NEWS

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BGGM 2.1.5 (2024-12-22)

Bug Fixes and Improvements

C++ search Function

1. Improved Initialization

   • The initial adjacency matrix now takes start_adj (the maximum likelihood solution) as the starting point to avoid inefficient sampling.

2. Adaptive Sampling

   • The sampling of zeros and nonzeros is now adapted to the newly accepted adjacency matrix (adj_s) rather than the static start_adj.

3. Efficiency Enhancements

   • Skip updates on rejection since the graph remains unchanged.
   • Use find_ids(adj_mat) instead of find_ids(start_adj) to ensure edge modifications are correctly tracked after acceptance.

Minor Changes:

• Example in bggm_missing.R reintroduced; Was removed due to irreproducible CRAN error.

BGGM 2.1.4 (2024-12-13)

• Addressed CRAN check error when building vignettes (removed example in bggm_missing.R -- will put it back once it's accepted to CRAN).
• Downgraded required R version to 4.0.0

BGGM 2.1.3 (2024-07-05)

• Replaced dprecated armadillo function conv_to<>::from with as_scalar
• prior_sd: Adjusted computation of delta. Also, changed default value for estimation: sqrt(1/3) resulting in delta = 2. For model testing default is more tight, at sigma_sd = 0.5, resulting in delta = 3.
• prior_sd is now limited to range 0 -- sqrt(1/2)

BGGM 2.1.2 (2024-06-22)

• The prior_sd (or rho_sd in var_estimate() ) is limited to ranges between 0 and sqrt(1/8). These values ensure that delta does not go below 1.
• Critical: select() did not return partial correlations, but Fisher-z values in summary(). Fisher values are transformed back to correlation metric. This fixes #90, see changes.
• Upgraded deprecated ggplot guides() argument
• Resolved non positive definite initialization matrix in wishrnd() in copula models when NA's are present in observed variables (fixes #89). See changes here

BGGM 2.1.1 (2024-02-23)

BFpack dependency error fixed.

BGGM 2.0.1 (2020-07-23)

This version of BGGM included changes based on the JOSS reviews: see here for the overview and here for specific issues.

BGGM 2.0.0 (2020-05-31)

BGGM was almost completely rewritten for version 2.0.0. This was due to adding support for binary, ordinal, and mixed data, which required that the methods be written in c ++. Unfortunately, as a result, lots of code from version 1.0.0 is broken.

Added features

• Full support for binary, ordinal, and mixed data. This is implemented with the argument type

• roll_your_own: compute custom network statistics from a weighted adjacency matrix or a partial correlation matrix

• pcor_to_cor: convert the sampled partial correlation matrices into correlation matrices.

• zero_order_cors: compute zero order correlations

• convergence: acf and trace plots

• posterior_samples: extract posterior samples

• regression_summary: summarize multivariate regression

• pcor_sum: Compute and compare partial correlation sums

• weighted_adj_mat: Extract the Weighted Adjacency Matrix

• pcor_mat: Extract the Partial Correlation Matrix

• Five additional data sets were added.

Extensions

• ggm_compare_ppc: added option for custom network statistics

• Added option to control for variables with formula

• A progress bar was added to many functions

BGGM 1.0.0 (2020-02-06)

Initial CRAN release