NEWS/ChangeLog for PLMIX -------------------------- 2.1.1 2019-09-02 NEW FEATURES o Added a new dataset called `d_gaming`. DOCUMENTATION o Removed some typos from the manual. 2.1.0 2019-08-01 MAJOR CHANGES o The pi_inv argument (formerly a numeric N*K matrix with the observed top-ordering) has been redefined as an object of class `top_ordering` or an object that can be coerced with the new function as.top_ordering. o gibbsPLMIX(...): o [::] added the element `objective` in the output list representing the objective function values (that is the kernel of the log-posterior distribution) sampled in the saved MCMC iterations. o mapPLMIX(...): o [::] recoded default value of the argument `plot_objective` from TRUE to FALSE. o make_complete(...), make_partial(...), paired_comparisons(...), rank_ord_switch(...) and rank_summaries(...): o [::] renamed argument `format` as `format_input`. o [::] deleted default value ("ordering") for the former argument `format`. o rPLMIX(...): o [::] renamed argument `format` as `format_output`. o selectPLMIX(...): o [::] renamed argument `post_summary` as `post_est`. o `d_apa`, `d_carconf`, `d_dublinwest`, `d_german`, `d_nascar`, `d_occup` and `d_rice` o [::] appended S3 class `top_ordering` to the supplied top-ordering datasets. o [::] renamed columns of the supplied top-ordering datasets. MINOR CHANGES o fixed a CRAN error due to the cleanEX(...) procedure in the R CMD check. o mapPLMIX(...): o [::] reversed order between the `P_map` and `W_map` elements in the output list. o rank_ord_switch(...): o [::] added names to the columns of the output matrix. o unit_to_freq(...): o [::] added name `freq` to the last column of the output matrix. NEW FEATURES o Added the new membership function is.top_ordering(...) that verifies whether the supplied data satisfy the conditions to be a top-ordering dataset (various object classes are accepted for the input data). o Added the new coercion function as.top_ordering(...) that attempts to coerce the supplied data into an object of S3 class `top_ordering` (various object classes and forms are accepted for the input data). o Appended S3 class `mpPLMIX` to the list returned by mapPLMIX(...) and mapPLMIX_multistart(...). o Added generic S3 class methods for objects of class `mpPLMIX` named as print.mpPLMIX(...), summary.mpPLMIX(...) and plot.mpPLMIX(...). o Appended S3 class `gsPLMIX` to the list returned by gibbsPLMIX(...). o Added generic S3 class methods for objects of class `gsPLMIX` named as print.gsPLMIX(...), summary.gsPLMIX(...) and plot.gsPLMIX(...). o Added the new function gsPLMIX_to_mcmc(...) to coerce an object of class `gsPLMIX` into an object of class `mcmc` as defined by the function as.mcmc(...) of the `coda` package. o Added two further datasets called `d_occup` and `d_rice`. o Added packages `coda`, `ggmcmc`, `ggplot2`, `radarchart`, `prefmod`, `rankdist`, `StatRank`, `pmr`, `PlackettLuce`, `utils` and `reshape2` in Imports. DOCUMENTATION o The manual has been globally reviewed and improved accordingly with the new changes and the additional implementations described in NEW FEATURES. o label_switchPLMIX(...): o [::] added the citation Papastamoulis, P. (2016). 2.0.1 2018-05-02 MINOR CHANGES o fixed former warnings using if() with conditions of length greater than one. We have also checked the current version with _R_CHECK_LENGTH_1_CONDITION_ set to true. o gibbsPLMIX(...): o [::] colnames added to output values labelled as `P` and `W`. o mapPLMIX(...): o [::] dimnames change for output value labelled as `P_map`. o [::] names added to output value labelled as `W_map`. o rank_summaries(...): o [::] format and label change for the former output value labelled as `missing_pos` now labelled as `na_or_not`. o [::] output values labelled as `mean_rank` and `marginals` now contain dimnames. 2.0 2018-01-31 BUG FIXES o mapPLMIX(...) o random_start(...) o rank_summaries(...) MAJOR CHANGES o bicPLMIX(...): o [::] replaced former argument `weights` as `G`. o [::] added default values for the arguments `ref_known` and `ref_vary`. o [::] added the reference Schwarz (1978). o gibbsPLMIX(...): o [::] added the `centered_start` argument for the random generation of the starting values, similarly to the mapPLMIX(...) and mapPLMIX_multistart(...) functions. o label_switchPLMIX(...): o [::] added new function to perform label switching adjustment of the posterior MCMC samples, formerly implemented by both the ppcheckPLMIX(...) and the ppcheckPLMIX_cond(...) functions. o mapPLMIX(...): o [::] modified the default value of the argument `eps` in accordance with that of the related mapPLMIX_multistart(...) function. o [::] modified the default value of the argument `plot_objective`. o [::] dropped object `Rho_map` from the output list. o [::] renamed object `z` of the output list as `z_hat`. o [::] renamed object `classification` of the output list as `class_map`. o [::] `bic` value is computed only for the default flat priors case, otherwise NULL is returned. o mapPLMIX_multistart(...): o [::] recoded default value of the argument `init`. o ppcheckPLMIX(...) and ppcheckPLMIX_cond(...): o [::] removed former arguments `MAPestP`, `MAPestW`, `ls_adj` and `adj_post_sample` needed for the label switching adjustment, which is currently implemented by the novel label_switchPLMIX(...) function. o [::] removed `final_sampleP` and `final_sampleW` objects from the output. o rank_summaries(...): o [::] renamed the argument and output object `pairedcomparisons` as `pc`. o [::] renamed the output object `missing_positions` as `missing_pos`, o rPLMIX(...): o [::] renamed former `rankingoutput` argument with `format`. o selectPLMIX: o [::] removed argument `log_lik`. MINOR CHANGES o ppcheckPLMIX(...) and ppcheckPLMIX_cond(...): o [::] added some messages. o "G=" replaced with "G_". o make_partial(...): o [::] renamed argument `probcensoring` as `probcens`. DOCUMENTATION o The manual has been globally reviewed and improved with additional implementation details and some new examples. o Added new examples for the three data objects `d_apa`, `d_carconf` and `d_dublinwest` showing how to extract the subset of complete orderings from the whole dataset. o Updated reference Mollica and Tardella (2016) as Mollica and Tardella (2017). o d_german dataset: modified the citation Croon (1989). o mapPLMIX(...) and mapPLMIX_multistart(...): o [::] added the citation Gormley and Murphy (2006). o ppcheckPLMIX(...) and ppcheckPLMIX_cond(...): o [::] removed example of label switching adjustment. o selectPLMIX(...): o [::] added Details section. o [::] renamed output objects `fitting_measures`, `effective_number_of_parameters` and `selection_criteria` as `fitting`, `penalties` and `select_criteria`. CITATION INFO o Added bibTex entries in the file CITATION. o Updated reference Mollica and Tardella (2016) as Mollica and Tardella (2017) in the CITATION info. NEW FEATURES o Removed package `combinat` from Imports. o Changed order in the namespace list (former: foreach abind rcdd FSA).