Update to package documentation to resolve further merge conflicts

Author: MaartenMarsman

DESCRIPTION

@@ -2,11 +2,7 @@ Package: bgms
 Type: Package
 Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
 Version: 0.1.5.0
-<<<<<<< HEAD
 Date: 2025-08-03
-=======
-Date: 2025-06-27
->>>>>>> adaMala
 Authors@R: c(
     person("Maarten", "Marsman", , "m.marsman@uva.nl", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5309-7502")),
@@ -43,4 +39,4 @@ Suggests:
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-Config/Needs/website: tidyverse/tidytemplate
+Config/Needs/website: tidyverse/tidytemplate

R/RcppExports.R

@@ -1,6 +1,14 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+run_bgmCompare_parallel <- function(observations, num_groups, counts_per_category, blume_capel_stats, pairwise_stats, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed, update_method, hmc_num_leapfrogs) {
+    .Call(`_bgms_run_bgmCompare_parallel`, observations, num_groups, counts_per_category, blume_capel_stats, pairwise_stats, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed, update_method, hmc_num_leapfrogs)
+}
+
+run_bgm_parallel <- function(observations, num_categories, pairwise_scale, edge_prior, inclusion_probability, beta_bernoulli_alpha, beta_bernoulli_beta, dirichlet_alpha, lambda, interaction_index_matrix, iter, burnin, counts_per_category, blume_capel_stats, main_alpha, main_beta, na_impute, missing_index, is_ordinal_variable, baseline_category, edge_selection, update_method, pairwise_effect_indices, target_accept, pairwise_stats, hmc_num_leapfrogs, nuts_max_depth, learn_mass_matrix, num_chains, nThreads, seed) {
+    .Call(`_bgms_run_bgm_parallel`, observations, num_categories, pairwise_scale, edge_prior, inclusion_probability, beta_bernoulli_alpha, beta_bernoulli_beta, dirichlet_alpha, lambda, interaction_index_matrix, iter, burnin, counts_per_category, blume_capel_stats, main_alpha, main_beta, na_impute, missing_index, is_ordinal_variable, baseline_category, edge_selection, update_method, pairwise_effect_indices, target_accept, pairwise_stats, hmc_num_leapfrogs, nuts_max_depth, learn_mass_matrix, num_chains, nThreads, seed)
+}
+
 get_explog_switch <- function() {
     .Call(`_bgms_get_explog_switch`)
 }
@@ -13,14 +21,6 @@ rcpp_ieee754_log <- function(x) {
     .Call(`_bgms_rcpp_ieee754_log`, x)
 }
 
-run_bgmCompare_parallel <- function(observations, num_groups, counts_per_category, blume_capel_stats, pairwise_stats, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed, update_method, hmc_num_leapfrogs) {
-    .Call(`_bgms_run_bgmCompare_parallel`, observations, num_groups, counts_per_category, blume_capel_stats, pairwise_stats, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed, update_method, hmc_num_leapfrogs)
-}
-
-run_bgm_parallel <- function(observations, num_categories, pairwise_scale, edge_prior, inclusion_probability, beta_bernoulli_alpha, beta_bernoulli_beta, dirichlet_alpha, lambda, interaction_index_matrix, iter, burnin, counts_per_category, blume_capel_stats, main_alpha, main_beta, na_impute, missing_index, is_ordinal_variable, baseline_category, edge_selection, update_method, pairwise_effect_indices, target_accept, pairwise_stats, hmc_num_leapfrogs, nuts_max_depth, learn_mass_matrix, num_chains, nThreads, seed) {
-    .Call(`_bgms_run_bgm_parallel`, observations, num_categories, pairwise_scale, edge_prior, inclusion_probability, beta_bernoulli_alpha, beta_bernoulli_beta, dirichlet_alpha, lambda, interaction_index_matrix, iter, burnin, counts_per_category, blume_capel_stats, main_alpha, main_beta, na_impute, missing_index, is_ordinal_variable, baseline_category, edge_selection, update_method, pairwise_effect_indices, target_accept, pairwise_stats, hmc_num_leapfrogs, nuts_max_depth, learn_mass_matrix, num_chains, nThreads, seed)
-}
-
 sample_omrf_gibbs <- function(no_states, no_variables, no_categories, interactions, thresholds, iter) {
     .Call(`_bgms_sample_omrf_gibbs`, no_states, no_variables, no_categories, interactions, thresholds, iter)
 }
@@ -31,4 +31,5 @@ sample_bcomrf_gibbs <- function(no_states, no_variables, no_categories, interact
 
 compute_Vn_mfm_sbm <- function(no_variables, dirichlet_alpha, t_max, lambda) {
     .Call(`_bgms_compute_Vn_mfm_sbm`, no_variables, dirichlet_alpha, t_max, lambda)
-}
+}
+