Changelog

Source: NEWS.md

emba 0.1.8 2021-01-07

• add option all.ss in function get_stable_state_from_models_dir() to include all stable states in the returned tibble object
• fix bug in get_stable_state_from_models_dir() (return empty tibble when no models had stable state)

emba 0.1.7 2020-09-22

• Input functions that read model directories with .gitsbe files, now disregard other kind of files that might be inside these directories.
• add minimum package dependencies in DESCRIPTION file
• add JOSS paper

emba 0.1.6 2020-07-08

• Fixed test for the update_biomarker_files function (writes to tmpdir() instead of the user’s library directory)

emba 0.1.5 2020-07-01

• Finally added tests to the package! Coverage is now 97%.
• Used the pkgdown package to create static html documentation for emba. Check it here!
• Change MCC calculation to return 0 when undefined/NaN MCC scores were produced (which is the correct limiting value - see Chicco at al. (2020)). Thus, the previous versions handling of NaN MCC scores, is now deprecated.
• Add the penalty parameter to account for the difference in model group size when calculating the average activity or link operator data differences. This minimizes the bias in the returned biomarkers.
  • For the implementation check the function emba::get_vector_diff and the corresponding StackOverflow question.
  • To get the same results as with previous versions of this library, use penalty=0 in the general emba::biomarker_* functions (though the results will probably be very biased and that’s why the default value for the penalty is now 0.1).
• Changed documentation to specify that the models.stable.state parameter used in various functions can take any values in the [0,1] interval and not just 0 (inactive) and 1 (active).
• The following functions do not take the redundant parameter models anymore:
  • emba::get_avg_link_operator_diff_mat_based_on_tp_predictions
  • emba::get_avg_activity_diff_mat_based_on_tp_predictions
  • emba::get_avg_activity_diff_based_on_tp_predictions
• Refactor several of the functions that load the results from the DrugLogics pipeline:
  • If a model has less or more than 1 stable state, it’s discarded and a message is printed.
  • Return value is now a data.frame object instead of a matrix.
  • The models names do not have the annoying .gitsbe extension anymore.
  • These changes affect the following functions: emba::get_link_operators_from_models_dir, emba::get_stable_state_from_models_dir and emba::get_model_names.
• The general functions emba::biomarker_mcc_analysis and emba::biomarker_tp_analysis do not use the calculate.subsets.stats input option anymore. The emba::biomarker_synergy_analysis continues to do so and now also calculates and returns all possible synergy set and subset pairs that miss just one of the model predicted synergies (emba::get_synergy_comparison_sets).
• Various small bug fixes and other code refactoring :)

emba 0.1.4 2020-04-14

• get_synergy_scores now supports reading both ensemble-wise and model-wise synergies files
• add calculate.subsets.stats option to the general analysis functions (biomarker_*) that decides if the powerset of the observed synergies and the number of models predicting each subset is going to be calculated. The default value is set to FALSE to save computation time :)

emba 0.1.3 Unreleased

• add function get_synergy_scores
• fixed test that used a randomly generated matrix

emba 0.1.2 2020-02-06

• add function get_avg_link_operator_diff_based_on_synergy_set_cmp
• add function get_avg_link_operator_diff_based_on_specific_synergy_prediction
• add function filter_network - to use for visualizing induced subgraphs
• update dependencies (set usefun min version to 0.4.3)

emba 0.1.1 2019-10-21

• Optimized count_models_that_predict_synergies function and added tests for it. For a benchmark see relative Stack Overflow thread

emba 0.1.0 Unreleased

• Added a NEWS.md file to track changes to the package
• Transferred functions from separate R scripts to the package
• Finished code refactoring and splitting to different modules
• Finished writing documentation for all functions