$by.self self.time self.pct total.time "gettext" 1.74 7.74 1.92 "deparse" 1.58 7.03 5.06 "gsub" 1.58 7.03 1.60 "match.arg" 1.08 4.80 2.86 ".deparseOpts" 0.98 4.36 2.18 "%in%" 0.86 3.83 2.14 "match.fun" 0.82 3.65 2.60 "assert_engine" 0.76 3.38 14.48 "paste0" 0.74 3.29 5.66 "pmatch" 0.72 3.20 0.74 "doTryCatch" 0.70 3.11 19.38 "eval" 0.70 3.11 1.02 "tryCatch" 0.66 2.94 19.54 "getExportedValue" 0.56 2.49 1.40 "do.call" 0.50 2.22 0.60 "get_name_in_parent" 0.38 1.69 6.92 "c" 0.36 1.60 0.36 "coerce_to" 0.32 1.42 2.68 "get" 0.30 1.33 0.32 "tryCatchList" 0.20 0.89 19.40 "assertive::assert_all_are_positive" 0.20 0.89 7.10 "is_in_range" 0.20 0.89 2.82 "::" 0.20 0.89 1.64 "asNamespace" 0.20 0.89 0.34 "dim<-" 0.20 0.89 0.20 "sys.frame" 0.20 0.89 0.20 "sys.parent" 0.20 0.89 0.20 "as.character" 0.18 0.80 0.18 "get0" 0.18 0.80 0.18 "parent.frame" 0.18 0.80 0.18 "sprintf" 0.16 0.71 2.08 ".getNamespaceInfo" 0.16 0.71 0.16 "getOption" 0.16 0.71 0.16 "isBaseNamespace" 0.16 0.71 0.16 "tryCatchOne" 0.14 0.62 19.38 "set_cause" 0.14 0.62 0.42 "structure" 0.14 0.62 0.14 "predicate" 0.12 0.53 5.32 "formals" 0.12 0.53 0.36 "length" 0.12 0.53 0.12 "sum" 0.12 0.53 0.12 "is2" 0.10 0.44 2.20 "mode" 0.10 0.44 1.40 "metric_fn" 0.10 0.44 0.24 "testit::assert" 0.10 0.44 0.20 "lapply" 0.10 0.44 0.14 "getNamespace" 0.10 0.44 0.10 "ifelse" 0.08 0.36 0.12 "check_n" 0.08 0.36 0.08 "environment" 0.08 0.36 0.08 "get_metric" 0.08 0.36 0.08 "use_first" 0.08 0.36 0.08 "safe_deparse" 0.06 0.27 5.38 "check_treelog_values" 0.06 0.27 5.30 "call_and_name" 0.06 0.27 0.84 "expectation_type" 0.06 0.27 0.56 "fn" 0.06 0.27 0.48 "bd_loglik" 0.06 0.27 0.34 "sys.function" 0.06 0.27 0.24 "noquote" 0.06 0.27 0.12 "$" 0.06 0.27 0.06 "all" 0.06 0.27 0.06 "assert2" 0.06 0.27 0.06 "beautier::is_one_na" 0.06 0.27 0.06 "conditionMessage" 0.06 0.27 0.06 "is.function" 0.06 0.27 0.06 "is.list" 0.06 0.27 0.06 "check_mcmc_values" 0.04 0.18 13.14 "check_tracelog_values" 0.04 0.18 5.16 "assertive::assert_is_character" 0.04 0.18 1.64 "is_scalar" 0.04 0.18 0.66 "sort.int" 0.04 0.18 0.26 "expr_label" 0.04 0.18 0.18 "cause<-" 0.04 0.18 0.16 "order" 0.04 0.18 0.10 "beautier::check_gamma_site_model" 0.04 0.18 0.08 "check_treelog_names" 0.04 0.18 0.08 "makeRestart" 0.04 0.18 0.06 "-" 0.04 0.18 0.04 "anyNA" 0.04 0.18 0.04 "attr" 0.04 0.18 0.04 "is.expectation" 0.04 0.18 0.04 "is.na" 0.04 0.18 0.04 "isNamespace" 0.04 0.18 0.04 "list" 0.04 0.18 0.04 "names<-" 0.04 0.18 0.04 "unlist" 0.04 0.18 0.04 "pirouette::check_experiments" 0.02 0.09 20.60 "pirouette::check_experiments_candidates_have_same_mcmcs" 0.02 0.09 16.70 "beautier::check_treelog" 0.02 0.09 5.40 "check_screenlog_values" 0.02 0.09 5.26 "are_equal_treelogs" 0.02 0.09 2.52 "are_equal_screenlogs" 0.02 0.09 2.14 "assertive::assert_is_numeric" 0.02 0.09 2.08 "gettextf" 0.02 0.09 2.08 "testthat::expect_true" 0.02 0.09 1.04 "expect" 0.02 0.09 0.94 "withRestarts" 0.02 0.09 0.80 "is_na" 0.02 0.09 0.76 "" 0.02 0.09 0.34 "is_logical" 0.02 0.09 0.32 "sort" 0.02 0.09 0.28 "is_character" 0.02 0.09 0.20 "signalCondition" 0.02 0.09 0.12 "makeRestartList" 0.02 0.09 0.08 "pirouette::check_experiments_all_inference_models_are_unique" 0.02 0.09 0.08 "check_tracelog_names" 0.02 0.09 0.06 "stopifnot" 0.02 0.09 0.06 "to_names" 0.02 0.09 0.06 "beautier::check_log_mode" 0.02 0.09 0.04 "beautier::check_log_sort" 0.02 0.09 0.04 "conditionCall" 0.02 0.09 0.04 ".getClassesFromCache" 0.02 0.09 0.02 ".makeMessage" 0.02 0.09 0.02 "@<-" 0.02 0.09 0.02 "any" 0.02 0.09 0.02 "check_mcmc_list_element_names" 0.02 0.09 0.02 "dimnames" 0.02 0.09 0.02 "invisible" 0.02 0.09 0.02 "is.atomic" 0.02 0.09 0.02 "is.expression" 0.02 0.09 0.02 "names" 0.02 0.09 0.02 "options" 0.02 0.09 0.02 "paste" 0.02 0.09 0.02 "stri_count_regex" 0.02 0.09 0.02 total.pct "gettext" 8.54 "deparse" 22.51 "gsub" 7.12 "match.arg" 12.72 ".deparseOpts" 9.70 "%in%" 9.52 "match.fun" 11.57 "assert_engine" 64.41 "paste0" 25.18 "pmatch" 3.29 "doTryCatch" 86.21 "eval" 4.54 "tryCatch" 86.92 "getExportedValue" 6.23 "do.call" 2.67 "get_name_in_parent" 30.78 "c" 1.60 "coerce_to" 11.92 "get" 1.42 "tryCatchList" 86.30 "assertive::assert_all_are_positive" 31.58 "is_in_range" 12.54 "::" 7.30 "asNamespace" 1.51 "dim<-" 0.89 "sys.frame" 0.89 "sys.parent" 0.89 "as.character" 0.80 "get0" 0.80 "parent.frame" 0.80 "sprintf" 9.25 ".getNamespaceInfo" 0.71 "getOption" 0.71 "isBaseNamespace" 0.71 "tryCatchOne" 86.21 "set_cause" 1.87 "structure" 0.62 "predicate" 23.67 "formals" 1.60 "length" 0.53 "sum" 0.53 "is2" 9.79 "mode" 6.23 "metric_fn" 1.07 "testit::assert" 0.89 "lapply" 0.62 "getNamespace" 0.44 "ifelse" 0.53 "check_n" 0.36 "environment" 0.36 "get_metric" 0.36 "use_first" 0.36 "safe_deparse" 23.93 "check_treelog_values" 23.58 "call_and_name" 3.74 "expectation_type" 2.49 "fn" 2.14 "bd_loglik" 1.51 "sys.function" 1.07 "noquote" 0.53 "$" 0.27 "all" 0.27 "assert2" 0.27 "beautier::is_one_na" 0.27 "conditionMessage" 0.27 "is.function" 0.27 "is.list" 0.27 "check_mcmc_values" 58.45 "check_tracelog_values" 22.95 "assertive::assert_is_character" 7.30 "is_scalar" 2.94 "sort.int" 1.16 "expr_label" 0.80 "cause<-" 0.71 "order" 0.44 "beautier::check_gamma_site_model" 0.36 "check_treelog_names" 0.36 "makeRestart" 0.27 "-" 0.18 "anyNA" 0.18 "attr" 0.18 "is.expectation" 0.18 "is.na" 0.18 "isNamespace" 0.18 "list" 0.18 "names<-" 0.18 "unlist" 0.18 "pirouette::check_experiments" 91.64 "pirouette::check_experiments_candidates_have_same_mcmcs" 74.29 "beautier::check_treelog" 24.02 "check_screenlog_values" 23.40 "are_equal_treelogs" 11.21 "are_equal_screenlogs" 9.52 "assertive::assert_is_numeric" 9.25 "gettextf" 9.25 "testthat::expect_true" 4.63 "expect" 4.18 "withRestarts" 3.56 "is_na" 3.38 "" 1.51 "is_logical" 1.42 "sort" 1.25 "is_character" 0.89 "signalCondition" 0.53 "makeRestartList" 0.36 "pirouette::check_experiments_all_inference_models_are_unique" 0.36 "check_tracelog_names" 0.27 "stopifnot" 0.27 "to_names" 0.27 "beautier::check_log_mode" 0.18 "beautier::check_log_sort" 0.18 "conditionCall" 0.18 ".getClassesFromCache" 0.09 ".makeMessage" 0.09 "@<-" 0.09 "any" 0.09 "check_mcmc_list_element_names" 0.09 "dimnames" 0.09 "invisible" 0.09 "is.atomic" 0.09 "is.expression" 0.09 "names" 0.09 "options" 0.09 "paste" 0.09 "stri_count_regex" 0.09 $by.total total.time total.pct self.time "create_std_pir_paramses" 22.48 100.00 0.00 "pirouette::check_experiments" 20.60 91.64 0.02 "tryCatch" 19.54 86.92 0.66 "tryCatchList" 19.40 86.30 0.20 "doTryCatch" 19.38 86.21 0.70 "tryCatchOne" 19.38 86.21 0.14 "pirouette::check_pir_params_data_types" 17.96 79.89 0.00 "pirouette::check_pir_params" 17.96 79.89 0.00 "pirouette::check_experiments_candidates_have_same_mcmcs" 16.70 74.29 0.02 "beautier::are_equal_mcmcs" 16.62 73.93 0.00 "create_std_pir_params" 14.88 66.19 0.00 "assert_engine" 14.48 64.41 0.76 "beautier::check_mcmc" 13.16 58.54 0.00 "check_mcmc_values" 13.14 58.45 0.04 "pirouette::has_twinning" 7.90 35.14 0.00 "renum_rng_seeds" 7.90 35.14 0.00 "assertive::assert_all_are_positive" 7.10 31.58 0.20 "get_name_in_parent" 6.92 30.78 0.38 "pir_rename_to_std" 6.84 30.43 0.00 "paste0" 5.66 25.18 0.74 "beautier::check_treelog" 5.40 24.02 0.02 "safe_deparse" 5.38 23.93 0.06 "predicate" 5.32 23.67 0.12 "check_treelog_values" 5.30 23.58 0.06 "check_screenlog_values" 5.26 23.40 0.02 "beautier::check_screenlog" 5.26 23.40 0.00 "beautier::check_tracelog" 5.22 23.22 0.00 "check_tracelog_values" 5.16 22.95 0.04 "deparse" 5.06 22.51 1.58 "create_all_bd_experiments" 4.28 19.04 0.00 "pirouette::create_all_experiments" 4.28 19.04 0.00 "assertive::assert_is_if_condition" 3.52 15.66 0.00 "create_pir_params" 3.28 14.59 0.00 "pirouette::check_experiment" 3.12 13.88 0.00 "match.arg" 2.86 12.72 1.08 "is_in_range" 2.82 12.54 0.20 "coerce_to" 2.68 11.92 0.32 "match.fun" 2.60 11.57 0.82 "are_equal_treelogs" 2.52 11.21 0.02 "is2" 2.20 9.79 0.10 ".deparseOpts" 2.18 9.70 0.98 "%in%" 2.14 9.52 0.86 "are_equal_screenlogs" 2.14 9.52 0.02 "assertive::assert_is_a_string" 2.10 9.34 0.00 "sprintf" 2.08 9.25 0.16 "assertive::assert_is_numeric" 2.08 9.25 0.02 "gettextf" 2.08 9.25 0.02 "are_equal_tracelogs" 2.04 9.07 0.00 "gettext" 1.92 8.54 1.74 "beautier::is_nested_sampling_mcmc" 1.68 7.47 0.00 "check_mcmc_nested_sampling" 1.68 7.47 0.00 "::" 1.64 7.30 0.20 "assertive::assert_is_character" 1.64 7.30 0.04 "gsub" 1.60 7.12 1.58 "getExportedValue" 1.40 6.23 0.56 "mode" 1.40 6.23 0.10 "beautier::check_inference_model" 1.40 6.23 0.00 "assertive::assert_all_are_whole_numbers" 1.38 6.14 0.00 "pirouette::check_candidates_save_to_same_files" 1.14 5.07 0.00 "beautier::check_store_every" 1.10 4.89 0.00 "testthat::expect_true" 1.04 4.63 0.02 "eval" 1.02 4.54 0.70 "expect" 0.94 4.18 0.02 "pirouette::create_experiment" 0.86 3.83 0.00 "call_and_name" 0.84 3.74 0.06 "withRestarts" 0.80 3.56 0.02 "exp_signal" 0.80 3.56 0.00 "is_na" 0.76 3.38 0.02 "pmatch" 0.74 3.29 0.72 "doWithOneRestart" 0.70 3.11 0.00 "withOneRestart" 0.70 3.11 0.00 "is_scalar" 0.66 2.94 0.04 "do.call" 0.60 2.67 0.50 "expectation_type" 0.56 2.49 0.06 "expectation_broken" 0.56 2.49 0.00 "pirouette::check_twinning_params" 0.56 2.49 0.00 "expectation_failure" 0.50 2.22 0.00 "fn" 0.48 2.14 0.06 "suppressWarnings" 0.44 1.96 0.00 "withCallingHandlers" 0.44 1.96 0.00 "set_cause" 0.42 1.87 0.14 "pirouette::check_sim_twin_tree_fun" 0.42 1.87 0.00 "sim_bd_twin_tree" 0.42 1.87 0.00 "sim_twin_tree_fun" 0.42 1.87 0.00 "beautier::create_inference_model" 0.38 1.69 0.00 "c" 0.36 1.60 0.36 "formals" 0.36 1.60 0.12 "beautier::create_ns_mcmc" 0.36 1.60 0.00 "combine_models" 0.36 1.60 0.00 "create_mcmc" 0.36 1.60 0.00 "DDD::bd_ML" 0.36 1.60 0.00 "asNamespace" 0.34 1.51 0.20 "bd_loglik" 0.34 1.51 0.06 "" 0.34 1.51 0.02 ".Call" 0.34 1.51 0.00 "assertive::assert_is_a_number" 0.34 1.51 0.00 "optimizer" 0.34 1.51 0.00 "subplex::subplex" 0.34 1.51 0.00 "get" 0.32 1.42 0.30 "is_logical" 0.32 1.42 0.02 "fun" 0.32 1.42 0.00 "sort" 0.28 1.25 0.02 "sort.int" 0.26 1.16 0.04 "sort.default" 0.26 1.16 0.00 "metric_fn" 0.24 1.07 0.10 "sys.function" 0.24 1.07 0.06 "dim<-" 0.20 0.89 0.20 "sys.frame" 0.20 0.89 0.20 "sys.parent" 0.20 0.89 0.20 "testit::assert" 0.20 0.89 0.10 "is_character" 0.20 0.89 0.02 "beastier::check_beast2_options" 0.20 0.89 0.00 "as.character" 0.18 0.80 0.18 "get0" 0.18 0.80 0.18 "parent.frame" 0.18 0.80 0.18 "expr_label" 0.18 0.80 0.04 "%||%" 0.18 0.80 0.00 "beastier::check_beast2_options_data_types" 0.18 0.80 0.00 "beautier::check_nested_sampling_mcmc" 0.18 0.80 0.00 "quasi_label" 0.18 0.80 0.00 ".getNamespaceInfo" 0.16 0.71 0.16 "getOption" 0.16 0.71 0.16 "isBaseNamespace" 0.16 0.71 0.16 "cause<-" 0.16 0.71 0.04 "ape::Ntip" 0.16 0.71 0.00 "structure" 0.14 0.62 0.14 "lapply" 0.14 0.62 0.10 "pirouette::check_sim_twal_fun" 0.14 0.62 0.00 "length" 0.12 0.53 0.12 "sum" 0.12 0.53 0.12 "ifelse" 0.12 0.53 0.08 "noquote" 0.12 0.53 0.06 "signalCondition" 0.12 0.53 0.02 "beautier::check_beauti_options" 0.12 0.53 0.00 "create_twinning_params" 0.12 0.53 0.00 "testthat::expect_equal" 0.12 0.53 0.00 "getNamespace" 0.10 0.44 0.10 "order" 0.10 0.44 0.04 "assertive::is_if_condition" 0.10 0.44 0.00 "beautier::check_site_model_types" 0.10 0.44 0.00 "beautier::check_site_model" 0.10 0.44 0.00 "beautier::is_one_bool" 0.10 0.44 0.00 "expectation" 0.10 0.44 0.00 "new_expectation" 0.10 0.44 0.00 "pirouette::sim_alignment_with_n_mutations" 0.10 0.44 0.00 "sim_twal_fun" 0.10 0.44 0.00 "sim_twal_with_same_n_mutation" 0.10 0.44 0.00 "check_n" 0.08 0.36 0.08 "environment" 0.08 0.36 0.08 "get_metric" 0.08 0.36 0.08 "use_first" 0.08 0.36 0.08 "beautier::check_gamma_site_model" 0.08 0.36 0.04 "check_treelog_names" 0.08 0.36 0.04 "makeRestartList" 0.08 0.36 0.02 "pirouette::check_experiments_all_inference_models_are_unique" 0.08 0.36 0.02 "beautier::check_clock_model" 0.08 0.36 0.00 "beautier::is_gamma_site_model" 0.08 0.36 0.00 "pirouette::sim_alignment_with_std_nsm" 0.08 0.36 0.00 "pirouette::sim_tral_with_std_nsm" 0.08 0.36 0.00 "$" 0.06 0.27 0.06 "all" 0.06 0.27 0.06 "assert2" 0.06 0.27 0.06 "beautier::is_one_na" 0.06 0.27 0.06 "conditionMessage" 0.06 0.27 0.06 "is.function" 0.06 0.27 0.06 "is.list" 0.06 0.27 0.06 "makeRestart" 0.06 0.27 0.04 "check_tracelog_names" 0.06 0.27 0.02 "stopifnot" 0.06 0.27 0.02 "to_names" 0.06 0.27 0.02 "beastier::check_os" 0.06 0.27 0.00 "create_gen_experiment" 0.06 0.27 0.00 "expectation_error" 0.06 0.27 0.00 "is_distr" 0.06 0.27 0.00 "phangorn::simSeq" 0.06 0.27 0.00 "rappdirs::app_dir" 0.06 0.27 0.00 "simSeq.phylo" 0.06 0.27 0.00 "-" 0.04 0.18 0.04 "anyNA" 0.04 0.18 0.04 "attr" 0.04 0.18 0.04 "is.expectation" 0.04 0.18 0.04 "is.na" 0.04 0.18 0.04 "isNamespace" 0.04 0.18 0.04 "list" 0.04 0.18 0.04 "names<-" 0.04 0.18 0.04 "unlist" 0.04 0.18 0.04 "beautier::check_log_mode" 0.04 0.18 0.02 "beautier::check_log_sort" 0.04 0.18 0.02 "conditionCall" 0.04 0.18 0.02 "...elt" 0.04 0.18 0.00 "appdirs$new" 0.04 0.18 0.00 "beautier::check_gamma_site_model_names" 0.04 0.18 0.00 "beautier::check_rln_clock_model" 0.04 0.18 0.00 "beautier::check_strict_clock_model" 0.04 0.18 0.00 "create_tracelog" 0.04 0.18 0.00 "create_treelog" 0.04 0.18 0.00 "initialize" 0.04 0.18 0.00 "methods::new" 0.04 0.18 0.00 ".getClassesFromCache" 0.02 0.09 0.02 ".makeMessage" 0.02 0.09 0.02 "@<-" 0.02 0.09 0.02 "any" 0.02 0.09 0.02 "check_mcmc_list_element_names" 0.02 0.09 0.02 "dimnames" 0.02 0.09 0.02 "invisible" 0.02 0.09 0.02 "is.atomic" 0.02 0.09 0.02 "is.expression" 0.02 0.09 0.02 "names" 0.02 0.09 0.02 "options" 0.02 0.09 0.02 "paste" 0.02 0.09 0.02 "stri_count_regex" 0.02 0.09 0.02 ".doSortWrap" 0.02 0.09 0.00 ".makeSortEnum" 0.02 0.09 0.00 "assertive::is_a_string" 0.02 0.09 0.00 "bd_loglik_choosepar" 0.02 0.09 0.00 "beautier::check_clock_models" 0.02 0.09 0.00 "beautier::check_mrca_prior" 0.02 0.09 0.00 "beautier::check_param" 0.02 0.09 0.00 "beautier::create_mcmc" 0.02 0.09 0.00 "beautier::is_gamma_distr" 0.02 0.09 0.00 "beautier::is_laplace_distr" 0.02 0.09 0.00 "beautier::is_param" 0.02 0.09 0.00 "calc_base_freq" 0.02 0.09 0.00 "compare.character" 0.02 0.09 0.00 "compare" 0.02 0.09 0.00 "comparison" 0.02 0.09 0.00 "conditionCall.condition" 0.02 0.09 0.00 "create_beauti_options" 0.02 0.09 0.00 "create_rate_matrix" 0.02 0.09 0.00 "DDD::phylo2L" 0.02 0.09 0.00 "edQt" 0.02 0.09 0.00 "getClass" 0.02 0.09 0.00 "getClassDef" 0.02 0.09 0.00 "is_numeric" 0.02 0.09 0.00 "match.call" 0.02 0.09 0.00 "no_difference" 0.02 0.09 0.00 "phyDat.DNA" 0.02 0.09 0.00 "pirouette::check_reconstructed_phylogeny" 0.02 0.09 0.00 "pirouette::create_inference_conditions" 0.02 0.09 0.00 "rownames" 0.02 0.09 0.00 "solve.default" 0.02 0.09 0.00 "stop" 0.02 0.09 0.00 "stringr::str_count" 0.02 0.09 0.00 "sys.call" 0.02 0.09 0.00 self.pct "create_std_pir_paramses" 0.00 "pirouette::check_experiments" 0.09 "tryCatch" 2.94 "tryCatchList" 0.89 "doTryCatch" 3.11 "tryCatchOne" 0.62 "pirouette::check_pir_params_data_types" 0.00 "pirouette::check_pir_params" 0.00 "pirouette::check_experiments_candidates_have_same_mcmcs" 0.09 "beautier::are_equal_mcmcs" 0.00 "create_std_pir_params" 0.00 "assert_engine" 3.38 "beautier::check_mcmc" 0.00 "check_mcmc_values" 0.18 "pirouette::has_twinning" 0.00 "renum_rng_seeds" 0.00 "assertive::assert_all_are_positive" 0.89 "get_name_in_parent" 1.69 "pir_rename_to_std" 0.00 "paste0" 3.29 "beautier::check_treelog" 0.09 "safe_deparse" 0.27 "predicate" 0.53 "check_treelog_values" 0.27 "check_screenlog_values" 0.09 "beautier::check_screenlog" 0.00 "beautier::check_tracelog" 0.00 "check_tracelog_values" 0.18 "deparse" 7.03 "create_all_bd_experiments" 0.00 "pirouette::create_all_experiments" 0.00 "assertive::assert_is_if_condition" 0.00 "create_pir_params" 0.00 "pirouette::check_experiment" 0.00 "match.arg" 4.80 "is_in_range" 0.89 "coerce_to" 1.42 "match.fun" 3.65 "are_equal_treelogs" 0.09 "is2" 0.44 ".deparseOpts" 4.36 "%in%" 3.83 "are_equal_screenlogs" 0.09 "assertive::assert_is_a_string" 0.00 "sprintf" 0.71 "assertive::assert_is_numeric" 0.09 "gettextf" 0.09 "are_equal_tracelogs" 0.00 "gettext" 7.74 "beautier::is_nested_sampling_mcmc" 0.00 "check_mcmc_nested_sampling" 0.00 "::" 0.89 "assertive::assert_is_character" 0.18 "gsub" 7.03 "getExportedValue" 2.49 "mode" 0.44 "beautier::check_inference_model" 0.00 "assertive::assert_all_are_whole_numbers" 0.00 "pirouette::check_candidates_save_to_same_files" 0.00 "beautier::check_store_every" 0.00 "testthat::expect_true" 0.09 "eval" 3.11 "expect" 0.09 "pirouette::create_experiment" 0.00 "call_and_name" 0.27 "withRestarts" 0.09 "exp_signal" 0.00 "is_na" 0.09 "pmatch" 3.20 "doWithOneRestart" 0.00 "withOneRestart" 0.00 "is_scalar" 0.18 "do.call" 2.22 "expectation_type" 0.27 "expectation_broken" 0.00 "pirouette::check_twinning_params" 0.00 "expectation_failure" 0.00 "fn" 0.27 "suppressWarnings" 0.00 "withCallingHandlers" 0.00 "set_cause" 0.62 "pirouette::check_sim_twin_tree_fun" 0.00 "sim_bd_twin_tree" 0.00 "sim_twin_tree_fun" 0.00 "beautier::create_inference_model" 0.00 "c" 1.60 "formals" 0.53 "beautier::create_ns_mcmc" 0.00 "combine_models" 0.00 "create_mcmc" 0.00 "DDD::bd_ML" 0.00 "asNamespace" 0.89 "bd_loglik" 0.27 "" 0.09 ".Call" 0.00 "assertive::assert_is_a_number" 0.00 "optimizer" 0.00 "subplex::subplex" 0.00 "get" 1.33 "is_logical" 0.09 "fun" 0.00 "sort" 0.09 "sort.int" 0.18 "sort.default" 0.00 "metric_fn" 0.44 "sys.function" 0.27 "dim<-" 0.89 "sys.frame" 0.89 "sys.parent" 0.89 "testit::assert" 0.44 "is_character" 0.09 "beastier::check_beast2_options" 0.00 "as.character" 0.80 "get0" 0.80 "parent.frame" 0.80 "expr_label" 0.18 "%||%" 0.00 "beastier::check_beast2_options_data_types" 0.00 "beautier::check_nested_sampling_mcmc" 0.00 "quasi_label" 0.00 ".getNamespaceInfo" 0.71 "getOption" 0.71 "isBaseNamespace" 0.71 "cause<-" 0.18 "ape::Ntip" 0.00 "structure" 0.62 "lapply" 0.44 "pirouette::check_sim_twal_fun" 0.00 "length" 0.53 "sum" 0.53 "ifelse" 0.36 "noquote" 0.27 "signalCondition" 0.09 "beautier::check_beauti_options" 0.00 "create_twinning_params" 0.00 "testthat::expect_equal" 0.00 "getNamespace" 0.44 "order" 0.18 "assertive::is_if_condition" 0.00 "beautier::check_site_model_types" 0.00 "beautier::check_site_model" 0.00 "beautier::is_one_bool" 0.00 "expectation" 0.00 "new_expectation" 0.00 "pirouette::sim_alignment_with_n_mutations" 0.00 "sim_twal_fun" 0.00 "sim_twal_with_same_n_mutation" 0.00 "check_n" 0.36 "environment" 0.36 "get_metric" 0.36 "use_first" 0.36 "beautier::check_gamma_site_model" 0.18 "check_treelog_names" 0.18 "makeRestartList" 0.09 "pirouette::check_experiments_all_inference_models_are_unique" 0.09 "beautier::check_clock_model" 0.00 "beautier::is_gamma_site_model" 0.00 "pirouette::sim_alignment_with_std_nsm" 0.00 "pirouette::sim_tral_with_std_nsm" 0.00 "$" 0.27 "all" 0.27 "assert2" 0.27 "beautier::is_one_na" 0.27 "conditionMessage" 0.27 "is.function" 0.27 "is.list" 0.27 "makeRestart" 0.18 "check_tracelog_names" 0.09 "stopifnot" 0.09 "to_names" 0.09 "beastier::check_os" 0.00 "create_gen_experiment" 0.00 "expectation_error" 0.00 "is_distr" 0.00 "phangorn::simSeq" 0.00 "rappdirs::app_dir" 0.00 "simSeq.phylo" 0.00 "-" 0.18 "anyNA" 0.18 "attr" 0.18 "is.expectation" 0.18 "is.na" 0.18 "isNamespace" 0.18 "list" 0.18 "names<-" 0.18 "unlist" 0.18 "beautier::check_log_mode" 0.09 "beautier::check_log_sort" 0.09 "conditionCall" 0.09 "...elt" 0.00 "appdirs$new" 0.00 "beautier::check_gamma_site_model_names" 0.00 "beautier::check_rln_clock_model" 0.00 "beautier::check_strict_clock_model" 0.00 "create_tracelog" 0.00 "create_treelog" 0.00 "initialize" 0.00 "methods::new" 0.00 ".getClassesFromCache" 0.09 ".makeMessage" 0.09 "@<-" 0.09 "any" 0.09 "check_mcmc_list_element_names" 0.09 "dimnames" 0.09 "invisible" 0.09 "is.atomic" 0.09 "is.expression" 0.09 "names" 0.09 "options" 0.09 "paste" 0.09 "stri_count_regex" 0.09 ".doSortWrap" 0.00 ".makeSortEnum" 0.00 "assertive::is_a_string" 0.00 "bd_loglik_choosepar" 0.00 "beautier::check_clock_models" 0.00 "beautier::check_mrca_prior" 0.00 "beautier::check_param" 0.00 "beautier::create_mcmc" 0.00 "beautier::is_gamma_distr" 0.00 "beautier::is_laplace_distr" 0.00 "beautier::is_param" 0.00 "calc_base_freq" 0.00 "compare.character" 0.00 "compare" 0.00 "comparison" 0.00 "conditionCall.condition" 0.00 "create_beauti_options" 0.00 "create_rate_matrix" 0.00 "DDD::phylo2L" 0.00 "edQt" 0.00 "getClass" 0.00 "getClassDef" 0.00 "is_numeric" 0.00 "match.call" 0.00 "no_difference" 0.00 "phyDat.DNA" 0.00 "pirouette::check_reconstructed_phylogeny" 0.00 "pirouette::create_inference_conditions" 0.00 "rownames" 0.00 "solve.default" 0.00 "stop" 0.00 "stringr::str_count" 0.00 "sys.call" 0.00 $sample.interval [1] 0.02 $sampling.time [1] 22.48