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Merged
MaartenMarsman merged 6 commits into from
Sep 22, 2025
Merged

parallel progress bar and interrupt #56

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671d3e1
parallel progress bar and interrupt
vandenman Sep 22, 2025
6198ad3
let's rebase first
vandenman Sep 22, 2025
1607723
fix rebase
vandenman Sep 22, 2025
33d55f9
almost done
vandenman Sep 22, 2025
029e7cf
cleanup
vandenman Sep 22, 2025
9c77cf2
fix rebase again
vandenman Sep 22, 2025
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8 changes: 4 additions & 4 deletions R/RcppExports.R
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
# 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_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, progress_type) {
.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, progress_type)
}

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)
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, progress_type) {
.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, progress_type)
}

get_explog_switch <- function() {
Expand Down
10 changes: 7 additions & 3 deletions R/bgm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ bgm = function(
dirichlet_alpha = 1,
lambda = 1,
na_action = c("listwise", "impute"),
display_progress = TRUE,
display_progress = c("per-chain", "total", "none"),
update_method = c("nuts", "adaptive-metropolis", "hamiltonian-mc"),
target_accept,
hmc_num_leapfrogs = 100,
Expand Down Expand Up @@ -324,7 +324,7 @@ bgm = function(
"."))

#Check display_progress ------------------------------------------------------
display_progress = check_logical(display_progress, "display_progress")
progress_type = progress_type_from_display_progress(display_progress)

#Format the data input -------------------------------------------------------
data = reformat_data(x = x,
Expand Down Expand Up @@ -428,7 +428,7 @@ bgm = function(
target_accept = target_accept, pairwise_stats = pairwise_stats,
hmc_num_leapfrogs = hmc_num_leapfrogs, nuts_max_depth = nuts_max_depth,
learn_mass_matrix = learn_mass_matrix, num_chains = chains,
nThreads = cores, seed = seed
nThreads = cores, seed = seed, progress_type = progress_type
)

# Main output handler in the wrapper function
Expand Down Expand Up @@ -457,5 +457,9 @@ bgm = function(
output$nuts_diag = nuts_diag
}

userInterrupt = any(vapply(out, FUN = `[[`, FUN.VALUE = logical(1L), "userInterrupt"))
if (userInterrupt)
warning("Stopped sampling after user interrupt, results are likely uninterpretable.")

return(output)
}
8 changes: 5 additions & 3 deletions R/bgmCompare.R
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ bgmCompare = function(
iter = 1e3,
burnin = 1e3,
na_action = c("listwise", "impute"),
display_progress = TRUE,
display_progress = c("per-chain", "total", "none"),
update_method = c("nuts", "adaptive-metropolis", "hamiltonian-mc"),
target_accept,
hmc_num_leapfrogs = 100,
Expand Down Expand Up @@ -202,7 +202,8 @@ bgmCompare = function(
}

# Check display_progress
display_progress = check_logical(display_progress, "display_progress")
progress_type = progress_type_from_display_progress(display_progress)


## Format data
data = compare_reformat_data(
Expand Down Expand Up @@ -340,7 +341,8 @@ bgmCompare = function(
inclusion_probability = model$inclusion_probability_difference,
num_chains = chains, nThreads = cores,
seed = seed,
update_method = update_method, hmc_num_leapfrogs = hmc_num_leapfrogs
update_method = update_method, hmc_num_leapfrogs = hmc_num_leapfrogs,
progress_type = progress_type
)

# Main output handler in the wrapper function
Expand Down
13 changes: 12 additions & 1 deletion R/function_input_utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -463,4 +463,15 @@ check_compare_model = function(
inclusion_probability_difference = inclusion_probability_difference
)
)
}
}

progress_type_from_display_progress <- function(display_progress = c("per-chain", "total", "none")) {
if (is.logical(display_progress) && length(display_progress) == 1) {
if (is.na(display_progress))
stop("The display_progress argument must be a single logical value, but not NA.")
display_progress = if (display_progress) "per-chain" else "none"
} else {
display_progress = match.arg(display_progress)
}
return(if (display_progress == "per-chain") 2L else if (display_progress == "total") 1L else 0L)
}
2 changes: 1 addition & 1 deletion src/Makevars.win
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
CXX_STD = CXX14
CXX_STD = CXX20

PKG_CPPFLAGS = \
$(shell "$(R_HOME)\bin\Rscript.exe" -e "cat(RcppParallel::CxxFlags())")
Expand Down
18 changes: 10 additions & 8 deletions src/RcppExports.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@ Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// run_bgmCompare_parallel
Rcpp::List run_bgmCompare_parallel(const arma::imat& observations, int num_groups, const std::vector<arma::imat>& counts_per_category, const std::vector<arma::imat>& blume_capel_stats, const std::vector<arma::mat>& pairwise_stats, const arma::ivec& num_categories, double main_alpha, double main_beta, double pairwise_scale, double difference_scale, double difference_selection_alpha, double difference_selection_beta, const std::string& difference_prior, int iter, int burnin, bool na_impute, const arma::imat& missing_data_indices, const arma::uvec& is_ordinal_variable, const arma::ivec& baseline_category, bool difference_selection, const arma::imat& main_effect_indices, const arma::imat& pairwise_effect_indices, double target_accept, int nuts_max_depth, bool learn_mass_matrix, const arma::mat& projection, const arma::ivec& group_membership, const arma::imat& group_indices, const arma::imat& interaction_index_matrix, const arma::mat& inclusion_probability, int num_chains, int nThreads, int seed, const std::string& update_method, int hmc_num_leapfrogs);
RcppExport SEXP _bgms_run_bgmCompare_parallel(SEXP observationsSEXP, SEXP num_groupsSEXP, SEXP counts_per_categorySEXP, SEXP blume_capel_statsSEXP, SEXP pairwise_statsSEXP, SEXP num_categoriesSEXP, SEXP main_alphaSEXP, SEXP main_betaSEXP, SEXP pairwise_scaleSEXP, SEXP difference_scaleSEXP, SEXP difference_selection_alphaSEXP, SEXP difference_selection_betaSEXP, SEXP difference_priorSEXP, SEXP iterSEXP, SEXP burninSEXP, SEXP na_imputeSEXP, SEXP missing_data_indicesSEXP, SEXP is_ordinal_variableSEXP, SEXP baseline_categorySEXP, SEXP difference_selectionSEXP, SEXP main_effect_indicesSEXP, SEXP pairwise_effect_indicesSEXP, SEXP target_acceptSEXP, SEXP nuts_max_depthSEXP, SEXP learn_mass_matrixSEXP, SEXP projectionSEXP, SEXP group_membershipSEXP, SEXP group_indicesSEXP, SEXP interaction_index_matrixSEXP, SEXP inclusion_probabilitySEXP, SEXP num_chainsSEXP, SEXP nThreadsSEXP, SEXP seedSEXP, SEXP update_methodSEXP, SEXP hmc_num_leapfrogsSEXP) {
Rcpp::List run_bgmCompare_parallel(const arma::imat& observations, int num_groups, const std::vector<arma::imat>& counts_per_category, const std::vector<arma::imat>& blume_capel_stats, const std::vector<arma::mat>& pairwise_stats, const arma::ivec& num_categories, double main_alpha, double main_beta, double pairwise_scale, double difference_scale, double difference_selection_alpha, double difference_selection_beta, const std::string& difference_prior, int iter, int burnin, bool na_impute, const arma::imat& missing_data_indices, const arma::uvec& is_ordinal_variable, const arma::ivec& baseline_category, bool difference_selection, const arma::imat& main_effect_indices, const arma::imat& pairwise_effect_indices, double target_accept, int nuts_max_depth, bool learn_mass_matrix, const arma::mat& projection, const arma::ivec& group_membership, const arma::imat& group_indices, const arma::imat& interaction_index_matrix, const arma::mat& inclusion_probability, int num_chains, int nThreads, int seed, const std::string& update_method, int hmc_num_leapfrogs, int progress_type);
RcppExport SEXP _bgms_run_bgmCompare_parallel(SEXP observationsSEXP, SEXP num_groupsSEXP, SEXP counts_per_categorySEXP, SEXP blume_capel_statsSEXP, SEXP pairwise_statsSEXP, SEXP num_categoriesSEXP, SEXP main_alphaSEXP, SEXP main_betaSEXP, SEXP pairwise_scaleSEXP, SEXP difference_scaleSEXP, SEXP difference_selection_alphaSEXP, SEXP difference_selection_betaSEXP, SEXP difference_priorSEXP, SEXP iterSEXP, SEXP burninSEXP, SEXP na_imputeSEXP, SEXP missing_data_indicesSEXP, SEXP is_ordinal_variableSEXP, SEXP baseline_categorySEXP, SEXP difference_selectionSEXP, SEXP main_effect_indicesSEXP, SEXP pairwise_effect_indicesSEXP, SEXP target_acceptSEXP, SEXP nuts_max_depthSEXP, SEXP learn_mass_matrixSEXP, SEXP projectionSEXP, SEXP group_membershipSEXP, SEXP group_indicesSEXP, SEXP interaction_index_matrixSEXP, SEXP inclusion_probabilitySEXP, SEXP num_chainsSEXP, SEXP nThreadsSEXP, SEXP seedSEXP, SEXP update_methodSEXP, SEXP hmc_num_leapfrogsSEXP, SEXP progress_typeSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Expand Down Expand Up @@ -52,13 +52,14 @@ BEGIN_RCPP
Rcpp::traits::input_parameter< int >::type seed(seedSEXP);
Rcpp::traits::input_parameter< const std::string& >::type update_method(update_methodSEXP);
Rcpp::traits::input_parameter< int >::type hmc_num_leapfrogs(hmc_num_leapfrogsSEXP);
rcpp_result_gen = Rcpp::wrap(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));
Rcpp::traits::input_parameter< int >::type progress_type(progress_typeSEXP);
rcpp_result_gen = Rcpp::wrap(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, progress_type));
return rcpp_result_gen;
END_RCPP
}
// run_bgm_parallel
Rcpp::List run_bgm_parallel(const arma::imat& observations, const arma::ivec& num_categories, double pairwise_scale, const std::string& edge_prior, const arma::mat& inclusion_probability, double beta_bernoulli_alpha, double beta_bernoulli_beta, double dirichlet_alpha, double lambda, const arma::imat& interaction_index_matrix, int iter, int burnin, const arma::imat& counts_per_category, const arma::imat& blume_capel_stats, double main_alpha, double main_beta, bool na_impute, const arma::imat& missing_index, const arma::uvec& is_ordinal_variable, const arma::ivec& baseline_category, bool edge_selection, const std::string& update_method, const arma::imat& pairwise_effect_indices, double target_accept, const arma::imat& pairwise_stats, int hmc_num_leapfrogs, int nuts_max_depth, bool learn_mass_matrix, int num_chains, int nThreads, uint64_t seed);
RcppExport SEXP _bgms_run_bgm_parallel(SEXP observationsSEXP, SEXP num_categoriesSEXP, SEXP pairwise_scaleSEXP, SEXP edge_priorSEXP, SEXP inclusion_probabilitySEXP, SEXP beta_bernoulli_alphaSEXP, SEXP beta_bernoulli_betaSEXP, SEXP dirichlet_alphaSEXP, SEXP lambdaSEXP, SEXP interaction_index_matrixSEXP, SEXP iterSEXP, SEXP burninSEXP, SEXP counts_per_categorySEXP, SEXP blume_capel_statsSEXP, SEXP main_alphaSEXP, SEXP main_betaSEXP, SEXP na_imputeSEXP, SEXP missing_indexSEXP, SEXP is_ordinal_variableSEXP, SEXP baseline_categorySEXP, SEXP edge_selectionSEXP, SEXP update_methodSEXP, SEXP pairwise_effect_indicesSEXP, SEXP target_acceptSEXP, SEXP pairwise_statsSEXP, SEXP hmc_num_leapfrogsSEXP, SEXP nuts_max_depthSEXP, SEXP learn_mass_matrixSEXP, SEXP num_chainsSEXP, SEXP nThreadsSEXP, SEXP seedSEXP) {
Rcpp::List run_bgm_parallel(const arma::imat& observations, const arma::ivec& num_categories, double pairwise_scale, const std::string& edge_prior, const arma::mat& inclusion_probability, double beta_bernoulli_alpha, double beta_bernoulli_beta, double dirichlet_alpha, double lambda, const arma::imat& interaction_index_matrix, int iter, int burnin, const arma::imat& counts_per_category, const arma::imat& blume_capel_stats, double main_alpha, double main_beta, bool na_impute, const arma::imat& missing_index, const arma::uvec& is_ordinal_variable, const arma::ivec& baseline_category, bool edge_selection, const std::string& update_method, const arma::imat& pairwise_effect_indices, double target_accept, const arma::imat& pairwise_stats, int hmc_num_leapfrogs, int nuts_max_depth, bool learn_mass_matrix, int num_chains, int nThreads, uint64_t seed, int progress_type);
RcppExport SEXP _bgms_run_bgm_parallel(SEXP observationsSEXP, SEXP num_categoriesSEXP, SEXP pairwise_scaleSEXP, SEXP edge_priorSEXP, SEXP inclusion_probabilitySEXP, SEXP beta_bernoulli_alphaSEXP, SEXP beta_bernoulli_betaSEXP, SEXP dirichlet_alphaSEXP, SEXP lambdaSEXP, SEXP interaction_index_matrixSEXP, SEXP iterSEXP, SEXP burninSEXP, SEXP counts_per_categorySEXP, SEXP blume_capel_statsSEXP, SEXP main_alphaSEXP, SEXP main_betaSEXP, SEXP na_imputeSEXP, SEXP missing_indexSEXP, SEXP is_ordinal_variableSEXP, SEXP baseline_categorySEXP, SEXP edge_selectionSEXP, SEXP update_methodSEXP, SEXP pairwise_effect_indicesSEXP, SEXP target_acceptSEXP, SEXP pairwise_statsSEXP, SEXP hmc_num_leapfrogsSEXP, SEXP nuts_max_depthSEXP, SEXP learn_mass_matrixSEXP, SEXP num_chainsSEXP, SEXP nThreadsSEXP, SEXP seedSEXP, SEXP progress_typeSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Expand Down Expand Up @@ -93,7 +94,8 @@ BEGIN_RCPP
Rcpp::traits::input_parameter< int >::type num_chains(num_chainsSEXP);
Rcpp::traits::input_parameter< int >::type nThreads(nThreadsSEXP);
Rcpp::traits::input_parameter< uint64_t >::type seed(seedSEXP);
rcpp_result_gen = Rcpp::wrap(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));
Rcpp::traits::input_parameter< int >::type progress_type(progress_typeSEXP);
rcpp_result_gen = Rcpp::wrap(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, progress_type));
return rcpp_result_gen;
END_RCPP
}
Expand Down Expand Up @@ -179,8 +181,8 @@ END_RCPP
}

static const R_CallMethodDef CallEntries[] = {
{"_bgms_run_bgmCompare_parallel", (DL_FUNC) &_bgms_run_bgmCompare_parallel, 35},
{"_bgms_run_bgm_parallel", (DL_FUNC) &_bgms_run_bgm_parallel, 31},
{"_bgms_run_bgmCompare_parallel", (DL_FUNC) &_bgms_run_bgmCompare_parallel, 36},
{"_bgms_run_bgm_parallel", (DL_FUNC) &_bgms_run_bgm_parallel, 32},
{"_bgms_get_explog_switch", (DL_FUNC) &_bgms_get_explog_switch, 0},
{"_bgms_rcpp_ieee754_exp", (DL_FUNC) &_bgms_rcpp_ieee754_exp, 1},
{"_bgms_rcpp_ieee754_log", (DL_FUNC) &_bgms_rcpp_ieee754_log, 1},
Expand Down
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