NEWS

mantar 0.3.2

Updated the vignette to gracefully handle unavailable external data, preventing errors during package checks.

Do not include the README in the installation.
Numerical tolerances in unit tests adjusted to avoid platform-specific test failures.
Regenerating documentation was with the current roxygen2 version.

Fixed issue where off-diagonal elements were counted twice when computing the average sample size.

When both mat and data are provided, mat is used for network estimation, while data is only used for additional calculations (e.g., for compatibility with bootnet).
cor_calc() now automatically scales raw data when no variables are treated as ordered. This was already the case when called indirectly, but now also applies when calling it directly. Only affects the returned means, not the estimated correlations.

Added means argument to regularization_net(). Not intended for typical use, but needed for integration with bootnet.
ns no longer accepts vectors in regularization_net(), instead accepts a matrix.
Added network_vars and auxiliary_vars arguments to cor_calc(), neighborhood_net(), and regularization_net(). These arguments accept both variable names and numeric indices referring to the provided data.

Functions now return imputed data as a mids object when using stacked multiple imputation.
With the new network_vars and auxiliary_vars arguments, users can now specify which variables are used for network estimation and which additional variables are included for correlation estimation in the presence of missing data.

Using only a single value for one of the regularization parameters in nonconvex regularization now results in a message rather than a warning.
Updated all dummy data sets, including the complete versions, and introduced varying amounts of missingness across variables in the incomplete data sets.

The argument k, which controlled the penalty term in information-criterion calculations, has been removed for security reasons. Instead, the penalty type is now specified via the argument ic_type (see the corresponding help pages).

Changed the default handling of the ridge penalty in the multiple-imputation pmm workflow when looking for donors through regressions (mice). Instead of forcing ridge = 0, the function now uses the default value defined by mice, ensuring consistent and method-appropriate regularization.

Added function reg_network() for network estimation using regularization, supporting both convex and non-convex penalties as well as multiple options for computing the likelihood in the information criterion when missing values are present.
Added function ordered_suggest(), a heuristic procedure for identifying variables that may be treated as ordered categorical based on their distribution and available information.
Added dummy data sets mantar_dummy_full_cat and mantar_dummy_mis_cat, containing only ordered categorical variables (with and without missing values).
Added dummy data sets mantar_dummy_full_mix and mantar_dummy_mis_mix, containing mixtures of ordered categorical and continuous variables (with and without missing values).

Added support for treating variables as ordered categorical in the estimation of correlations.
Renamed dummy data sets to mantar_dummy_full_cont and mantar_dummy_mis_cont to better reflect that they contain only continuous variables.
Improved documentation for several functions and updated the README to reflect new functionality.