Changelog • gips

gips 1.2.3.9000

Performance gain

project_matrix() is now implemented in C++ internally. Additionally, several internal calculations used by log_posteriori_of_gips() and find_MAP(optimizer = "BF") were optimized.

For Brute Force optimization:

permutation size	6	7	8	9
v1.2.3	1.26 s	4.06 s	30.19 s	4.35 min
v1.2.3.9000	0.64 s	2.66 s	16.31 s	2.17 min

For log_posteriori_of_gips() evaluated on 1000 random permutations of a given size:

permutation size	30	50	100	200	300
v1.2.3	2.31 s	2.31 s	11.70 s	46.49 s	110.17 s
v1.2.3.9000	0.84 s	1.26 s	3.24 s	15.73 s	39.47 s

The above tables based on the code from Pull Request #99.

Update to functions

plot.gips() now uses ggplot2 for all plot types.

Bugfix:

Documentation improvements: grammar and style corrections in roxygen comments, vignettes, and error messages.

gips 1.2.3

CRAN release: 2025-03-18

Performance gain

There was a significant speed improvement in get_structure_constants(), which is used internally by posterior calculations. For 1000 random permutations of a given size:

permutation size	30	50	100	200	300
v1.2.2	0.09 s	0.10 s	0.25 s	~10 s	~25 s
v1.2.3	0.07 s	0.08 s	0.10 s	0.17 s	~0.20 s

This change consequently improved log_posteriori_of_gips(). For 1000 random permutations of a given size:

permutation size	30	50	100	200	300
v1.2.2	1.50 s	2.49 s	7.08 s	55.25 s	169.77 s
v1.2.3	1.29 s	2.24 s	6.84 s	31.73 s	85.10 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.

gips 1.2.2

Bugfix:

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

gips 1.2.1

CRAN release: 2023-08-12

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

CRAN release: 2023-08-07

New functions

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

CRAN release: 2022-10-13

This is the first release of gips.