Why is `create_std_pir_paramses` slow?

[richelbilderbeek]

test_that("use", {
  skip("No profiling")
  path <- file.path(rappdirs::user_cache_dir(), "create_std_pir_paramses.Rprof")
  Rprof(path)
  create_std_pir_paramses(n = n)
  Rprof(NULL)
  summaryRprof(path)
}

results in:

$by.self
                                                 self.time self.pct total.time total.pct
"getExportedValue"                                   10.90     3.95      33.06     11.98
"simSeq.phylo"                                        8.70     3.15     137.66     49.88
"!="                                                  7.28     2.64       7.28      2.64
"stri_match_first_regex"                              7.16     2.59       7.30      2.65
"%in%"                                                6.08     2.20      13.18      4.78
"::"                                                  5.80     2.10      39.84     14.44
"asNamespace"                                         5.60     2.03      11.52      4.17
"sample.int"                                          5.38     1.95       6.12      2.22
"gsub"                                                5.38     1.95       5.44      1.97
"get0"                                                4.96     1.80       4.96      1.80
"deparse"                                             4.84     1.75      13.62      4.94
"assert2"                                             4.64     1.68      21.96      7.96
"gettext"                                             4.32     1.57       4.64      1.68
"stri_count_regex"                                    4.06     1.47       4.44      1.61
"eval"                                                3.92     1.42      20.44      7.41
"beautier::check_gamma_site_model"                    3.68     1.33       9.14      3.31
"match.arg"                                           3.64     1.32      10.02      3.63
"options"                                             3.34     1.21       3.34      1.21
"getNamespace"                                        3.28     1.19       3.28      1.19
"[.data.frame"                                        3.12     1.13       9.58      3.47
"isBaseNamespace"                                     3.12     1.13       3.12      1.13
"structure"                                           2.94     1.07       4.74      1.72
".getNamespaceInfo"                                   2.92     1.06       2.92      1.06
"length"                                              2.74     0.99       2.74      0.99
"phyDat.DNA"                                          2.72     0.99      48.30     17.50
"[["                                                  2.70     0.98       8.34      3.02
"$"                                                   2.64     0.96       2.64      0.96
"isNamespace"                                         2.64     0.96       2.64      0.96
"pirouette::count_n_mutations"                        2.62     0.95      22.30      8.08
"testit::assert"                                      2.54     0.92      31.84     11.54
"paste0"                                              2.50     0.91      11.66      4.22
"c"                                                   2.36     0.86       2.36      0.86
"sys.call"                                            2.30     0.83       2.42      0.88
"sample"                                              2.26     0.82       8.48      3.07
"eigen"                                               2.20     0.80       8.90      3.22
".deparseOpts"                                        2.20     0.80       5.50      1.99
"create_rate_matrix"                                  2.18     0.79      46.00     16.67
"pmatch"                                              2.16     0.78       2.32      0.84
"getP"                                                2.12     0.77       3.64      1.32
"data.frame"                                          2.10     0.76      15.28      5.54
"edQt"                                                2.06     0.75      18.10      6.56
"as.DNAbin.phyDat"                                    1.98     0.72       4.44      1.61
"doTryCatch"                                          1.96     0.71     269.40     97.62
"tryCatch"                                            1.94     0.70     269.86     97.78
"as.character"                                        1.92     0.70       3.52      1.28
"names"                                               1.86     0.67       1.86      0.67
"as.data.frame.matrix"                                1.78     0.64       3.10      1.12
"matrix"                                              1.76     0.64       5.86      2.12
"match.fun"                                           1.76     0.64       5.20      1.88
"match.call"                                          1.72     0.62       3.78      1.37
"is.matrix"                                           1.70     0.62       1.70      0.62
"dim"                                                 1.68     0.61       2.56      0.93
"as.matrix"                                           1.62     0.59       8.00      2.90
"[[.data.frame"                                       1.62     0.59       5.64      2.04
"as.matrix.data.frame"                                1.60     0.58       5.72      2.07
"pirouette::get_alignment_sequences"                  1.56     0.57       8.22      2.98
"as.list"                                             1.52     0.55       1.96      0.71
"solve.default"                                       1.44     0.52       3.04      1.10
"order"                                               1.42     0.51       5.20      1.88
"assert_engine"                                       1.36     0.49      29.52     10.70
"vapply"                                              1.32     0.48       2.52      0.91
"pirouette::sim_alignment_with_std_nsm"               1.30     0.47     204.64     74.15
"do.call"                                             1.28     0.46       2.34      0.85
"sum"                                                 1.28     0.46       1.28      0.46
"<Anonymous>"                                         1.26     0.46       2.92      1.06
"one_expression"                                      1.26     0.46       2.00      0.72
"type"                                                1.26     0.46       1.62      0.59
"levels"                                              1.22     0.44       1.42      0.51
"parent.frame"                                        1.16     0.42       1.16      0.42
"sys.function"                                        1.14     0.41       1.96      0.71
"anyDuplicated"                                       1.14     0.41       1.52      0.55
"all"                                                 1.14     0.41       1.14      0.41
"fast.table"                                          1.06     0.38      10.66      3.86
"stopifnot"                                           1.06     0.38       1.70      0.62
"as.data.frame"                                       1.04     0.38       4.38      1.59
"calc_base_freq"                                      1.02     0.37      17.70      6.41
"pirouette::sim_alignment_with_n_mutations"           1.00     0.36     231.40     83.85
"any"                                                 1.00     0.36       1.00      0.36
"coerce_to"                                           0.98     0.36       6.30      2.28
"colSums"                                             0.98     0.36       1.28      0.46
"mode"                                                0.96     0.35       4.40      1.59
"paste"                                               0.94     0.34       1.60      0.58
"is.data.frame"                                       0.94     0.34       0.94      0.34
"sys.parent"                                          0.94     0.34       0.94      0.34
"t"                                                   0.90     0.33       1.06      0.38
"unique"                                              0.84     0.30       1.28      0.46
"sprintf"                                             0.82     0.30       5.60      2.03
"makeRestartList"                                     0.82     0.30       2.10      0.76
"enquo"                                               0.80     0.29       1.64      0.59
"strsplit"                                            0.80     0.29       0.82      0.30
"$<-"                                                 0.80     0.29       0.80      0.29
"as.vector"                                           0.80     0.29       0.80      0.29
"dimnames"                                            0.78     0.28       1.62      0.59
"na.omit.data.frame"                                  0.76     0.28       7.40      2.68
"unlist"                                              0.74     0.27       2.50      0.91
"beautier::check_gamma_site_model_names"              0.74     0.27       1.60      0.58
"pirouette::is_dna_seq"                               0.72     0.26      11.44      4.15
"lapply"                                              0.72     0.26       1.60      0.58
"sort.list"                                           0.70     0.25       4.42      1.60
"make.names"                                          0.70     0.25       3.30      1.20
"seq"                                                 0.70     0.25       1.34      0.49
"tryCatchList"                                        0.68     0.25     269.52     97.66
"rownames<-"                                          0.66     0.24       0.90      0.33
"get_name_in_parent"                                  0.64     0.23      13.50      4.89
"pirouette::get_alignment_sequence_length"            0.64     0.23       6.96      2.52
"phangorn::simSeq"                                    0.62     0.22     138.28     50.11
"testthat::expect_equal"                              0.62     0.22      24.14      8.75
"conditionMessage"                                    0.62     0.22       1.06      0.38
"conditionCall"                                       0.62     0.22       0.92      0.33
"as.numeric"                                          0.62     0.22       0.62      0.22
"get"                                                 0.60     0.22       0.64      0.23
"getCallingDLLe"                                      0.56     0.20       0.96      0.35
"FUN"                                                 0.56     0.20       0.80      0.29
"duplicated"                                          0.56     0.20       0.78      0.28
"pirouette::check_alignment"                          0.56     0.20       0.68      0.25
"seq.default"                                         0.56     0.20       0.64      0.23
"nchar"                                               0.56     0.20       0.56      0.20
"doWithOneRestart"                                    0.54     0.20       7.10      2.57
"attr"                                                0.54     0.20       0.54      0.20
"tryCatchOne"                                         0.52     0.19     269.44     97.63
"expect"                                              0.52     0.19      13.72      4.97
"stringr::str_match"                                  0.52     0.19       8.52      3.09
"tolower"                                             0.52     0.19       6.48      2.35
"colnames<-"                                          0.52     0.19       0.72      0.26
"quasi_label"                                         0.50     0.18       7.90      2.86
"reorder"                                             0.50     0.18       1.44      0.52
"names<-"                                             0.50     0.18       0.50      0.18
"all_true"                                            0.48     0.17       1.10      0.40
"beautier::is_one_na"                                 0.48     0.17       0.50      0.18
"as.integer"                                          0.48     0.17       0.48      0.17
"as.symbol"                                           0.48     0.17       0.48      0.17
"formals"                                             0.46     0.17       1.56      0.57
"f"                                                   0.46     0.17       1.54      0.56
"factor"                                              0.44     0.16       0.58      0.21
"stringr::str_count"                                  0.42     0.15       5.78      2.09
"opts"                                                0.42     0.15       0.52      0.19
"is2"                                                 0.40     0.14       5.38      1.95
"rownames"                                            0.40     0.14       1.64      0.59
"beautier::check_site_model_names"                    0.40     0.14       1.14      0.41
"diag<-"                                              0.40     0.14       0.84      0.30
"sys.frame"                                           0.40     0.14       0.40      0.14
"labels"                                              0.38     0.14       0.94      0.34
"anyDuplicated.default"                               0.38     0.14       0.38      0.14
"unname"                                              0.36     0.13       3.16      1.15
"row.names<-"                                         0.36     0.13       1.36      0.49
"pirouette::check_mutation_rate"                      0.36     0.13       0.40      0.14
"as.list.default"                                     0.36     0.13       0.36      0.13
"cbind"                                               0.36     0.13       0.36      0.13
"type.character"                                      0.36     0.13       0.36      0.13
"compare"                                             0.34     0.12       3.12      1.13
".reorder_ape"                                        0.34     0.12       0.60      0.22
"attributes"                                          0.34     0.12       0.34      0.12
"pirouette::check_root_sequence"                      0.32     0.12       8.20      2.97
"is_in_range"                                         0.32     0.12       6.52      2.36
"set_cause"                                           0.32     0.12       0.80      0.29
"row.names"                                           0.32     0.12       0.38      0.14
"predicate"                                           0.30     0.11      11.70      4.24
"na.omit"                                             0.30     0.11       7.70      2.79
"ape::as.DNAbin"                                      0.30     0.11       4.74      1.72
"diag"                                                0.30     0.11       0.42      0.15
"eval_bare"                                           0.30     0.11       0.42      0.15
"anyNA"                                               0.30     0.11       0.30      0.11
"is.factor"                                           0.30     0.11       0.30      0.11
"is.na"                                               0.30     0.11       0.30      0.11
"list"                                                0.30     0.11       0.30      0.11
"pirouette::sim_tral_with_std_nsm"                    0.28     0.10     206.02     74.65
"beautier::check_site_model"                          0.28     0.10      20.28      7.35
"signalCondition"                                     0.28     0.10       2.26      0.82
"nrow"                                                0.28     0.10       1.50      0.54
"...elt"                                              0.28     0.10       0.46      0.17
"unique.default"                                      0.28     0.10       0.44      0.16
".row_names_info"                                     0.28     0.10       0.28      0.10
".subset2"                                            0.28     0.10       0.28      0.10
"getOption"                                           0.28     0.10       0.28      0.10
"beautier::check_site_model_types"                    0.26     0.09      16.12      5.84
"["                                                   0.26     0.09       9.84      3.57
"force"                                               0.26     0.09       1.98      0.72
"ncol"                                                0.26     0.09       0.94      0.34
".rowNamesDF<-"                                       0.26     0.09       0.88      0.32
"lower.tri"                                           0.26     0.09       0.42      0.15
"tabulate"                                            0.26     0.09       0.26      0.09
"withRestarts"                                        0.24     0.09       9.46      3.43
"reorder.phylo"                                       0.24     0.09       0.94      0.34
"ape::Ntip"                                           0.24     0.09       0.86      0.31
"expectation_type"                                    0.22     0.08       3.88      1.41
"comparison"                                          0.22     0.08       2.50      0.91
"safe_deparse"                                        0.20     0.07      10.42      3.78
"expectation_broken"                                  0.20     0.07       4.20      1.52
"logical"                                             0.20     0.07       0.58      0.21
"as.data.frame.data.frame"                            0.20     0.07       0.22      0.08
"environment"                                         0.20     0.07       0.20      0.07
"quo_is_missing"                                      0.20     0.07       0.20      0.07
"beautier::is_gamma_site_model"                       0.18     0.07      11.98      4.34
"%||%"                                                0.18     0.07       4.76      1.72
"dimnames.data.frame"                                 0.18     0.07       0.84      0.30
"levels.default"                                      0.18     0.07       0.20      0.07
"=="                                                  0.18     0.07       0.18      0.07
"is.expectation"                                      0.18     0.07       0.18      0.07
"compare.character"                                   0.16     0.06       2.76      1.00
"beautier::is_site_model_name"                        0.16     0.06       1.80      0.65
"as.pairlist"                                         0.16     0.06       0.22      0.08
"duplicated.default"                                  0.16     0.06       0.22      0.08
"character"                                           0.16     0.06       0.16      0.06
"t.default"                                           0.16     0.06       0.16      0.06
"assertive::assert_is_if_condition"                   0.14     0.05       7.30      2.65
"expr_label"                                          0.14     0.05       4.58      1.66
"call_and_name"                                       0.14     0.05       1.44      0.52
"conditionMessage.condition"                          0.14     0.05       0.44      0.16
".set_row_names"                                      0.14     0.05       0.16      0.06
"/"                                                   0.14     0.05       0.14      0.05
"is.list"                                             0.14     0.05       0.14      0.05
"make.unique"                                         0.14     0.05       0.14      0.05
"numeric"                                             0.14     0.05       0.14      0.05
"check_mcmc_values"                                   0.12     0.04      25.94      9.40
"pirouette::get_alignment_n_taxa"                     0.12     0.04       1.72      0.62
"is_scalar"                                           0.12     0.04       1.20      0.43
"row.names<-.data.frame"                              0.12     0.04       1.00      0.36
"dim.data.frame"                                      0.12     0.04       0.88      0.32
"Ntip.phylo"                                          0.12     0.04       0.34      0.12
"conditionCall.condition"                             0.12     0.04       0.30      0.11
"check_tracelog_names"                                0.12     0.04       0.20      0.07
"class"                                               0.12     0.04       0.12      0.04
"max"                                                 0.12     0.04       0.12      0.04
"noquote"                                             0.12     0.04       0.12      0.04
"quo_get_env"                                         0.12     0.04       0.12      0.04
"use_first"                                           0.12     0.04       0.12      0.04
"assertive::assert_all_are_positive"                  0.10     0.04      14.66      5.31
"check_screenlog_values"                              0.10     0.04      12.02      4.36
"exp_signal"                                          0.10     0.04       9.56      3.46
"no_difference"                                       0.10     0.04       2.60      0.94
"fn"                                                  0.10     0.04       0.86      0.31
"bd_loglik"                                           0.10     0.04       0.58      0.21
"as.matrix.DNAbin"                                    0.10     0.04       0.56      0.20
"check_screenlog_names"                               0.10     0.04       0.16      0.06
"-"                                                   0.10     0.04       0.10      0.04
"!"                                                   0.10     0.04       0.10      0.04
"dim<-"                                               0.10     0.04       0.10      0.04
"is.pairlist"                                         0.10     0.04       0.10      0.04
"Mod"                                                 0.10     0.04       0.10      0.04
"nargs"                                               0.10     0.04       0.10      0.04
"quo_get_expr"                                        0.10     0.04       0.10      0.04
"assertive::assert_is_a_string"                       0.08     0.03       3.76      1.36
"expectation"                                         0.08     0.03       2.38      0.86
"pirouette::check_candidates_save_to_same_files"      0.08     0.03       1.46      0.53
"is_na"                                               0.08     0.03       1.30      0.47
".Call"                                               0.08     0.03       0.72      0.26
"labels.DNAbin"                                       0.08     0.03       0.56      0.20
"beautier::check_log_sort"                            0.08     0.03       0.16      0.06
"ifelse"                                              0.08     0.03       0.16      0.06
"metric_fn"                                           0.08     0.03       0.16      0.06
 [ reached 'max' / getOption("max.print") -- omitted 81 rows ]

$by.total
                                                          total.time total.pct self.time
"create_std_pir_paramses"                                     275.98    100.00      0.00
"tryCatch"                                                    269.86     97.78      1.94
"tryCatchList"                                                269.52     97.66      0.68
"tryCatchOne"                                                 269.44     97.63      0.52
"doTryCatch"                                                  269.40     97.62      1.96
"pirouette::check_twinning_params"                            232.36     84.19      0.00
"suppressWarnings"                                            232.14     84.11      0.00
"withCallingHandlers"                                         232.14     84.11      0.00
"pirouette::check_pir_params_data_types"                      231.78     83.98      0.00
"pirouette::check_pir_params"                                 231.78     83.98      0.00
"pirouette::check_sim_twal_fun"                               231.52     83.89      0.00
"sim_twal_fun"                                                231.48     83.88      0.00
"sim_twal_with_same_n_mutation"                               231.48     83.88      0.00
"pirouette::sim_alignment_with_n_mutations"                   231.40     83.85      1.00
"create_std_pir_params"                                       225.06     81.55      0.00
"pirouette::sim_tral_with_std_nsm"                            206.02     74.65      0.28
"pirouette::sim_alignment_with_std_nsm"                       204.64     74.15      1.30
"phangorn::simSeq"                                            138.28     50.11      0.62
"simSeq.phylo"                                                137.66     49.88      8.70
"pir_rename_to_std"                                           126.70     45.91      0.00
"pirouette::has_twinning"                                      59.00     21.38      0.00
"renum_rng_seeds"                                              59.00     21.38      0.00
"phyDat.DNA"                                                   48.30     17.50      2.72
"create_pir_params"                                            46.10     16.70      0.00
"create_rate_matrix"                                           46.00     16.67      2.18
"pirouette::check_experiments"                                 40.76     14.77      0.00
"::"                                                           39.84     14.44      5.80
"create_twinning_params"                                       35.06     12.70      0.00
"pirouette::check_experiments_candidates_have_same_mcmcs"      33.72     12.22      0.00
"beautier::are_equal_mcmcs"                                    33.52     12.15      0.02
"getExportedValue"                                             33.06     11.98     10.90
"testit::assert"                                               31.84     11.54      2.54
"assert_engine"                                                29.52     10.70      1.36
"beautier::check_mcmc"                                         26.00      9.42      0.00
"check_mcmc_values"                                            25.94      9.40      0.12
"testthat::expect_equal"                                       24.14      8.75      0.62
"pirouette::count_n_mutations"                                 22.30      8.08      2.62
"assert2"                                                      21.96      7.96      4.64
"eval"                                                         20.44      7.41      3.92
"beautier::check_site_model"                                   20.28      7.35      0.28
"edQt"                                                         18.10      6.56      2.06
"calc_base_freq"                                               17.70      6.41      1.02
"beautier::check_site_model_types"                             16.12      5.84      0.26
"data.frame"                                                   15.28      5.54      2.10
"assertive::assert_all_are_positive"                           14.66      5.31      0.10
"expect"                                                       13.72      4.97      0.52
"deparse"                                                      13.62      4.94      4.84
"get_name_in_parent"                                           13.50      4.89      0.64
"%in%"                                                         13.18      4.78      6.08
"beautier::check_screenlog"                                    12.18      4.41      0.00
"check_screenlog_values"                                       12.02      4.36      0.10
"beautier::is_gamma_site_model"                                11.98      4.34      0.18
"predicate"                                                    11.70      4.24      0.30
"paste0"                                                       11.66      4.22      2.50
"asNamespace"                                                  11.52      4.17      5.60
"pirouette::is_dna_seq"                                        11.44      4.15      0.72
"beautier::check_treelog"                                      10.70      3.88      0.02
"fast.table"                                                   10.66      3.86      1.06
"check_treelog_values"                                         10.56      3.83      0.04
"safe_deparse"                                                 10.42      3.78      0.20
"match.arg"                                                    10.02      3.63      3.64
"["                                                             9.84      3.57      0.26
"[.data.frame"                                                  9.58      3.47      3.12
"exp_signal"                                                    9.56      3.46      0.10
"withRestarts"                                                  9.46      3.43      0.24
"beautier::check_tracelog"                                      9.42      3.41      0.02
"check_tracelog_values"                                         9.20      3.33      0.06
"beautier::check_gamma_site_model"                              9.14      3.31      3.68
"create_all_bd_experiments"                                     8.94      3.24      0.00
"pirouette::create_all_experiments"                             8.92      3.23      0.00
"eigen"                                                         8.90      3.22      2.20
"stringr::str_match"                                            8.52      3.09      0.52
"sample"                                                        8.48      3.07      2.26
"[["                                                            8.34      3.02      2.70
"pirouette::get_alignment_sequences"                            8.22      2.98      1.56
"pirouette::check_root_sequence"                                8.20      2.97      0.32
"as.matrix"                                                     8.00      2.90      1.62
"quasi_label"                                                   7.90      2.86      0.50
"na.omit"                                                       7.70      2.79      0.30
"na.omit.data.frame"                                            7.40      2.68      0.76
"stri_match_first_regex"                                        7.30      2.65      7.16
"assertive::assert_is_if_condition"                             7.30      2.65      0.14
"!="                                                            7.28      2.64      7.28
"withOneRestart"                                                7.12      2.58      0.02
"doWithOneRestart"                                              7.10      2.57      0.54
"pirouette::get_alignment_sequence_length"                      6.96      2.52      0.64
"is_in_range"                                                   6.52      2.36      0.32
"tolower"                                                       6.48      2.35      0.52
"coerce_to"                                                     6.30      2.28      0.98
"pirouette::check_experiment"                                   6.30      2.28      0.00
"sample.int"                                                    6.12      2.22      5.38
"matrix"                                                        5.86      2.12      1.76
"stringr::str_count"                                            5.78      2.09      0.42
"as.matrix.data.frame"                                          5.72      2.07      1.60
"[[.data.frame"                                                 5.64      2.04      1.62
"sprintf"                                                       5.60      2.03      0.82
".deparseOpts"                                                  5.50      1.99      2.20
"gsub"                                                          5.44      1.97      5.38
"is2"                                                           5.38      1.95      0.40
"are_equal_screenlogs"                                          5.32      1.93      0.02
"match.fun"                                                     5.20      1.88      1.76
"order"                                                         5.20      1.88      1.42
"get0"                                                          4.96      1.80      4.96
"gettextf"                                                      4.96      1.80      0.04
"%||%"                                                          4.76      1.72      0.18
"structure"                                                     4.74      1.72      2.94
"ape::as.DNAbin"                                                4.74      1.72      0.30
"gettext"                                                       4.64      1.68      4.32
"expr_label"                                                    4.58      1.66      0.14
"are_equal_treelogs"                                            4.50      1.63      0.00
"stri_count_regex"                                              4.44      1.61      4.06
"as.DNAbin.phyDat"                                              4.44      1.61      1.98
"sort.list"                                                     4.42      1.60      0.70
"mode"                                                          4.40      1.59      0.96
"as.data.frame"                                                 4.38      1.59      1.04
"expectation_broken"                                            4.20      1.52      0.20
"are_equal_tracelogs"                                           4.10      1.49      0.00
"assertive::assert_is_character"                                4.02      1.46      0.04
"expectation_type"                                              3.88      1.41      0.22
"match.call"                                                    3.78      1.37      1.72
"assertive::assert_is_a_string"                                 3.76      1.36      0.08
"getP"                                                          3.64      1.32      2.12
"beautier::is_nested_sampling_mcmc"                             3.62      1.31      0.00
"check_mcmc_nested_sampling"                                    3.62      1.31      0.00
"as.character"                                                  3.52      1.28      1.92
"assertive::assert_is_numeric"                                  3.48      1.26      0.04
"options"                                                       3.34      1.21      3.34
"make.names"                                                    3.30      1.20      0.70
"getNamespace"                                                  3.28      1.19      3.28
"unname"                                                        3.16      1.15      0.36
"isBaseNamespace"                                               3.12      1.13      3.12
"compare"                                                       3.12      1.13      0.34
"as.data.frame.matrix"                                          3.10      1.12      1.78
"solve.default"                                                 3.04      1.10      1.44
".getNamespaceInfo"                                             2.92      1.06      2.92
"<Anonymous>"                                                   2.92      1.06      1.26
"assertive::assert_all_are_whole_numbers"                       2.88      1.04      0.06
"compare.character"                                             2.76      1.00      0.16
"length"                                                        2.74      0.99      2.74
"beautier::check_inference_model"                               2.70      0.98      0.02
"$"                                                             2.64      0.96      2.64
"isNamespace"                                                   2.64      0.96      2.64
"no_difference"                                                 2.60      0.94      0.10
"dim"                                                           2.56      0.93      1.68
"vapply"                                                        2.52      0.91      1.32
"unlist"                                                        2.50      0.91      0.74
"comparison"                                                    2.50      0.91      0.22
"expectation_failure"                                           2.50      0.91      0.06
"sys.call"                                                      2.42      0.88      2.30
"expectation"                                                   2.38      0.86      0.08
"c"                                                             2.36      0.86      2.36
"do.call"                                                       2.34      0.85      1.28
"beautier::check_store_every"                                   2.34      0.85      0.00
"pmatch"                                                        2.32      0.84      2.16
"new_expectation"                                               2.30      0.83      0.06
"signalCondition"                                               2.26      0.82      0.28
"makeRestartList"                                               2.10      0.76      0.82
"one_expression"                                                2.00      0.72      1.26
"force"                                                         1.98      0.72      0.26
"as.list"                                                       1.96      0.71      1.52
"sys.function"                                                  1.96      0.71      1.14
"names"                                                         1.86      0.67      1.86
"beautier::is_site_model_name"                                  1.80      0.65      0.16
"pirouette::create_experiment"                                  1.76      0.64      0.00
"pirouette::get_alignment_n_taxa"                               1.72      0.62      0.12
"is.matrix"                                                     1.70      0.62      1.70
"stopifnot"                                                     1.70      0.62      1.06
"enquo"                                                         1.64      0.59      0.80
"rownames"                                                      1.64      0.59      0.40
"type"                                                          1.62      0.59      1.26
"dimnames"                                                      1.62      0.59      0.78
"paste"                                                         1.60      0.58      0.94
"beautier::check_gamma_site_model_names"                        1.60      0.58      0.74
"lapply"                                                        1.60      0.58      0.72
"as.character.DNAbin"                                           1.60      0.58      0.06
"formals"                                                       1.56      0.57      0.46
"f"                                                             1.54      0.56      0.46
"anyDuplicated"                                                 1.52      0.55      1.14
"nrow"                                                          1.50      0.54      0.28
"expectation_error"                                             1.50      0.54      0.06
"pirouette::check_candidates_save_to_same_files"                1.46      0.53      0.08
"reorder"                                                       1.44      0.52      0.50
"call_and_name"                                                 1.44      0.52      0.14
"levels"                                                        1.42      0.51      1.22
"row.names<-"                                                   1.36      0.49      0.36
"seq"                                                           1.34      0.49      0.70
"is_na"                                                         1.30      0.47      0.08
"sum"                                                           1.28      0.46      1.28
"colSums"                                                       1.28      0.46      0.98
"unique"                                                        1.28      0.46      0.84
"testthat::expect_true"                                         1.26      0.46      0.02
"is_scalar"                                                     1.20      0.43      0.12
"parent.frame"                                                  1.16      0.42      1.16
"all"                                                           1.14      0.41      1.14
"beautier::check_site_model_names"                              1.14      0.41      0.40
"all_true"                                                      1.10      0.40      0.48
"t"                                                             1.06      0.38      0.90
"conditionMessage"                                              1.06      0.38      0.62
"any"                                                           1.00      0.36      1.00
"row.names<-.data.frame"                                        1.00      0.36      0.12
"getCallingDLLe"                                                0.96      0.35      0.56
"is.data.frame"                                                 0.94      0.34      0.94
"sys.parent"                                                    0.94      0.34      0.94
"labels"                                                        0.94      0.34      0.38
"ncol"                                                          0.94      0.34      0.26
"reorder.phylo"                                                 0.94      0.34      0.24
"conditionCall"                                                 0.92      0.33      0.62
"beautier::create_inference_model"                              0.92      0.33      0.00
"rownames<-"                                                    0.90      0.33      0.66
"create_mcmc"                                                   0.90      0.33      0.02
".rowNamesDF<-"                                                 0.88      0.32      0.26
"dim.data.frame"                                                0.88      0.32      0.12
"combine_models"                                                0.88      0.32      0.02
"ape::Ntip"                                                     0.86      0.31      0.24
"fn"                                                            0.86      0.31      0.10
"makeRestart"                                                   0.86      0.31      0.02
"diag<-"                                                        0.84      0.30      0.40
"dimnames.data.frame"                                           0.84      0.30      0.18
"pirouette::check_sim_twin_tree_fun"                            0.84      0.30      0.00
"strsplit"                                                      0.82      0.30      0.80
"assertive::assert_is_a_number"                                 0.82      0.30      0.04
"sim_bd_twin_tree"                                              0.82      0.30      0.00
"sim_twin_tree_fun"                                             0.82      0.30      0.00
"$<-"                                                           0.80      0.29      0.80
"as.vector"                                                     0.80      0.29      0.80
"FUN"                                                           0.80      0.29      0.56
"set_cause"                                                     0.80      0.29      0.32
"duplicated"                                                    0.78      0.28      0.56
"DDD::bd_ML"                                                    0.76      0.28      0.00
"colnames<-"                                                    0.72      0.26      0.52
".Call"                                                         0.72      0.26      0.08
"is_logical"                                                    0.72      0.26      0.00
"pirouette::check_alignment"                                    0.68      0.25      0.56
"beautier::create_ns_mcmc"                                      0.68      0.25      0.00
"optimizer"                                                     0.66      0.24      0.00
"subplex::subplex"                                              0.66      0.24      0.00
"get"                                                           0.64      0.23      0.60
"seq.default"                                                   0.64      0.23      0.56
"fun"                                                           0.64      0.23      0.04
"as.numeric"                                                    0.62      0.22      0.62
".reorder_ape"                                                  0.60      0.22      0.34
"factor"                                                        0.58      0.21      0.44
"logical"                                                       0.58      0.21      0.20
"bd_loglik"                                                     0.58      0.21      0.10
"nchar"                                                         0.56      0.20      0.56
"as.matrix.DNAbin"                                              0.56      0.20      0.10
"labels.DNAbin"                                                 0.56      0.20      0.08
"attr"                                                          0.54      0.20      0.54
"opts"                                                          0.52      0.19      0.42
"sort"                                                          0.52      0.19      0.04
                                                          self.pct
"create_std_pir_paramses"                                     0.00
"tryCatch"                                                    0.70
"tryCatchList"                                                0.25
"tryCatchOne"                                                 0.19
"doTryCatch"                                                  0.71
"pirouette::check_twinning_params"                            0.00
"suppressWarnings"                                            0.00
"withCallingHandlers"                                         0.00
"pirouette::check_pir_params_data_types"                      0.00
"pirouette::check_pir_params"                                 0.00
"pirouette::check_sim_twal_fun"                               0.00
"sim_twal_fun"                                                0.00
"sim_twal_with_same_n_mutation"                               0.00
"pirouette::sim_alignment_with_n_mutations"                   0.36
"create_std_pir_params"                                       0.00
"pirouette::sim_tral_with_std_nsm"                            0.10
"pirouette::sim_alignment_with_std_nsm"                       0.47
"phangorn::simSeq"                                            0.22
"simSeq.phylo"                                                3.15
"pir_rename_to_std"                                           0.00
"pirouette::has_twinning"                                     0.00
"renum_rng_seeds"                                             0.00
"phyDat.DNA"                                                  0.99
"create_pir_params"                                           0.00
"create_rate_matrix"                                          0.79
"pirouette::check_experiments"                                0.00
"::"                                                          2.10
"create_twinning_params"                                      0.00
"pirouette::check_experiments_candidates_have_same_mcmcs"     0.00
"beautier::are_equal_mcmcs"                                   0.01
"getExportedValue"                                            3.95
"testit::assert"                                              0.92
"assert_engine"                                               0.49
"beautier::check_mcmc"                                        0.00
"check_mcmc_values"                                           0.04
"testthat::expect_equal"                                      0.22
"pirouette::count_n_mutations"                                0.95
"assert2"                                                     1.68
"eval"                                                        1.42
"beautier::check_site_model"                                  0.10
"edQt"                                                        0.75
"calc_base_freq"                                              0.37
"beautier::check_site_model_types"                            0.09
"data.frame"                                                  0.76
"assertive::assert_all_are_positive"                          0.04
"expect"                                                      0.19
"deparse"                                                     1.75
"get_name_in_parent"                                          0.23
"%in%"                                                        2.20
"beautier::check_screenlog"                                   0.00
"check_screenlog_values"                                      0.04
"beautier::is_gamma_site_model"                               0.07
"predicate"                                                   0.11
"paste0"                                                      0.91
"asNamespace"                                                 2.03
"pirouette::is_dna_seq"                                       0.26
"beautier::check_treelog"                                     0.01
"fast.table"                                                  0.38
"check_treelog_values"                                        0.01
"safe_deparse"                                                0.07
"match.arg"                                                   1.32
"["                                                           0.09
"[.data.frame"                                                1.13
"exp_signal"                                                  0.04
"withRestarts"                                                0.09
"beautier::check_tracelog"                                    0.01
"check_tracelog_values"                                       0.02
"beautier::check_gamma_site_model"                            1.33
"create_all_bd_experiments"                                   0.00
"pirouette::create_all_experiments"                           0.00
"eigen"                                                       0.80
"stringr::str_match"                                          0.19
"sample"                                                      0.82
"[["                                                          0.98
"pirouette::get_alignment_sequences"                          0.57
"pirouette::check_root_sequence"                              0.12
"as.matrix"                                                   0.59
"quasi_label"                                                 0.18
"na.omit"                                                     0.11
"na.omit.data.frame"                                          0.28
"stri_match_first_regex"                                      2.59
"assertive::assert_is_if_condition"                           0.05
"!="                                                          2.64
"withOneRestart"                                              0.01
"doWithOneRestart"                                            0.20
"pirouette::get_alignment_sequence_length"                    0.23
"is_in_range"                                                 0.12
"tolower"                                                     0.19
"coerce_to"                                                   0.36
"pirouette::check_experiment"                                 0.00
"sample.int"                                                  1.95
"matrix"                                                      0.64
"stringr::str_count"                                          0.15
"as.matrix.data.frame"                                        0.58
"[[.data.frame"                                               0.59
"sprintf"                                                     0.30
".deparseOpts"                                                0.80
"gsub"                                                        1.95
"is2"                                                         0.14
"are_equal_screenlogs"                                        0.01
"match.fun"                                                   0.64
"order"                                                       0.51
"get0"                                                        1.80
"gettextf"                                                    0.01
"%||%"                                                        0.07
"structure"                                                   1.07
"ape::as.DNAbin"                                              0.11
"gettext"                                                     1.57
"expr_label"                                                  0.05
"are_equal_treelogs"                                          0.00
"stri_count_regex"                                            1.47
"as.DNAbin.phyDat"                                            0.72
"sort.list"                                                   0.25
"mode"                                                        0.35
"as.data.frame"                                               0.38
"expectation_broken"                                          0.07
"are_equal_tracelogs"                                         0.00
"assertive::assert_is_character"                              0.01
"expectation_type"                                            0.08
"match.call"                                                  0.62
"assertive::assert_is_a_string"                               0.03
"getP"                                                        0.77
"beautier::is_nested_sampling_mcmc"                           0.00
"check_mcmc_nested_sampling"                                  0.00
"as.character"                                                0.70
"assertive::assert_is_numeric"                                0.01
"options"                                                     1.21
"make.names"                                                  0.25
"getNamespace"                                                1.19
"unname"                                                      0.13
"isBaseNamespace"                                             1.13
"compare"                                                     0.12
"as.data.frame.matrix"                                        0.64
"solve.default"                                               0.52
".getNamespaceInfo"                                           1.06
"<Anonymous>"                                                 0.46
"assertive::assert_all_are_whole_numbers"                     0.02
"compare.character"                                           0.06
"length"                                                      0.99
"beautier::check_inference_model"                             0.01
"$"                                                           0.96
"isNamespace"                                                 0.96
"no_difference"                                               0.04
"dim"                                                         0.61
"vapply"                                                      0.48
"unlist"                                                      0.27
"comparison"                                                  0.08
"expectation_failure"                                         0.02
"sys.call"                                                    0.83
"expectation"                                                 0.03
"c"                                                           0.86
"do.call"                                                     0.46
"beautier::check_store_every"                                 0.00
"pmatch"                                                      0.78
"new_expectation"                                             0.02
"signalCondition"                                             0.10
"makeRestartList"                                             0.30
"one_expression"                                              0.46
"force"                                                       0.09
"as.list"                                                     0.55
"sys.function"                                                0.41
"names"                                                       0.67
"beautier::is_site_model_name"                                0.06
"pirouette::create_experiment"                                0.00
"pirouette::get_alignment_n_taxa"                             0.04
"is.matrix"                                                   0.62
"stopifnot"                                                   0.38
"enquo"                                                       0.29
"rownames"                                                    0.14
"type"                                                        0.46
"dimnames"                                                    0.28
"paste"                                                       0.34
"beautier::check_gamma_site_model_names"                      0.27
"lapply"                                                      0.26
"as.character.DNAbin"                                         0.02
"formals"                                                     0.17
"f"                                                           0.17
"anyDuplicated"                                               0.41
"nrow"                                                        0.10
"expectation_error"                                           0.02
"pirouette::check_candidates_save_to_same_files"              0.03
"reorder"                                                     0.18
"call_and_name"                                               0.05
"levels"                                                      0.44
"row.names<-"                                                 0.13
"seq"                                                         0.25
"is_na"                                                       0.03
"sum"                                                         0.46
"colSums"                                                     0.36
"unique"                                                      0.30
"testthat::expect_true"                                       0.01
"is_scalar"                                                   0.04
"parent.frame"                                                0.42
"all"                                                         0.41
"beautier::check_site_model_names"                            0.14
"all_true"                                                    0.17
"t"                                                           0.33
"conditionMessage"                                            0.22
"any"                                                         0.36
"row.names<-.data.frame"                                      0.04
"getCallingDLLe"                                              0.20
"is.data.frame"                                               0.34
"sys.parent"                                                  0.34
"labels"                                                      0.14
"ncol"                                                        0.09
"reorder.phylo"                                               0.09
"conditionCall"                                               0.22
"beautier::create_inference_model"                            0.00
"rownames<-"                                                  0.24
"create_mcmc"                                                 0.01
".rowNamesDF<-"                                               0.09
"dim.data.frame"                                              0.04
"combine_models"                                              0.01
"ape::Ntip"                                                   0.09
"fn"                                                          0.04
"makeRestart"                                                 0.01
"diag<-"                                                      0.14
"dimnames.data.frame"                                         0.07
"pirouette::check_sim_twin_tree_fun"                          0.00
"strsplit"                                                    0.29
"assertive::assert_is_a_number"                               0.01
"sim_bd_twin_tree"                                            0.00
"sim_twin_tree_fun"                                           0.00
"$<-"                                                         0.29
"as.vector"                                                   0.29
"FUN"                                                         0.20
"set_cause"                                                   0.12
"duplicated"                                                  0.20
"DDD::bd_ML"                                                  0.00
"colnames<-"                                                  0.19
".Call"                                                       0.03
"is_logical"                                                  0.00
"pirouette::check_alignment"                                  0.20
"beautier::create_ns_mcmc"                                    0.00
"optimizer"                                                   0.00
"subplex::subplex"                                            0.00
"get"                                                         0.22
"seq.default"                                                 0.20
"fun"                                                         0.01
"as.numeric"                                                  0.22
".reorder_ape"                                                0.12
"factor"                                                      0.16
"logical"                                                     0.07
"bd_loglik"                                                   0.04
"nchar"                                                       0.20
"as.matrix.DNAbin"                                            0.04
"labels.DNAbin"                                               0.03
"attr"                                                        0.20
"opts"                                                        0.15
"sort"                                                        0.01
 [ reached 'max' / getOption("max.print") -- omitted 225 rows ]

$sample.interval
[1] 0.02

$sampling.time
[1] 275.98

[richelbilderbeek]

Ah, sim_alignment_with_n_mutations takes up 86% of all time. Clear: it needs to simulate exactly the right number of mutations.