Changes in version 1.2.3 (2025-03-18)                  

Performance gain

There was a significant improvement in the speed of calculation. Details
in the table below for 1000 random permutations of a given size:

| permutation size | 30 | 50 | 100 | 200 | 300 |
|---|---|---|---|---|---| | old computation time | 0.09 s | 0.10 s
| 0.25 s | ~10 s | ~25 s | | new computation time | 0.07 s | 0.08 s
| 0.10 s | 0.17 s | ~0.20 s |

Update to functions

  - plot.gips() can get type = "n0", which will plot the change of n0
    along the "MH" optimization. Handy for deciding of burn-in time;
  - find_MAP(optimizer = "MH") tracks the n0 along the optimization;
  - summary.gips() calculates Likelihood-Ratio test.

                        Changes in version 1.2.2                        

Bugfix:

  - logLik.gips() will return an object of class logLik;
  - Better Vignettes titles.

                 Changes in version 1.2.1 (2023-08-12)                  

Bugfix:

  - One test on alternative BLAS/LAPACK has an alternative check for a
    singular matrix. Found by CRAN's ATLAS test.

                 Changes in version 1.2.0 (2023-08-07)                  

New functions

  - BIC.gips()
  - AIC.gips()
  - logLik.gips()
  - as.character.gips()

Update to functions

  - gips() has a new default D_matrix = mean(diag(S)) * diag(p);
  - summary.gips() calculates AIC, BIC, and n_parameters (number of free
    parameters in the covariance matrix);
  - get_probabilities_from_gips() will return a sorted vector;
  - compare_posteriories_of_perms() and
    compare_log_posteriories_of_perms() have a new parameter digits;
  - Everywhere a permutation was expected, the gips object can now be
    passed and interpreted as a permutation. Those are:
      - perm in gips(), project_matrix(), prepare_orthogonal_matrix(),
        get_structure_constants(), calculate_gamma_function();
      - perm1 and perm2 in compare_posteriories_of_perms(),
        compare_log_posteriories_of_perms();
      - x in gips_perm();
  - plot.gips() can get type = "MLE", which is an alias for type =
    "heatmap";
  - find_MAP(optimizer = "BF") is 3 times faster;
  - find_MAP(optimizer = "BF") is default for perm_size <= 9.

Bugfixes:

  - Sometimes, post_probabilities underflows to 0. This is appropriately
    validated now;
  - NaNs should not occur in find_MAP() for D_matrix <- diag(ncol(S)) *
    d when 1000 < d < 1e300;
  - When NaNs do occur in find_MAP(), they will throw an error (used to
    show a warning);
  - Inf better handled in print.gips();
  - print.*() functions will print \n in the end;
  - Slightly different punctuation in print.gips();
  - Tremendous vignettes and documentation improvements;
  - Proper testing of examples;
  - delta parameter of gips() has to be bigger than 1. We used to
    restrict it to bigger than 2;
  - project_matrix() shows a warning when the non-positive-semi-definite
    matrix is passed as an S argument;
  - project_matrix() preserves colnames() and rownames() of a matrix;
  - D_matrix is checked for containing any NaN or Inf values;
  - Absurdly long structure constants vectors may overflow an integer.
    Now we use double;
  - compare_log_posteriories_of_perms() and
    compare_posteriories_of_perms() show an error when given two
    incomparable gips objects (with different parameters).

                 Changes in version 1.0.0 (2022-10-13)                  

  - This is the first release of gips.