality of the core org.vikamine.kernel package of the VIKAMINE system
+for subgroup discovery and analytics.
+
+VIKAMINE is licensed under LGPL >= 2.1.
+Copyright (C) 2003-2008 by Martin Atzmueller, and contributors.
+Copyright (C) 2008-2019 by Martin Atzmueller, Florian Lemmerich, and contributors.
+
+The source code can be obtained at www.vikamine.org, and the SVN repository
+sourceforge.net/p/vikamine/code/HEAD/tree/trunk/ => org.vikamine.kernel
+
+Below, we include an excerpt from the org.vikamine.kernel README-COPYING.txt
+file:
+------------------------
+The org.vikamine.kernel package (this package), called the "software" from now on,
+is provided under the terms of the GNU Lesser General Public (LGPL) version 2.1
+(see file lgpl-license.txt) or (at your option) any later version.
+
+Thus, we require that a product containing any parts of this software
+announces that the software has been used.
+
+The latest version of the software can always be obtained on
+ >>> http://www.vikamine.org <<<.
+
+This package utilizes the libraries:
+- Apache commons-math
+- jdom (jdom.org)
- opencsv
\ No newline at end of file
Modified: pkg/rsubgroup/man/SDTaskConfig-class.Rd
===================================================================
--- pkg/rsubgroup/man/SDTaskConfig-class.Rd 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/man/SDTaskConfig-class.Rd 2020-02-24 09:15:57 UTC (rev 64)
@@ -14,6 +14,16 @@
\section{Slots}{
\describe{
+ \item{\code{attributes}:}{The list of attributes to consider for mining.
+ Either a vector of attribute names, or NULL (the default),
+ which includes all attributes.}
+ \item{\code{method}:}{A mining method; one of
+ Beam-Search \code{beam},
+ BSD \code{bsd},
+ SD-Map \code{sdmap},
+ SD-Map enabling internal disjunctions \code{sdmap-dis}.
+ The default is \code{method = "sdmap"}.
+ }
\item{\code{qf}:}{A quality function; one of:
Adjusted Residuals \code{ares},
Binomial Test \code{bin},
@@ -24,14 +34,7 @@
Relative Gain \code{relgain},
Weighted Relative Accuracy \code{wracc}.
The default is \code{qf = "ps"}.
- }
- \item{\code{method}:}{A mining method; one of
- Beam-Search \code{beam},
- BSD \code{bsd},
- SD-Map \code{sdmap},
- SD-Map enabling internal disjunctions \code{sdmap-dis}.
- The default is \code{method = "sdmap"}.
- }
+ }
\item{\code{k}:}{The maximum number (top-k) of patterns
to discover. The default is \code{k = 20}}
\item{\code{minqual}:}{The minimal quality (default \code{minqual = 0}).}
@@ -59,19 +62,20 @@
are strictly irrelevant,
Significant Improvement (Global) \code{sig-improve-global},
removes patterns that do not significantly improve
- (0.05 level) w.r.t. all their possible generalizations,
+ (default 0.01 level) w.r.t. all their possible generalizations,
Significant Improvement (Set) \code{sig-improve-set},
removes patterns that do not significantly improve
- (0.05 level) w.r.t. all generalizations in the result set,
+ (default 0.01 level) w.r.t. all generalizations in the result set,
Weighted Covering \code{weighted-covering}, performs weighted
covering on the data in order to select a covering set of
subgroups while reducing the overlap on the data.
By default no postfilter is set, i.e., \code{postfilter = ""}.
}
- \item{\code{attributes}:}{The list of attributes to consider for mining.
- Either a vector of attribute names, or NULL (the default),
- which includes all attributes.}
+ \item{\code{parfilter}:}{Provides the minimal improvement value for the
+ postfilter (for min-improve-* filters), or the significance level (P) for
+ sig-improve-* filters.
}
+ }
}
\seealso{
\code{\link{DiscoverSubgroups}}.
Modified: pkg/rsubgroup/tests/test.R
===================================================================
--- pkg/rsubgroup/tests/test.R 2015-07-01 19:51:32 UTC (rev 63)
+++ pkg/rsubgroup/tests/test.R 2020-02-24 09:15:57 UTC (rev 64)
@@ -2,7 +2,7 @@
# rsubgroup package R classes
#
# This file is part of the rsubgroup package.
-# Copyright (C) 2011-2015 by Martin Atzmueller
+# Copyright (C) 2011-2019 by Martin Atzmueller
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -19,7 +19,15 @@
#
# Contact: Martin Atzmueller (martin at atzmueller.net)
###############################################################################
+library(rJava)
+.jinit()
+jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
+if(substr(jv, 1L, 1L) == "1") {
+ jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))
+ if(jvn < 1.8) stop("Java 8 is needed for this package but not available")
+}
+
library(rsubgroup)
data(credit.data)
Modified: www/index.php
===================================================================
--- www/index.php 2015-07-01 19:51:32 UTC (rev 63)
+++ www/index.php 2020-02-24 09:15:57 UTC (rev 64)
@@ -1,5 +1,5 @@
-<?php
-header("HTTP/1.1 301 Moved Permanently");
-header("Location:http://www.subgroup.cc");
-exit;
+<?php
+header("HTTP/1.1 301 Moved Permanently");
+header("Location:http://www.rsubgroup.org");
+exit;
?>
\ No newline at end of file
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