HEMDAG 2.6.1

CHANGES

• fixed stringsAsFactors issue – link;

HEMDAG 2.6.0

CHANGES

• fixed NAMESPACE notes in CRAN checks;
• added link to the GitHub repository obogaf::parser;
• adjusted link to read the docs;

HEMDAG 2.5.9

NEW FEATURES

• added build.consistent.graph;

CHANGES

• added some warning checks in functions that compute performance metrics;
• improved some graph utility functions;
• improved manual;
• improved tutorial on read the docs – link;
• namespace made clearer;
• fixed minor bugs;
• removed defunct functions;

HEMDAG 2.4.8

CHANGES

• fixed a minor bug in Do.GPAV.holdout;
• improved package description;

HEMDAG 2.4.7

NEW FEATURES

• fixed degenerate case in precision.at.all.recall.levels.single.class (labels are all negatives/positives);
• fixed degenerate case in precision.at.given.recall.levels.over.classes (labels in a fold are all negatives/positives);
• fixed degenerate case in do.stratified.cv.data.single.class (sampling of the labels with just one positive/negative);
• added input variable compute.performance to the following high level functions:
  • Do.TPR.DAG and Do.TPR.DAG.holdout;
  • Do.HTD and Do.HTD.holdout;
  • Do.GPAV and Do.GPAV.holdout;
  • Do.heuristic.methods and Do.heuristic.methods.holdout;

CHANGES

• improved manual;

HEMDAG 2.3.6

NEW FEATURES

• added lexicographical.topological.sort;

CHANGES

• fixed minor bugs;
• improved manual;

HEMDAG 2.2.5

NEW FEATURES

• precision-recall performance computed through precrec package:
  • added precision.at.all.recall.levels.single.class;
  • PXR.at.multiple.recall.levels.over.classes substituted with precision.at.given.recall.levels.over.classes;
• improved IO functions: the extension of the input or output file can be or plain text (.txt) or compressed (.gz);

CHANGES

• fixed minor bugs;
• improved manual;

HEMDAG 2.2.4

CHANGES

• fixed CRAN Package Check Results: removed unneeded header and define from GPAV C++ source code

HEMDAG 2.2.3

NEW FEATURES

• Added GPAV algorithm (Burdakov et al., Journal of Computational Mathematics, 2006 – link);
• Embedded GPAV algorithm in the top-down step of the functions TPR.DAG, Do.TPR.DAG and Do.TPR.DAG.holdout;
• Some functions have been defunct. To know the defunct functions just typing in the R environment: help("HEMDAG-defunct");

CHANGES

• improved manual;

AUTHOR

• Added Alessandro Petrini as author for his contribution in writing the C++ code of GPAV algorithm;

HEMDAG 2.1.3

CHANGES

• various fixes from 2.1.2

HEMDAG 2.1.2

NEW FEATURES

• Improved performance metrics:
  • added compute.Fmeasure.multilabel;
  • added PXR.at.multiple.recall.levels.over.classes;
  • all the performance metrics (AUPRC, AUROC, FMM, PXR) can be computed either one-shot or averaged across folds;
• Improved the high-level hierarchical ensemble functions:
  • embedded the new performance metric functions;
  • added the parameter metric: maximization by FMAX or PRC (see manual for further details);
  • added some checkers (warning/stop messages) to make the library more user-friendly;

CHANGES

• improved manual;

HEMDAG 2.0.1

CHANGES

• fixed bug in do.stratified.cv.data.single.class;

HEMDAG 2.0.0

NEW FEATURES

• Added TPR-DAG: function gathering several hierarchical ensemble variants;

• Added Do.TPR.DAG: high-level function to run TPR-DAG cross-validated experiments;

• Added Do.TPR.DAG.holdout: high-level functions to run TPR-DAG holdout experiments;

• The following TPR-DAG and DESCENS high-level functions were removed:

  • Do.tpr.threshold.free;
  • Do.tpr.threshold.cv;
  • Do.tpr.weighted.threshold.free.cv;
  • Do.tpr.weighted.threshold.cv;
  • Do.descens.threshold.free;
  • Do.descens.threshold.cv;
  • Do.descens.weighted.threshold.free.cv;
  • Do.descens.tau.cv;
  • Do.descens.weighted.threshold.cv;
  • Do.tpr.threshold.free.holdout;
  • Do.tpr.threshold.holdout;
  • Do.tpr.weighted.threshold.free.holdout;
  • Do.tpr.weighted.threshold.holdout;
  • Do.descens.threshold.free.holdout;
  • Do.descens.threshold.holdout;
  • Do.descens.weighted.threshold.free.holdout;
  • Do.descens.tau.holdout;
  • Do.descens.weighted.threshold.holdout;

NOTE: all the removed functions can be run opportunely setting the input parameters of the new high-level function Do.TPR.DAG (for cross-validated experiments) and Do.TPR.DAG.holdout (for hold-out experiments);

CHANGES

• improved manual;

HEMDAG 1.1.1

NEW FEATURES

• Added DESCENS algorithm;
• Added Heuristic Methods MAX, AND, OR (Obozinski et al., Genome Biology, 2008 – link);
• Added tupla.matrix function;

CHANGES

• improved manual;
• Added link to the GitHub repository HPOparser (note: from version 2.6.0 HPOparser was changed in obogaf::parser);
• Added CITATION file;

HEMDAG 1.0.0

PACKAGE GENESIS