NEWS

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tna 1.2.3 (2026-04-26)

• Resolved CRAN warning "Data files with namespace references not in the recursive strong package dependencies" by rebuilding engagement_mmm as a tna_mmm object that carries no foreign class references. The new sibling S3 methods group_model.tna_mmm() and mmm_stats.tna_mmm() preserve all existing example behaviour without requiring seqHMM at example-run time. Real mhmm objects from seqHMM continue to work via the original *.mhmm methods.
• Added random_tna(), random_group_tna(), random_tna_mmm(), and list_random_state_pools() for constructing synthetic TNA models with no external dependencies.
• Lowered the minimum required R version from 4.4.0 to 4.1.0 (the floor set by the native |> pipe used in the package).

tna 1.2.2 (2026-04-15)

• Fix bug in plot.tna_sequence_comparison

tna 1.2.1

• The test argument of compare_sequences() is now TRUE by default for backward compatibility.
• Fixed an issue with bootstrap() when the model contained weights that were zero.
• Fixed issues with several distance measures in cluster_sequences().
• Fixed edge ordering in betweenness_network().
• The packages no longer depends on qgraph.
• Network plotting functionality now relies on cograph instead.

tna 1.2.0 (2026-02-12)

• Added the function reliability() for reliability analysis of tna models.
• The import_onehot() function has been redesigned with new features.
• Replaced the Z tests and chi-squared tests in compare_sequences() with a permutation test.
• Removed the chi-squared test from plot_mosaic().
• The correct argument of compare_sequences() has been renamed to adjust to align with other similar arguments.
• Added several new arguments to the plot method of tna objects for plotting heterogeneous networks.
• The plot method for communities now uses the first available method by default.
• The stringdist package has been moved to Suggests.
• Added additional checks for missing columns when using tidy selections in various functions that were previously silently ignored.

tna 1.1.0 (2025-10-18)

• Added the function cluster_sequences() to cluster sequence data using string distance measures of the stringdist package.
• Added the function compare_sequences() to compare the frequencies of patterns between groups for sequence data.
• prepare_data() now accepts a character vector for the actor argument.

tna 1.0.0 (2025-07-15)

• CRAN release

tna 0.7.0

• Added the function import_onehot() to read one-hot data.
• The function plot_sequences() gains the argument ncol for selecting the number of columns of the facets.

tna 0.6.1

• The group column is now automatically removed from cols in group_model().

tna 0.6.0

• Added a new method plot_sequences() for sequence index plots and state distribution plots.

tna 0.5.1

• Fixed the handling of missing values in group_model() with stslist objects.
• Fixed an issue with plot.group_tna_permutation() that resulted in plotting arguments not being passed to qgraph.

tna 0.5.0 (2025-05-26)

• Added a new dataset group_regulation_long.

tna 0.4.9

• Switched to matrix as the internal data format used by TNA models for performance improvements across all functions.

tna 0.4.8

• Fixed an issue with prepare_data() that resulted in excessive console output.

tna 0.4.7

• Added the function import_data() to read wide format sequence data into long format.

tna 0.4.6

• Added the function plot_frequencies() that can be used to plot the state frequency distribution for both tna and group_tna objects.

tna 0.4.5

• The function permutation_test() is now a method for both ungrouped (build_model()) and grouped (group_model()) models. For grouped models, the function performs the test between every unique pair of groups.
• A new argument adjust has been added for permutation_test() to optionally adjust p-values using p.adjust. By default, the p-values are not adjusted (adjust = "none").
• A new argument groupwise has been added for group_model(). When FALSE (the default), scaling methods listed in scaling are performed globally over the groups. When TRUE, the scaling is performed within each group instead (this was the default behavior in previous versions of the package).
• Added a simulate() method for tna objects. For models with type = "relative", this function simulates sequence data based on the initial probabilities and transition probability matrix.

tna 0.4.4

• The plot.tna_centralities() and plot.group_tna_centralities() functions now plot the centralities in the same order as provided in the measures argument.
• The plot.tna() and plot_model() functions now use the median edge weight as the default value for the cut argument.
• Fixed the from and to columns in bootstrap() output, which were inverted from the true edge direction.
• A plot method has been added for the bootstrap() output, which plots the corresponding network where non-significant edges have been pruned.

tna 0.4.3

• The permutation_test() function now properly checks that its arguments x and y can be compared.
• The p-value calculations of permutation_test() and bootstrap() have been adjusted by adding 1 to both the number of permutations/bootstrap samples and the number of extreme events so that these estimates are never zero. The documentation has also been clarified regarding p-values emphasizing that these are estimates only.

tna 0.4.2

• The plot_compare() function now supports negCol and posCol for specifying the color of the positive and negative differences in transition and initial probabilities.
• The plot_mosaic() function now plots the x-axis on the top and rotates the labels 90 degrees only when there are more than three groups.

tna 0.4.1

• The detailed argument of estimate_centrality_stability() has been removed. Previously this argument had no effect on the output of the function.
• Removed several duplicated entries in the documentation.

tna 0.4.0 (2025-03-01)

• The prepare_data() function now produces an object of class tna_data, which can be directly used as an argument to build_model() and other methods.
• The prepare_data() function now supports order when used together with time and actor.
• The prepare_data() function gains the unused_fn argument of tidyr::pivot_wider() to process any extra columns. The default is to keep all columns and use the first value.
• Added the function compare() to compare tna models and weight matrices. This function produces an object of class tna_comparison which has print() and plot() methods.
• Added the function plot_mosaic() which can be used to produce mosaic plots of transition counts for frequency-based transition network models and to contrast the state counts between groups.
• Fixed an issue with plot.tna_communities() which now checks for the availability of a particular community detection method before plotting.
• Made several arguments in the plot methods of the package accessible to the user.

tna 0.3.2

• event2sequence() has been renamed to prepare_data(). The function is now also more general and can process more date formats.
• Added a method argument to bootstrap(). The new default option "stability" implements a bootstrapping scheme where the edge weights are compared against a range of "consistent" weights (see the documentation for details). The old functionality can be accessed with method = "threshold".
• Fixed an issue with permutatation_test() when x and y had a differing number of columns.
• Community detection methods can now be selected using the methods argument in communities().
• The build_model() function has gained the argument cols which can be used to subset the columns of the data for stslist and data.frame inputs.
• Removed all verbose arguments in favor of options(rlib_message_verbosity = "quiet"). and options(rlib_warning_verbosity = "quiet").

tna 0.3.1

• Fixed an issue when checking the validity of character type arguments.
• Improved the bootstrap() function to determine edge significance based on deviation from the observed value, rather than a fixed threshold.
• Added a helper function event2sequence() to parse event data into sequence data.

tna 0.3.0 (2024-12-11)

• Added support for grouped sequence data (clusters).

tna 0.2.0

• Added bootstrapping, permutation test, and centrality stability functionalities.

tna 0.1.0

• Initial version.