[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/clock_model_to_xml_prior_distr.R#L14) *warning:* **no visible global function definition for ‘rln_clock_model_to_xml_mean_rate_prior’**
```r
      text <- c(text, rln_clock_model_to_xml_mean_rate_prior(clock_model)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:32:23:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/clock_models_to_xml_state.R#L32) *warning:* **no visible global function definition for ‘clock_model_to_xml_state’**
```r
    line_to_remove <- clock_model_to_xml_state(clock_models[[1]]) # nolint
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:9:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_distr.R#L9) *warning:* **no visible global function definition for ‘tree_priors_to_xml_prior_distr’**
```r
  text <- c(text, tree_priors_to_xml_prior_distr(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:10:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_distr.R#L10) *warning:* **no visible global function definition for ‘gamma_site_models_to_xml_prior_distr’**
```r
  text <- c(text, gamma_site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:11:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_distr.R#L11) *warning:* **no visible global function definition for ‘site_models_to_xml_prior_distr’**
```r
  text <- c(text, site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:27:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_operators.R#L27) *warning:* **no visible global function definition for ‘site_models_to_xml_operators’**
```r
  text <- c(text, site_models_to_xml_operators(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_run.R:23:11:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_run.R#L23) *warning:* **no visible global function definition for ‘mcmc_to_xml_run’**
```r
  text <- mcmc_to_xml_run(mcmc) # nolint beautier function
          ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:24:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_state.R#L24) *warning:* **no visible global function definition for ‘site_models_to_xml_state’**
```r
  text <- c(text, site_models_to_xml_state(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:33:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_beast2_input_state.R#L33) *warning:* **no visible global function definition for ‘tree_priors_to_xml_state’**
```r
  text <- c(text, tree_priors_to_xml_state(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_clock_models_from_names.R:5:26:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_clock_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_clock_model_from_name’**
```r
    clock_models[[i]] <- create_clock_model_from_name(clock_model_name) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:41:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_mcmc_nested_sampling.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @aliases create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:42:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_mcmc_nested_sampling.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
#' @export create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_site_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_site_model_from_name’**
```r
    site_models[[i]] <- create_site_model_from_name(site_model_name) # nolint beautier function
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:17:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_tracelog_xml.R#L17) *warning:* **no visible global function definition for ‘tree_models_to_xml_tracelog’**
```r
  text <- c(text, tree_models_to_xml_tracelog(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:32:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/create_tracelog_xml.R#L32) *warning:* **no visible global function definition for ‘tree_priors_to_xml_tracelog’**
```r
  text <- c(text, tree_priors_to_xml_tracelog(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_operators_from_lines.R:13:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/extract_xml_operators_from_lines.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
  last_line <- beautier::find_last_regex_line(lines, "(<operator id=\")|(</operator>)")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/extract_xml_section_from_lines.R#L7) *warning:* **no visible global function definition for ‘extract_xml_operators_from_lines’**
```r
    return(extract_xml_operators_from_lines(lines)) # nolint beautier function
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_last_xml_closing_tag_line.R:6:3:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/find_last_xml_closing_tag_line.R#L6) *warning:* **no visible global function definition for ‘find_last_regex_line’**
```r
  find_last_regex_line(lines, paste0("</", section, ">")) # nolint beautier function
  ^~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_id.R:5:9:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/get_alignment_id.R#L5) *warning:* **no visible global function definition for ‘get_file_base_sans_ext’**
```r
  id <- get_file_base_sans_ext(fasta_filename) # nolint beautier function
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_id.R:9:3:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/get_alignment_id.R#L9) *warning:* **no visible global function definition for ‘check_alignment_id’**
```r
  check_alignment_id(id)
  ^~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/has_xml_opening_tag.R#L11) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
    tag <- get_xml_opening_tag(lines) # nolint
           ^~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:14:24:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/has_xml_opening_tag.R#L14) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !beautier::is_one_na(find_first_xml_opening_tag_line(lines, section))
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:10:10:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_clock_models.R#L10) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames) # nolint beautier function
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:13:26:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_clock_models.R#L13) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(ucldstdev_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:20:26:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_clock_models.R#L20) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(mean_rate_prior_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/init_inference_model.R:39:22:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_inference_model.R#L39) *warning:* **no visible global function definition for ‘init_mrca_prior’**
```r
  inference_model <- init_mrca_prior(input_filename, inference_model)
                     ^~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:8:50:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_mrca_prior.R#L8) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
      inference_model$mrca_prior$alignment_id <- get_alignment_id(input_filename) # nolint beautier function
                                                 ^~~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:11:48:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_mrca_prior.R#L11) *warning:* **no visible global function definition for ‘get_taxa_names’**
```r
      inference_model$mrca_prior$taxa_names <- get_taxa_names(input_filename) # nolint beautier function
                                               ^~~~~~~~~~~~~~
```
[R/init_site_models.R:44:28:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_site_models.R#L44) *warning:* **no visible global function definition for ‘get_site_model_n_params’**
```r
    param_id <- param_id + get_site_model_n_params(site_model) # nolint beautier function
                           ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:198:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_site_models.R#L198) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(gtr_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:220:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_site_models.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
  if (!beautier::is_one_na(hky_site_model$gamma_site_model$gamma_shape_prior_distr)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:299:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_site_models.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(jc69_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:327:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/init_site_models.R#L327) *style:* **Lines should not be more than 80 characters.**
```r
    !beautier::is_one_na(tn93_site_model$gamma_site_model$gamma_shape_prior_distr)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/interspace.R:6:11:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/interspace.R#L6) *warning:* **no visible global function definition for ‘count_trailing_spaces’**
```r
  nsni <- count_trailing_spaces(lines[1]) # nolint beautier function
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_clock_model_name.R:2:13:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_clock_model_name.R#L2) *warning:* **no visible global function definition for ‘get_clock_model_names’**
```r
  name %in% get_clock_model_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_default_mcmc.R:2:8:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_default_mcmc.R#L2) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(mcmc)) return(FALSE) # nolint beautier function
       ^~~~~~~
```
[R/is_default_mcmc.R:3:39:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_default_mcmc.R#L3) *warning:* **no visible global function definition for ‘create_mcmc’**
```r
  length(names(mcmc)) == length(names(create_mcmc()))
                                      ^~~~~~~~~~~
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_freq_equilibrium_name.R:4:13:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_freq_equilibrium_name.R#L4) *warning:* **no visible global function definition for ‘get_freq_equilibrium_names’**
```r
  name %in% get_freq_equilibrium_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_id.R:4:32:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_id.R#L4) *warning:* **no visible global function definition for ‘is_one_int’**
```r
  assertive::is_a_string(x) || is_one_int(x) # nolint beautier function
                               ^~~~~~~~~~
```
[R/is_init_distr.R:26:20:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_init_distr.R#L26) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(x))
                   ^~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_init_site_model.R#L36) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
is_init_gtr_site_model <- function(
^
```
[R/is_mrca_align_id_in_fasta.R:6:9:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_mrca_align_id_in_fasta.R#L6) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
  id <- get_alignment_id(fasta_filename)
        ^~~~~~~~~~~~~~~~
```
[R/is_mrca_align_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_mrca_align_ids_in_fastas.R#L6) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:8:8:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L8) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE) # nolint beautier function
       ^~~~~~~~
```
[R/is_site_model.R:10:8:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L10) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:18:10:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L18) *warning:* **no visible global function definition for ‘is_distr’**
```r
    if (!is_distr(expected_distr)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:24:10:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L24) *warning:* **no visible global function definition for ‘is_param’**
```r
    if (!is_param(expected_param)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:27:8:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L27) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/is_tree_prior_name.R:2:13:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_tree_prior_name.R#L2) *warning:* **no visible global function definition for ‘get_tree_prior_names’**
```r
  name %in% get_tree_prior_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/mcmc_to_xml_run.R:47:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/mcmc_to_xml_run.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    xml <- paste0(xml, " numInitializationAttempts=\"", mcmc$n_init_attempts, "\"")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mrca_prior_to_xml_lh_distr.R:6:34:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/mrca_prior_to_xml_lh_distr.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_prior) == 1 && is_one_na(mrca_prior)) return(NULL) # nolint beautier function
                                 ^~~~~~~~~
```
[R/mrca_priors_to_xml_state.R:6:35:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/mrca_priors_to_xml_state.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_priors) == 1 && is_one_na(mrca_priors)) return(NULL) # nolint beautier function
                                  ^~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_model_to_xml_state.R#L25) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_model_to_xml_state.R#L51) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_2_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_subst_model.R:6:18:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_model_to_xml_subst_model.R#L6) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/site_model_to_xml_subst_model.R:7:18:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_model_to_xml_subst_model.R#L7) *warning:* **no visible global function definition for ‘is_jc69_site_model’**
```r
  testit::assert(is_jc69_site_model(site_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_models_to_xml_operators.R#L4) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_tracelog.R:6:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/site_models_to_xml_tracelog.R#L6) *warning:* **no visible global function definition for ‘site_model_to_xml_tracelog’**
```r
    text <- c(text, site_model_to_xml_tracelog(site_model)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:10:22:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_prior_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior) # nolint beautier function
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:7:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_prior_to_xml_prior_distr.R#L7) *warning:* **no visible global function definition for ‘bd_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, bd_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:9:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_prior_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘cbs_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cbs_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:11:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_prior_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘ccp_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, ccp_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:13:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_prior_to_xml_prior_distr.R#L13) *warning:* **no visible global function definition for ‘cep_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cep_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:16:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_prior_to_xml_prior_distr.R#L16) *warning:* **no visible global function definition for ‘yule_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, yule_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_distr.R:8:21:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_priors_to_xml_distr.R#L8) *warning:* **no visible global function definition for ‘tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_operators.R:6:18:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/R/tree_priors_to_xml_operators.R#L6) *warning:* **no visible global function definition for ‘are_tree_priors’**
```r
  testit::assert(are_tree_priors(tree_priors)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[tests/testthat/test-are_equal_mcmcs.R:57:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/tests/testthat/test-are_equal_mcmcs.R#L57) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-check_file_and_model_agree.R:16:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/tests/testthat/test-check_file_and_model_agree.R#L16) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-check_file_and_model_agree.R:35:19:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/tests/testthat/test-check_file_and_model_agree.R#L35) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-create_treelog_xml.R:15:1:](https://github.com/ropensci/beautier/blob/e5f33d61385c822a9d40498ad9f9a5bc9b097eb6/tests/testthat/test-create_treelog_xml.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
    "    <log id=\"TreeWithMetaDataLogger.t:test_output_0\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:test_output_0\"/>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://commercetools-docs-kit-9bu4c4ay9.now.sh
* https://commercetools-docs-kit.now.sh
* https://commercetools-docs-kit.commercetools.now.sh
* https://commercetools-docs-kit-git-master.commercetools.now.sh


Successfully deployed to following URLs:

* https://pdfswitch-docs-qchwjvehc.now.sh
* https://pdfswitch-docs.pdfswitch.now.sh
* https://pdfswitch-docs-git-master.pdfswitch.now.sh


if you put this in one RUN command with concatenated cmds with && the image would be slightly smaller.


This is what I use in my skin:
<widget name="icon" pixmaps="icons/input_question.png,icons/input_info.png,icons/input_warning.png,icons/input_error.png,icons/input_message.png" position="0,0" size="53,53" alphatest="blend" transparent="1" />

What did you try?


test added!


Số vòng được định nghĩa là 1 số tự nhiên sao cho chữ số đầu bằng chữ số cuối. Cần đếm số vòng
Ví dụ: 8, 121, 22 là các số vòng
Input: Hai số nguyên dương L, R ( 1<= L, R <= 10^18)
Output: Số vòng trong [L; R]


Так описываются переменные внутри шаблона


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


林翠波-2019011272-应用统计研
dataliti3.2<- data.frame(x1 <- c(25,20,6,1001,525,825,120,28,7,532,75,40,187,122,74),
                         x2 <- c(3547.79,896.34,750.32,2087.05,1639.31,3357.7,808.47,520.27,671.13,2863.32,1160,862.75,672.99,901.76,3546.18),
                         y <- c(553.96,208.55,3.1,2815.4,1052.12,3427,442.82,70.12,122.24,1400,464,7.5,224.18,538.94,2442.79)
)                                       ##创建一个数据框，命名为=dataliti3.2

lm.bj <- lm(y~x1+x2,data3.2)            ##~右边为自变量x1,x2，~左边为因变量y,lm()回归模型
lm.bj                                   #查看一下回归
summary(lm.bj)                          #k可知残差的标准差估计为 475.8约等于476
y1 <- fitted(lm.bj)                     #拟合模型预测值
y1
options(digits=1)                       #指定小数点后有效数，保留1位小数
ei<- y-y1
ei                                      #residuals(lm.eco)#拟合模型 普通残差值ei    #####课本表4-8第5列数据

a <- rep(1,15)                          ##对1重复15次
a
X <- cbind(a,x1,x2);X                   #构造设计矩阵
hii <- X%*%solve(t(X)%*%X)%*%t(X)       #计算帽子矩阵
hii
chii <- diag(H)
chii                                    #求杠杆值
options(digits=2)
SRE <- (ei/(475.8*sqrt(1-chii)))        #学生化残差#####课本表4-8第6列数据
SRE
options(digits = 1)
DRE <- ei/(1-chii)                      #删除残差#####课本表4-8第7列数据
DRE
options(digits=3)
SREi <- SRE*sqrt((15-2-2)/(15-2-1-SRE^2))  #得到删除的学生化残差 #####课本表4-8第8列数据
SREi
options(digits=2)
ch_ii <- chii-1/15                  #中心化杠杆值ch_ii #####课本表4-8第9列数据
ch_ii
Di <- (chii*ei^2)/((2+1)*475.8^2*(1-hii)^2)  #计算库克距离  #####课本表4-8第10列数据
Di
table_48 <- data.frame(x1,x2,y,ei = ei,SRE = SRE,e_i =DRE ,SREi = SDR,ch_ii = ch_ii,Di = Di)  #得到表4-8
table_48


Why not?


Resolved additional requirement from issue #37


두더지 게임 만들기 1st version.

- start button(smile 이미지) 클릭하면 랜덤으로 지뢰 5개 생성,
  생성된 지뢰 위치에 따라 힌트(1~5점)가 생성


Yup, you are right.
Somehow, I can't commit to develop right now / nor pull it.


[R/calc_required_node_time.R:15:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_required_node_time.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
calc_required_node_time <- function(phy,
^
```
[R/calc_required_node_time.R:50:18:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_required_node_time.R#L50) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:51:16:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_required_node_time.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_required_node_time.R:66:18:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_required_node_time.R#L66) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:67:16:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_required_node_time.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_summary_statistics.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  output <- c( calc_beta(focal_tree),
              ^
```
[R/calc_time_spent_at_node.R:15:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_time_spent_at_node.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
calc_time_spent_at_node <- function(phy,
^
```
[R/calc_time_spent_at_node.R:53:36:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                   ^
```
[R/calc_time_spent_at_node.R:53:57:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                                        ^
```
[R/calc_time_spent_at_node.R:69:37:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                    ^
```
[R/calc_time_spent_at_node.R:69:58:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/count_hidden.R:10:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/count_hidden.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
  extinct_species <- tree$tip.label[(num_extant_species+1):length(tree$tip.label)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:10:56:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/count_hidden.R#L10) *style:* **Put spaces around all infix operators.**
```r
  extinct_species <- tree$tip.label[(num_extant_species+1):length(tree$tip.label)]
                                                      ~^~
```
[R/count_hidden.R:20:15:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/count_hidden.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    b <- desc[ desc %in% extinct_species]
              ^
```
[R/count_hidden.R:27:9:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/count_hidden.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(n == root_node && length(b) == 1)  {
        ^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_independent.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:187:7:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L187) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:207:42:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_linked.R#L207) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:43:15:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/util.R#L43) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (compress){
              ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-calc-dist.R:19:26:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:22:26:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-create_equal_alignment.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/1cb5575685456e70266ad75006b136943fea7439/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


Successfully deployed to following URLs:

* https://zq-blog-9jr7zvhaw.now.sh
* https://zq-blog.zq-blog.now.sh
* https://zq-blog-git-master.zq-blog.now.sh


Số vòng là số mà có chữ số đầu trùng với chữ số cuối. Cho 1 đoạN [L, R]
đếm số vòng trong đoạn trên biết 1 <= L, R<= 10^18
Input: L, R
Output: Số vòng


ok toto


Hmm, try:

```
git pull
git checkout develop
```

or, if that fails, what does this command give you:

```
git branch --list --all
```

?


toto


Hi,
Sorry, There was a bug that I couldn't distribute on Sunday.😭
This fix is almost complete and will be released this week.


unload gameobject


That change of one word from "lowest" to "highest" doesn't explain anything.

> the active link with the highest priority will be used. If one or more

The highest priority will always be 1. Everything else is lower priority.
So, when something is named as priority everyone is assuming decelerating importance.
May be because I'm not a native english speaker, I would rather named it "weight" over "priority".
That would imply: more weighted route is more important.


For reference, my output:

```
richel@sonic:~/GitHubs/nodeSub$ git branch --list --all
* develop
  master
  remotes/origin/HEAD -> origin/master
  remotes/origin/develop
  remotes/origin/master
  remotes/origin/richel
```

Note that I have not checked out the `richel` branch.


99% of the time, a db is sufficient, much better in terms of performance, and easy to maintain and set up. the use case of a blockchain is really limited


You can also define properties as auto-property whenever you don't have any specific logic or validation in set or get methods; in this case compiler will generate the backing field (private string name; private string countryCode, etc.) and the trivial logic for setter and getter methods.


Well done!


Successfully deployed to following URLs:

* https://picker-i2qzs4ny0.now.sh
* https://picker-omega-five.now.sh
* https://picker.react-component.now.sh
* https://picker-git-master.react-component.now.sh


fix any? warning


![](https://github.trello.services/images/mini-trello-icon.png) [Comparar detecção de defeitos](https://trello.com/c/C9L6tUIf/5-comparar-detec%C3%A7%C3%A3o-de-defeitos)


[崔静-2019011248-回归.zip](https://github.com/zhenyan56/Applied-linear-regression/files/3891008/-2019011248-.zip)


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

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why import that whole strings file for only 2 strings?


[R/calc_required_node_time.R:15:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_required_node_time.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
calc_required_node_time <- function(phy,
^
```
[R/calc_required_node_time.R:50:18:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_required_node_time.R#L50) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:51:16:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_required_node_time.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_required_node_time.R:66:18:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_required_node_time.R#L66) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:67:16:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_required_node_time.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_summary_statistics.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  output <- c( calc_beta(focal_tree),
              ^
```
[R/calc_time_spent_at_node.R:15:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_time_spent_at_node.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
calc_time_spent_at_node <- function(phy,
^
```
[R/calc_time_spent_at_node.R:53:36:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                   ^
```
[R/calc_time_spent_at_node.R:53:57:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                                        ^
```
[R/calc_time_spent_at_node.R:69:37:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                    ^
```
[R/calc_time_spent_at_node.R:69:58:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/count_hidden.R:10:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/count_hidden.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
  extinct_species <- tree$tip.label[(num_extant_species+1):length(tree$tip.label)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:10:56:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/count_hidden.R#L10) *style:* **Put spaces around all infix operators.**
```r
  extinct_species <- tree$tip.label[(num_extant_species+1):length(tree$tip.label)]
                                                      ~^~
```
[R/count_hidden.R:20:15:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/count_hidden.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    b <- desc[ desc %in% extinct_species]
              ^
```
[R/count_hidden.R:27:9:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/count_hidden.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(n == root_node && length(b) == 1)  {
        ^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_independent.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:187:7:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L187) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:207:42:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_linked.R#L207) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:43:15:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/util.R#L43) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (compress){
              ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-calc-dist.R:19:26:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:22:26:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-create_equal_alignment.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/184c3f060bc785fa9d5fd69a20a0d83b875accf0/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


So beautiful!!!
You're great!


> 99% of the time, a db is sufficient, much better in terms of performance, and easy to maintain and set up. the use case of a blockchain is really limited

Would AWS QLDB only make 1% of the profits?


s


Successfully deployed to following URLs:

* https://commercetools-docs-kit-krt0431r0.now.sh
* https://commercetools-docs-kit.now.sh
* https://commercetools-docs-kit.commercetools.now.sh
* https://commercetools-docs-kit-git-master.commercetools.now.sh


> broken"putfootdownyay"."lovebigballs":


Successfully deployed to following URLs:

* https://pdfswitch-docs-7mijbmlik.now.sh
* https://pdfswitch-docs.pdfswitch.now.sh
* https://pdfswitch-docs-git-master.pdfswitch.now.sh


Simple script for unpacking Vools miner archive file.


### `timeforfight[up](url)**justmoveit**`


better set it after post boot