Smc issue 306

.gitignore

@@ -4,7 +4,6 @@
 .DS_Store
 .Ruserdata
 inst/doc
-work-docs/
 doc
 Meta
 /doc/

DESCRIPTION

@@ -56,8 +56,7 @@ Imports: Rcpp (>= 1.0.0),
   relations (>= 0.6-8),
   rlang (>= 0.3.1),
   HDInterval (>= 0.2.0),
-  cowplot (>= 1.0.0),
-  methods
+  cowplot (>= 1.0.0)
 LinkingTo: Rcpp, RcppArmadillo, testthat
 Suggests:
   R.rsp,

NAMESPACE

@@ -1,24 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(compute_consensus,BayesMallows)
-S3method(compute_consensus,SMCMallows)
 S3method(compute_posterior_intervals,BayesMallows)
-S3method(compute_posterior_intervals,SMCMallows)
 S3method(plot,BayesMallows)
 S3method(plot,SMCMallows)
 S3method(print,BayesMallows)
 S3method(print,BayesMallowsMixtures)
+S3method(update_mallows,BayesMallows)
+S3method(update_mallows,SMCMallows)
 export(assess_convergence)
 export(assign_cluster)
-export(calculate_backward_probability)
-export(calculate_forward_probability)
 export(compute_consensus)
 export(compute_mallows)
 export(compute_mallows_mixtures)
 export(compute_posterior_intervals)
-export(compute_posterior_intervals_alpha)
-export(compute_posterior_intervals_rho)
-export(compute_rho_consensus)
 export(create_ordering)
 export(create_ranking)
 export(estimate_partition_function)
@@ -35,11 +30,9 @@ export(prepare_partition_function)
 export(rank_distance)
 export(rank_freq_distr)
 export(sample_mallows)
-export(smc_mallows_new_item_rank)
-export(smc_mallows_new_users)
+export(update_mallows)
 importFrom(Rcpp,sourceCpp)
 importFrom(Rdpack,reprompt)
-importFrom(methods,is)
 importFrom(rlang,.data)
 importFrom(stats,aggregate)
 importFrom(utils,head)

NEWS.md

@@ -1,17 +1,51 @@
 # BayesMallows (development versions)
 
+## Changes to sequential Monte Carlo methods
+
+* BREAKING CHANGE: "C" argument removed from plot.SMCMallows() since clustering
+  is currently not supported for these models.
+* BREAKING CHANGE: argument "mcmc_kernel_app" renamed to "mcmc_steps", to 
+  better explain what it is doing.
+* BREAKING CHANGE: argument "nmc" to plot.SMCMallows has been removed because it
+  is now a part of the objects of class "SMCMallows", and hence does not need to
+  be explicitly provided.
+* BREAKING CHANGE: argument "burnin" to plot.SMCMallows has been removed because
+  burnin is not relevant with sequential Monte Carlo.
+* BREAKING CHANGE: arguments "timesteps" and "n_items" to 
+  smc_mallows_new_item_rank() have been removed, since they are given by the 
+  dimension of the rankings argument.
+* function smc_mallows_update() has been added, which allows updating existing
+  models as new data arrive.
+* BREAKING CHANGE: Argument "N" in SMC Mallows functions has been change to 
+  "n_particles".
+* BREAKING CHANGE: Argument "Time" in SMC Mallows functions has been changed to
+  "timesteps", to better describe what it means.
+* BREAKING CHANGE: smc_mallows_new_users() no longer takes the argument 
+  "n_items", as it is given by the number of columns in its "rankings" argument.
+* BREAKING CHANGE: Functions smc_mallows_new_users() and 
+  smc_mallows_new_item_rank() are now wrappers in R, which call the underlying 
+  C++ functions. These functions are now able to compute the partition function
+  automatically, not requiring the user to do this manually. As a consequence,
+  the argument "cardinalities" has been removed, and the argument 
+  "logz_estimate" has changed its expectation, to be consistent with the use
+  in compute_mallows().
+* BREAKING CHANGE: compute_rho_consensus() for SMC Mallows has been deprecated 
+  in favor of compute_consensus().
+* BREAKING CHANGE: compute_posterior_intervals_rho() and compute_posterior_intervals_alpha()
+  for SMC Mallows have been deprecated in factor of 
+  compute_posterior_intervals() with argument parameter = "rho" and
+  parameter = "alpha".
+* Plot title "Implemented SMC scheme" removed from plot.SMCMallows() with 
+  argument parameter = "alpha".
+
+## Other changes
+
 * Argument obs_freq to internal function rmallows() is removed, as it is not 
   being used. Thanks to Lorenzo Zuccato for pointing this our 
   (https://github.com/ocbe-uio/BayesMallows/issues/337).
 * Argument save_clus to compute_mallows() has been removed, as it was not used.
 * compute_mallows() now supports parallel chains, by providing a 'cl' argument.
   See vignette "MCMC with Parallel Chains" for a tutorial.
-* compute_rho_consensus() for SMC Mallows has been deprecated in favor of 
-  compute_consensus().
-* compute_posterior_intervals_rho() and compute_posterior_intervals_alpha()
-  for SMC Mallows have been deprecated in factor of 
-  compute_posterior_intervals() with argument parameter = "rho" and
-  parameter = "alpha".
 * Documentation of functions are now grouped in families.
 * lik_db_mix() is now deprecated in favor of get_mallows_loglik()
 * Unusued argument removed from internal function augment_pairwise(). Thanks to

R/BayesMallows.R

@@ -23,7 +23,7 @@
 #'  \code{\link{estimate_partition_function}}.
 #'  \item For sequential Monte Carlo algorithms developed in
 #'  \insertCite{steinSequentialInferenceMallows2023;textual}{BayesMallows}, see
-#'  \code{\link{smc_mallows_new_users}} and \code{\link{smc_mallows_new_item_rank}}.
+#'  \code{\link{update_mallows}}.
 #' }
 #'
 #'