Merge pull request #42 from osorensen/aider-test

Aider test

Author: osorensen

.Rbuildignore

@@ -4,3 +4,4 @@
 ^data-raw$
 ^dev$
 ^\.github$
+^cran-comments\.md$

.gitignore

@@ -2,4 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
-parameter_trace
+.aider*

DESCRIPTION

@@ -7,13 +7,16 @@ Authors@R: c(person("Oystein", "Sorensen",
                     role = c("aut", "cre"),
                     comment = c(ORCID = "0000-0003-0724-3542")))
 Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
-Description: Nested sequential Monte Carlo algorithms for the Bayesian Mallows
-    model.
+Description: Provides nested sequential Monte Carlo (SMC^2) algorithms for 
+    performing Bayesian inference in the Mallows model for ranking data. 
+    The package implements efficient algorithms for sequential learning 
+    with both complete and partial rankings, supporting multiple distance 
+    metrics including Kendall, Spearman, Cayley, Hamming, and footrule distances.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 LinkingTo: 
     Rcpp,
     RcppArmadillo

NEWS.md

@@ -0,0 +1,7 @@
+# BayesMallowsSMC2 0.1.1
+
+* Initial CRAN submission
+* Implements nested sequential Monte Carlo (SMC^2) algorithms for Bayesian Mallows model
+* Supports multiple distance metrics: Kendall, Spearman, Cayley, Hamming, and footrule
+* Handles both complete and partial rankings
+* Includes functions for hyperparameter setting and SMC options configuration

R/RcppExports.R

@@ -17,7 +17,7 @@
 #' The function generates all possible topological sorts for the provided preference matrix
 #' and saves approximately `save_frac` of the sorts in a matrix which is returned.
 #'
-#' @return This function returns the number of topological sorts.
+#' @return A list containing the number of topological sorts and optionally a matrix of sorts.
 #'
 #' @export
 #' @examples

cran-comments.md

@@ -0,0 +1,17 @@
+## Test environments
+* local R installation, R 4.3.2
+* ubuntu 20.04 (on GitHub Actions), R 4.1.0, 4.2.0, 4.3.0
+* win-builder (devel and release)
+* macOS (on GitHub Actions), R 4.3.0
+
+## R CMD check results
+
+0 errors | 0 warnings | 0 notes
+
+## Downstream dependencies
+
+There are currently no downstream dependencies for this package.
+
+## Comments
+
+This is a new submission of BayesMallowsSMC2, providing nested sequential Monte Carlo algorithms for the Bayesian Mallows model.

man/precompute_topological_sorts.Rd

@@ -7,7 +7,7 @@
 #include <list>
 #include <string>
 #include <sstream>
-#include <filesystem>
+#include <R_ext/Utils.h>
 using namespace std;
 
 class Graph {
@@ -37,6 +37,11 @@ void Graph::alltopologicalSortUtil(
     std::vector<arma::ivec>& sorts, double save_frac) {
   bool flag = false;
 
+  // Check for user interrupts in long-running recursive function
+  if (sort_count % 1000 == 0) {
+    R_CheckUserInterrupt();
+  }
+
   for (size_t i{}; i < n_items; i++) {
     if (indegree[i] == 0 && !visited[i]) {
       list<int>::iterator j;
@@ -102,7 +107,7 @@ arma::imat Graph::alltopologicalSort(long long int& sort_count, double save_frac
 //' The function generates all possible topological sorts for the provided preference matrix
 //' and saves approximately `save_frac` of the sorts in a matrix which is returned.
 //'
-//' @return This function returns the number of topological sorts.
+//' @return A list containing the number of topological sorts and optionally a matrix of sorts.
 //'
 //' @export
 //' @examples

src/all_topological_sorts.cpp

@@ -36,6 +36,9 @@ unsigned int CayleyDistance::d(const uvec& r1, const uvec& r2) {
 }
 
 unsigned int FootruleDistance::d(const uvec& r1, const uvec& r2) {
+  if(r1.size() != r2.size()) {
+    Rcpp::stop("Rankings must have the same length");
+  }
   unsigned int value{};
   for(size_t i{}; i < r1.size(); i++) {
     value += r1[i] > r2[i] ? r1[i] - r2[i] : r2[i] - r1[i];
@@ -61,6 +64,9 @@ unsigned int KendallDistance::d(const uvec& r1, const uvec& r2) {
 }
 
 unsigned int SpearmanDistance::d(const uvec& r1, const uvec& r2) {
+  if(r1.size() != r2.size()) {
+    Rcpp::stop("Rankings must have the same length");
+  }
   unsigned int value{};
   for(size_t i{}; i < r1.size(); i++) {
     value += r1[i] > r2[i] ? pow(r1[i] - r2[i], 2) : pow(r2[i] - r1[i], 2);

src/distances.cpp

@@ -1,5 +1,6 @@
 // [[Rcpp::depends(RcppArmadillo)]]
 #include <RcppArmadillo.h>
+#include <R_ext/Utils.h>
 #include "prior.h"
 #include "data.h"
 #include "distances.h"
@@ -42,6 +43,7 @@ Rcpp::List run_smc(
   std::vector<double> iteration_times;
 
   for(size_t t{}; t < T; t++) {
+    R_CheckUserInterrupt();
     reporter.report_time(t);
 
     for(auto& p : particle_vector) {