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Releases: miicTeam/miic_R_package

v2.0.3

24 Sep 09:05
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v2.0.3

Features

  • Release to CRAN.

  • tMIIC version for temporal causal discovery on stationary time series:
    new mode of miic() to reconstruct networks from temporal stationary
    datasets (Simon et al., eLife 2024).
    The temporal mode of miic() is not activated by default and can be enabled by
    setting the newly added parameter mode to "TS"(Temporal Stationary).
    A tuning of the temporal mode is possible through a set of new parameters:
    max_nodes, n_layers, delta_t, mov_avg and keep_max_data.

  • Addition of the 'is consequence' prior knowledge. Consequence variables are
    excluded from the possible contributors, edges between consequences are
    ignored and edges between a non consequence and a consequence are pre-oriented
    toward the consequence.
    Information about consequence variables can be provided to miic()
    in the state_order, by supplying an is_consequence column.

  • iMIIC version introducing contextual variables, genuine vs putative causes
    and multiple enhancements to deal with very large datasets (Ribeiro-Dantas et al., iScience 2024).
    Information on contextual variables can be provided to miic()
    in the state_order, by supplying an is_contextualcolumn and
    genuine vs putative causes can be tuned by the newly added parameter
    ort_consensus_ratio.

  • Enhancement of orientations using mutual information supremum principle for
    finite datasets (Cabeli et al., Why21 at NeurIPS 2021).
    The use of enhanced orientations is controlled by the newly added parameter
    negative_info of miic() and is activated by default.

Fixes and improvements

  • Faster post-processing in R for datasets with large number of variables.

  • Fix for memory overflow on shared memory space.

  • The discretization of continuous variables has been improved when dealing
    with variables having a large number of identical values.

Breaking changes

As part of this major release, consolidation of long-pending breaking changes:

  • Harmonization of exported function names using camel case.

  • Harmonization of parameters and return values using snake case.

  • Harmonization of abbreviations.

All the documentation has been updated accordingly, in case of issue when
upgrading to this version, please consult the help of the relevant function
for more information about its interface.

For the core miic() function, the main breaking changes in the interface
when upgrading from the 1.5.3 release are:

in the parameters:

  • cplx: renaming of the complexity term "mdl""bic"

  • ori_proba_ratioort_proba_ratio

in the miic object returned:

  • all.edges.summarysummary

    • Nxy_ain_xy_ai
    • log_confidenceinfo_shifted
    • infOrtort_inferred
    • trueOrtort_ground_truth
    • isOrtOkis_inference_correct
    • isCausalis_causal
    • probap_y2x, p_x2y
    • consensusort_consensus
  • orientations.probtriples

    • NI3ni3
    • Errorconflict

Still compared to 1.5.3, another important change in the behavior of miic()
is that, by default, miic() no longer propagates orientations
and allows latent variables discovery during orientation step.

Known issues

  • Conditioning on a (very) large number of contributors can lead to a memory
    fault.

v1.5.3

04 Nov 12:29
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Fixes and improvements

  • Apply proper conditions to determine if a directed edge represents a causal relation

  • Fix the check error on CRAN Solaris

  • Fix some edge case bugs

v1.5.2

01 Oct 12:51
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Fixes and improvements

  • Further refactoring of the C++ code for the computation of information

  • Fix minor bugs in the continuous computation

  • Fix incompatibility with older versions of GCC (std::align)

v1.5.1

01 Oct 12:42
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Fixes and improvements

  • Fix various bugs in the computation of information in the presence of NA
    values in the dataset.

  • An overhaul of the C++ code base, better memory management, computation time
    and code readability.

v1.5.1-rc1

17 Sep 15:34
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v1.5.1-rc1 Pre-release
Pre-release

Fixes and improvements

  • Fix various bugs in the computation of information in the presence of NA
    values in the dataset.

  • An overhaul of the C++ code base, better memory management, computation time
    and code readability.

v1.5.0

11 Sep 17:04
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Features

  • Add a column consensus to the reconstructed graph's edges summary associated
    with the option consistent, and a new parameter consensus_threshold
    accordingly.

  • Add a parameter ori_proba_ratio to have more control on the orientation of
    edges.

Fixes and improvements

  • Faster post processing in R

  • Rework plot functionality

  • Fix a bug in the orientation part about the log score

  • Refactor of the C++ code base (orientation).

v1.5.0 submission

17 Aug 09:47
4684ea9
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v1.5.0 submission Pre-release
Pre-release

Features

  • Add a column consensus to the reconstructed graph's edges summary associated
    with the option consistent, and a new parameter consensus_threshold
    accordingly.

  • Add a parameter ori_proba_ratio to have more control on the orientation of
    edges.

Fixes and improvements

  • Faster post processing in R

  • Rework plot functionality

  • Fix a bug in the orientation part about the log score

  • Refactor of the C++ code base (orientation).

v1.4.2

31 Jul 11:56
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  • Various fixes of memory leaks
  • Refactoring of confidence cut code

v1.4.2

28 Jul 10:57
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v1.4.2 Pre-release
Pre-release

Last fixes before CRAN resubmission

v1.4.0

24 Jul 14:02
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v1.4.0 submitted to CRAN