Small fixes #350
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Small fixes #350
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* fixed issue 342 * updating linter
* updating label switching docs * checking clustering * trying to fix clustering bug * closing in on clustering bug * added long-running cluster test * used algorithm setdiff and updated tests * fixed missing header * got rid of sample.h * got rid of more sample * changing more sampling * got rid of all sample * got rid of all sample things * updated tests * updated test for CRAN * getting rid of more arma sampling * added seed in example * deleted potato_partial * made small clustering dataset and added documentation * added simple cluster test * made more examples * simplified arguments to estimate_partition_function * removed degree argument * default K to 20 * added example to get_transitive_closure * corrected error in example * more documentation updating * updating docs * updating and still passing tests * made simple print methods * many documentation improvements * removed some tests * fixing some types * fixed strange bug * fixed another type * example * parenthesized initialization of List fixed issue on Windows * fixing some codefactor issues * trying to update linter rules * styling * added plot test * added test * added test for theta * removed 'rho' option for BayesMallowsMixtures assess_convergence * removed confusing message * increasing the coverage * increasing tests * more testing * high coverage in assess_convergence * no longer dependent on cowplot * updated raw vignette * bugfix * styling * added tests of setup_rank_data * more tests * fixed some induced errors * added tests for set_compute_options * updating docs * added tests for model options * styling * added initial values test * added test for readLines * some renaming * updating plot_top_k * updated sample_mallows * styling * added simulated Bernoulli data * added Bernoulli test * styling * tests passing, back to R random numbers * removing sample.* * simplifying initialization * simplified constructors * better prior in bernoulli example * added test for assign_cluster * turned off plotting in tests * added tests for compute_consensus * fixing long running example issue * updating longrunning example * cleaning code * changing to pragma once * removing a print statement * removing cran skip * adding some compute_mallows tests * refactored posterior intervals function * added test for compute_intervals for SMC * updating docs * increasing test coverage * styling * increasing test coverage * added test for get_transitive_closure * protecting against overflow in aug prob * added tests for heat_plot * moving around * added test for ties in MAP * added tests for print * updating test * turning off user option test on CI and CRAN * added tests for plot * tests passing * added test for plot.SMCMallows * added skip * styling * some updates * improving distance tests * added some tests * refactoring * running vignettes * checking platform independence * test * adding test * adding test * fix * added test for update_mallows * print * mm * checking platform dependence * adding test * updating * updating makevars * switching to Rcpp::sample * test update * updating test * hopefully having platform independent random numbers * fixing compiler warning * updating test * updating test * getting rid of more arma random * update test * removing more arma::shuffle * updating tests again * updating more tests * adding tests * some final hopefully, test changes * styling * updating tests * test update * trying to bypass seed things * Revert "test update" This reverts commit 18cfaf5. * giving up * tests are fine now * adding test * adding plot_top_k test * adding test for top-k * adding more tests * increasing tests * adding tests for plot_elbow * fixing error in bernoulli_data docs * added function for getting cardinalities * getting it right for Ulam distance * changed part of the logz things * fixed error in _pkgdown.yml * styling * styling * all working with exact distances * updating docs * functionality working for estimated partition function * fixed bug in updated partial rankings * rebuilt vignettes * added handling of estimated logz * added estimated partition function to update_mallows * some cleaning * refactoring * put the header where it belongs * refactoring all distances * styling * added some fixes * updated test * update url * exporting cardinalities that were missing * updating docs * fixing data issue * some readability improvements * simplification and overloading * refactoring aug_prob * refactoring * removed forward argument * renaming * updating tests * added speedup trick for augmented ranks * removed unused definition * removed redundant casts * some really serious refactoring of pairwise * more refactoring * got rid of list-list-list-list of constraints * pulled out a function * fixing pragma once * vectorized * updated Bernoulli example data * styling * correcting the Bernoulli model * removed cast * consting * forgot something * split out distributions in own files * removing some unnecessary code * moving a member between classes * improving initialization of missing ranks * reorganized source code * refactoring * Many updates * fixing parallel SMC * rebuilt vignettes * rebuilt parallel chains vignette with proper seeds * fixing S3 error * pleasing the linter * small typo * added pseudo aug distance option * vignette update * improved code * privatized * privatized more * styling * improving pointer initialization * privatized * updated tests * privatized * more class improvement * one platform independent sampler * simplifying syntax * deduplication * styling * betting on return value optimization * updating tests because random number sequence has changed * correcting a bug * updating tests * adding Mac exception * adding architecture specification for skip * added note about prior sampling * switch to call-by-reference * small bug fix in pseudo-likelihood proposal * removing a line break * small steps towards the goal * removed unnecessary line * made consistent vector part of particles * made aug_distance a separate object * changed to one foreach * removed commented code * refactoring * for each in reweight * changed to pointer for matrix * completed transition * got rid of parallel approach for SMC as it is incorrect * rebuilt SMC vignette * removing header file from work-docs * cleaning the work docs
wleoncio
approved these changes
Jan 12, 2024
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