[Subgroup-commits] r15 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 2 21:21:39 CEST 2014
Author: atzmueller
Date: 2014-08-02 21:21:38 +0200 (Sat, 02 Aug 2014)
New Revision: 15
Added:
pkg/man/Pattern-class.Rd
pkg/man/credit.data.Rd
Modified:
pkg/NAMESPACE
pkg/R/classes.R
pkg/R/subgroup.R
Log:
* improve documentation
* fix visibility (internal functions), cf. bug #5827
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2014-08-02 06:51:24 UTC (rev 14)
+++ pkg/NAMESPACE 2014-08-02 19:21:38 UTC (rev 15)
@@ -1 +1 @@
-exportPattern(".")
\ No newline at end of file
+exportPattern("^[^\\.]")
\ No newline at end of file
Modified: pkg/R/classes.R
===================================================================
--- pkg/R/classes.R 2014-08-02 06:51:24 UTC (rev 14)
+++ pkg/R/classes.R 2014-08-02 19:21:38 UTC (rev 15)
@@ -20,15 +20,7 @@
# Contact: Martin Atzmueller (martin at atzmueller.net)
###############################################################################
-setClass("SDOptions",
- representation(
- verbose = "logical",
- debug = "logical"
- ),
- prototype(verbose = FALSE, debug = FALSE)
-)
-
setClass("SDTaskConfig",
representation(
qf = "character",
Modified: pkg/R/subgroup.R
===================================================================
--- pkg/R/subgroup.R 2014-08-02 06:51:24 UTC (rev 14)
+++ pkg/R/subgroup.R 2014-08-02 19:21:38 UTC (rev 15)
@@ -23,13 +23,13 @@
library(foreign)
library(rJava)
-setGeneric("CreateARFFProvider",
+setGeneric(".CreateARFFProvider",
function(source, name, ...) {
- standardGeneric("CreateARFFProvider")
+ standardGeneric(".CreateARFFProvider")
}
)
-setMethod("CreateARFFProvider", signature(source = "data.frame", name = "character"),
+setMethod(".CreateARFFProvider", signature(source = "data.frame", name = "character"),
function(source, name, ...) {
# Creates a dataset provider (converting the dataframe)
con <- textConnection("arffVector", "w")
@@ -43,7 +43,7 @@
}
)
-setMethod("CreateARFFProvider", signature(source = "character", name = "character"),
+setMethod(".CreateARFFProvider", signature(source = "character", name = "character"),
function(source, name, ...) {
# Creates a dataset provider given a file name
provider <- .jnew("org/vikamine/kernel/xpdl/FileDatasetProvider", source)
@@ -51,15 +51,15 @@
}
)
-CreateOntologyForData <- function(provider, dataset) {
+.CreateOntologyForData <- function(provider, dataset) {
# Creates the ontology object for the respective dataset
ontology <- .jcall(provider, "Lorg/vikamine/kernel/data/Ontology;","getDataset", dataset)
return(ontology)
}
-CreateSimpleSDTask <- function(ontology, target) {
+.CreateSimpleSDTask <- function(ontology, target) {
# Creates a simple subgroup discovery task
- freeMemory()
+ .FreeMemory()
simpleTask <- new(J("org/vikamine/kernel/subgroup/search/SDSimpleTask"), ontology)
if (!is.null(target$value)) {
selector <- new(J("org/vikamine/kernel/subgroup/selectors/DefaultSGSelector"), ontology, target$attribute, target$value)
@@ -82,10 +82,10 @@
#
# Returns:
# A subgroup discovery task
- freeMemory()
- provider <- CreateARFFProvider(source, "data")
- ontology <- CreateOntologyForData(provider, "data")
- task <- CreateSimpleSDTask(ontology, target)
+ .FreeMemory()
+ provider <- .CreateARFFProvider(source, "data")
+ ontology <- .CreateOntologyForData(provider, "data")
+ task <- .CreateSimpleSDTask(ontology, target)
J(task, "setQualityFunction", config at qf)
J(task, "setSDMethod", config at method)
J(task, "setMaxSGCount", as.integer(config at k))
@@ -120,7 +120,7 @@
return(NULL)
}
-GetParameters <- function(task, sg) {
+.GetParameters <- function(task, sg) {
target <- J(task, "getTarget")
if (J(target, "isBoolean")) {
size <- J(J(sg, "getStatistics"), "getSubgroupSize")
@@ -137,7 +137,7 @@
}
}
-ConvertDescription <- function(sgDescription) {
+.ConvertDescription <- function(sgDescription) {
# Internal function for converting a (Java) SGDescription consisting
# of a set of selection expressions into a character vector of strings
# representing these
@@ -166,10 +166,10 @@
for (sg in sgArray) {
#description <- as.character(J(J(sg, "getSGDescription"), "getDescription"))
sgDescription <- J(sg, "getSGDescription")
- description <- ConvertDescription(sgDescription)
+ description <- .ConvertDescription(sgDescription)
quality <- J(sg, "getQuality")
size <- J(J(sg, "getStatistics"), "getSubgroupSize")
- parameters = GetParameters(task, sg)
+ parameters = .GetParameters(task, sg)
pattern <- new("Pattern", description=description, quality=quality, size=size, parameters=parameters)
patterns = append(patterns, pattern)
}
@@ -198,7 +198,7 @@
}
-FormatDoubleSignificantDigits <- function(double, ndigits=2) {
+.FormatDoubleSignificantDigits <- function(double, ndigits=2) {
# Internal function: Prints double according to
if (is.numeric(ndigits)) {
sprintf(paste("%.", ndigits, "f", sep=""), double)
@@ -230,13 +230,13 @@
i = 1
for (pattern in patterns) {
descriptions[i] = paste(pattern at description, collapse=", ")
- qualities[i] = FormatDoubleSignificantDigits(pattern at quality, ndigits)
+ qualities[i] = .FormatDoubleSignificantDigits(pattern at quality, ndigits)
sizes[i] = pattern at size
if (!is.null(pattern at parameters$mean)) {
- ps[i] = FormatDoubleSignificantDigits(pattern at parameters$mean, ndigits)
+ ps[i] = .FormatDoubleSignificantDigits(pattern at parameters$mean, ndigits)
isNumeric = TRUE
} else {
- ps[i] = FormatDoubleSignificantDigits(pattern at parameters$p, ndigits)
+ ps[i] = .FormatDoubleSignificantDigits(pattern at parameters$p, ndigits)
isNumeric = FALSE
}
i = i + 1
@@ -257,7 +257,7 @@
return(dataframe)
}
-freeMemory <- function(...) {
+.FreeMemory <- function(...) {
# Call the R garbage collection
# Then call Java garbage collection
gc(...)
Added: pkg/man/Pattern-class.Rd
===================================================================
--- pkg/man/Pattern-class.Rd (rev 0)
+++ pkg/man/Pattern-class.Rd 2014-08-02 19:21:38 UTC (rev 15)
@@ -0,0 +1,34 @@
+\name{Pattern-class}
+\docType{class}
+\alias{Pattern-class}
+\alias{Pattern}
+
+\title{Class ``Pattern'' --- A Simple Subgroup Description Container}
+\description{A Simple Container holding the results (subgroups, description and
+ parameters) for the Subgroup and Pattern Mining Algorithms}
+
+\section{Objects from the Class}{
+ Objects are created by calls of the form
+ \code{new("Pattern", ...)}.
+}
+
+\section{Slots}{
+ \describe{
+ \item{\code{description}:}{The subgroup description,
+ as a character vector.
+ }
+ \item{\code{quality}:}{The numeric value denoting the
+ quality of the subgroup pattern as determined by the applied
+ quality function.
+ }
+ \item{\code{size}:}{The size of the subgroup.}
+ \item{\code{parameters}}{Additional quality parameters of the subgroup.}
+ }
+ }
+\seealso{
+\code{\link{DiscoverSubgroups}}.
+\code{\link{DiscoverSubgroupsByTask}}
+\code{\link{CreateSDTask}}
+}
+
+\keyword{classes}
Added: pkg/man/credit.data.Rd
===================================================================
--- pkg/man/credit.data.Rd (rev 0)
+++ pkg/man/credit.data.Rd 2014-08-02 19:21:38 UTC (rev 15)
@@ -0,0 +1,11 @@
+\name{credit.data}
+\docType{data}
+\alias{credit}
+\title{Statlog (German Credit Data) Data Set}
+\description{
+ This dataset classifies people described by a set of attributes as good or bad credit risks.
+}
+\usage{credit.data}
+\format{A vector containing 1000 observations.}
+\source{UCI Repository, https://archive.ics.uci.edu/ml/datasets/Statlog+(German+Credit+Data).}
+\keyword{datasets}
\ No newline at end of file
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