Changes in version 2021-05-16                      

minor CRAN fixes

                     Changes in version 2021-01-26                      

minor changes

  - minor change in rule_based_RandomForest print method
  - default of k_range in train_one_vs_rest_TSP set to 10:50 instead
    of 2:50
  - default of genes_altogether and genes_one_vs_rest in sort_rules_RF
    set to 50 instead of 200
  - default of rules_altogether and rules_one_vs_rest in train_RF set
    to 50 instead of 200
  - Update the tutorial with time and accuracy comparisons

                     Changes in version 2020-11-19                      

changes

  - train_RF has optimized gene_repetition method

                     Changes in version 2020-11-16                      

changes

  - replace the mode imputation method by kNN method in predict_RF
    function.
  - train_RF now stores the whole binary matrix instead of mode matrix.
  - change work-flow figures in the tutorial.
  - the predict_RF function can predict matrix with one sample with no
    error

                     Changes in version 2020-11-02                      

changes:

  - proximity_matrix_RF replaced cocluster_RF function and it can return
    and plot the proximity matrix

Bug fixes:

  - FIXED: plot_binary_RF does not get the predictions and scores when
    using as_training=TRUE and top_anno="platfrom" or "prediction"

                     Changes in version 2020-10-09                      

Additions:

  - Tutorial is available now.

Minor changes:

  - easier access to switchBox disjoint argument in
    train_one_vs_rest_TSP function.
  - Update examples.

Bug fixes:

  - plot_binary_TSP when using ExpressionSet as input with no ref or
    platform.
  - passing additional arguments to SB training function by the user.
  - printing number of rules in the print function for sorted rules.
  - border = NA instead of border = FALSE in plotting functions.
  - optimize_RF can handle two classes problems without errors
  - num.trees = num.trees missed in ranger for featureNo_altogether
    slots

                     Changes in version 2020-09-28                      

Dependencies:

  - Dependency issue solved (switchBox and Biobase packages are
    installed separately).

Minor changes:

  - Update examples.

                     Changes in version 2020-09-24                      

Additions:

  - additional function summary_genes_RF to summarize genes to rules
    stats.
  - additional function optimize_RF to help in train_RF parameters
    optimization.

Changes:

  - plot_binary_RF now supports when RF model is trained with
    probability = FALSE.
  - plot_binary_RF extracts prediction labels for training data from the
    classifier object.
  - imputation is implemented in predict_RF function.
  - NA is not allowed for class and platforms labels.

Optimizations:

  - stats for gene repetition in rules are stored in the sorted rules
    object to make training process faster.

Minor changes:

  - Update examples.
  - minor bug fixes.

                     Changes in version 2020-09-08                      

  - first release on CRAN servers