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gips 1.2.2.9000

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:

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.

gips 1.2.2

Bugfix:

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

gips 1.2.1

Bugfix:

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

gips 1.2.0

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).

gips 1.0.0

• This is the first release of gips.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.