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rmcfs - changes

Version 1.3.6

• iGraph >2.0.3 compatibility updates
• various memory optimization changes (mode=2 OutOfMemoryError fixed)
• reference links to publication updated

Version 1.3.5

• fixed a java 17 compatibility issue

Version 1.3.4

• fixed a nullpointerexception for numeric target variable
• fixed a buildId param setting (always True)
• fixed a splitSetSize param setting for numeric target variable

Version 1.3.3

• Extreme speedup and memory optimization for the data with large number of rows
• mcfs help Alizadeh data link updated

Version 1.3.2

• closeAllConnections() removed from the code
• final data pruning is processed on R side (memory optimization)

Version 1.3.1

• fixed an issue in fix.data() - function works faster
• fixed an issue with tempdir on some old R versions and OS

Version 1.3.0

• two-stage feature selection implemented
• function mcfs() has new parameter mode - if mode = 2 mcfs runs 2 stage filtering that is much faster and gives more detailed ID-Graphs
• two-stage feature selection - rankings from both phases are saved () and combined together to create the final one
• in function mcfs there is a new cutoff method cutoffMethod - if cutoffMethod = “contrast” then cutoff value is determined based on contrast attributes
• mcfs now supports weighting of input attributes - new parameter ‘attrWeights’ in mcfs()
• read/write to/from adx/adh now supports data.frame attributes: ‘attr_weights’ and ‘target’
• in result$RI data.frame column ‘RI_norm’ is replaced by ‘RI’
• all RI data.frames contains normalized values of the following columns: ‘RI’, ‘classifiers’ and ‘nodes’
• plots ‘ri’, ‘id’, ‘heatmap’, ‘cmatrix’, ‘features’ support color parameter
• plot.idgraph supports color parameter
• plots: ‘features’ and ‘cv’ are created in ggplot2 by default
• new function export.plots()
• in functions ‘import.result()’ and ‘export.result()’ - path can now define full path to the zip result file and label can be set to NA
• function export.result() saves the ranking in original order (as it is in input data)
• updated vignette file to be consistent with JSS article
• function build.idgraph() works much faster now
• fix.data() works much faster now
• data export/import are improved
• some default parameters changed to speed up calculations: featureFreq, splitSetSize, threadsNumber
• removed ‘progressInterval’ parameter
• removed ‘finalCVRepetitions’ parameter
• various minor fixes in plots for some extreme situations
• minor fix in internal function drop.file.extension()
• minor fix in recognition of JAVA version (version 9/10)
• minor fixes in plots for numeric decision MCFS result
• minor fix in adx/adh export for big data
• rmcfs is working on JAVA 7 and above
• dmLab.jar version 2.3.0

Version 1.2.15

• fixed an issue for Java 11

Version 1.2.14

• updated onLoad info

Version 1.2.13

• updated vignette

Version 1.2.12

• updated vignette and citation info to JSS article

Version 1.2.11

• function build.idgraph() has a new parameter ‘outer_ID’
• in function build.idgraph() parameter ‘plot_all_nodes’ is now ‘orphan_nodes’
• fix and efficiency improvement in importing ID-graph from file

Version 1.2.10

• fix for Open JDK 9

Version 1.2.9

• Java version in description file fixed
• minor fix of input parameter ‘seed’
• onLoad info changed

Version 1.2.8

• vignette - bibliography file removed

Version 1.2.7

• mcfs check whether decision attribute contains NA values
• alizadeh dataset has been removed from the package and can be downloaded from the internet
• function refine.data() is now prune.data()
• new vignette article that has been accepted for publication in Jourlan of Statistical Software

Version 1.2.6

• function filter.data() is now refine.data()
• testthat environment added

Version 1.2.5

• function import.result() is fixed for empty results
• functions import.result() and export.result() have default value for parameer: path = “./”
• heatmaps are more readable now
• parameter projectionSize by default is set on sqrt(d)
• parameter featureFreq by default is set on 150

Version 1.2.4

• minor fix in processing temporary paths

Version 1.2.3

• minor fix in cleaning temporary files

Version 1.2.2

• minor fix in uncompression input zip files

Version 1.2.1

• new functions write.adh() and read.adh()
• functions read.adx() and read.adh() can read zipped files
• functions write.adx(), write.arff(), write.adh() have new parameter ‘zip’ and they may produce zipped data
• in plot(type = ‘features’) by default ‘size = NA’ and it means ‘cutoff_value’ * 1.2 features
• in plot(type = ‘ri’) and plot(type = ‘id’) by default ‘size = NA’ and it means ‘cutoff_value’ * 10 features
• few minor fixes
• dmLab.jar version 2.2.1

Version 1.2.0

• new featureFreq parameter - it determines how many times each input feature must be randomly selected when projections = ‘auto’.
• parameter ‘balanceRatio’ is now ‘balance’
• parameters balance, projectionSize, projections are set on ‘auto’ value by default
• in function plot.mcfs() has new updated parameters: plot_permutations, plot_diff_bars, cv_measure
• in function plot.idgraph() parameter ‘label.dist’ is now ‘label_dist’
• in function write.adx() parameter ‘chunk.size’ is now ‘chunk_size’
• in function write.arff() parameter ‘chunk.size’ is now ‘chunk_size’
• in function fix.data() parameter ‘source.chars’ is now ‘source_chars’, ‘destination.char’->‘destination_char’, ‘numeric.class’->‘numeric_class’, ‘nominal.class’->‘nominal_class’
• in function export.result() parameter ‘save.rds’ is now ‘save_rds’
• in function artificial.data() parameter ‘rnd.features’ is now ‘rnd_features’
• new function read.adx()
• fixed some small problems when important features set is empty
• mcfs_result contains input data data.frame
• new plot type: plot(type=‘heatmap’)
• import and export of zipped result
• dmLab.jar version 2.2.0

Version 1.1.2

• MCFS-ID works on numeric target (new classifier M5 (regression tree) is implemented in MCFS-ID)
• fix.data replaces value ‘?’ by NA
• fix in write.arff
• dmLab.jar version 2.1.2

Version 1.1.1

• function info() is now showme()
• minor fixes
• dmLab.jar version 2.1.1

Version 1.1.0

• first official CRAN release
• functionality of the package is highly simplified - available 12 basic functions
• new names of functions: save.result()/read.result() are now export.result()/import.result(); build.ID.graph() is now build.idgraph()
• removed useles prefix ‘mcfs.’ from input params in function mcfs()
• function fix.data() combines all functionality of: fix.data.values(), fix.data.names() and fix.data.types()
• function mcfc() returns ‘mcfs’ object - one plot() function (parameter ‘type’) and one print() function for ‘mcfs’ object
• function build.idgraph() returns ‘idgraph’ object - new plot() function for ‘idgraph’ object
• function plot(type=“ri”) implements plot.permutations functionality - now it shows maxRI values(if ‘plot_permutations’ = TRUE)
• fixed margins in plot.idgraph() - now idgraph uses entire plot space
• removed curved_edges param from plot.idgraph() - curved_edges are always on
• plot.idgraph() has new parameter label.dist() that defines distance of labels to corresponding nodes
• build.idgraph() implements get.min.ID() functionality - get.min.ID() is not visible
• new function ‘artificial.data(1000)’ that creates example data used in JSS paper
• many minor fixes to meet CRAN rules
• RD files updated by artificial.data example
• function mcfc() has new seed parameter - now it is possible to replicate the result
• dmLab.jar version 2.1.0

Version 1.0.6

• function write.adx is reiplemented and now it uses a smart exporting (chunk based) for huge datasets
• function write.arff is reiplemented and now it uses a smart exporting (chunk based) for huge datasets
• function info() extended and changed - better for huge data.frames
• function fix.data.names added (colNames are cleaned from various unwanted chars e.g. “|”, “#”, “,”)
• fix.data.types and fix.data.values works much faster on huge data
• fixed plot.distances (x axis shows correct values projections(s))
• dmLab.jar version 2.0.6

Version 1.0.5

• useless parameter ‘iType’ is removed from plot.ID.graph function
• in mcfs function removed parameter ‘splitSetSizeLimit’ splitSetSize does the job
• new parameter in mcfs function ‘cutoffMethod’
• fix of helps (mcfs, build.ID.graph, plot.ID.graph)
• running mcfs on one class data is not allowed
• function ‘model.frame’ replaced by faster and more stable own implementation
• updated and improved help *.rd files
• dmLab.jar version 2.0.5

Version 1.0.4

• new parameter in plot.permutations (parameter ‘type’)
• cleaning of temporary files after reading result by mcfs function
• dmLab.jar version 2.0.4

Version 1.0.3

• parameters u & v are available in mcfs function

Version 1.0.2

• new parameter in plot.ID.graph (curved.edges=T)
• refactoring: importances -> RI, interactions -> ID [plot.ID.graph, build.ID.graph, plot.RI, plot.ID]

Version 1.0.1

• new function build.rules
• updated help *.rd files (in mcfs introduced parameters s,t according to official papers about MCFS-ID)

Version 1.0.0

• first version of rmcfs

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.