[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:220:1:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/init_site_models.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
  if (!beautier::is_one_na(hky_site_model$gamma_site_model$gamma_shape_prior_distr)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:299:1:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/init_site_models.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(jc69_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:327:1:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_site_model.R#L8) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE) # nolint beautier function
       ^~~~~~~~
```
[R/is_site_model.R:10:8:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_site_model.R#L10) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:18:10:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_site_model.R#L27) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/is_tree_prior_name.R:2:13:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_tree_prior_name.R#L2) *warning:* **no visible global function definition for ‘get_tree_prior_names’**
```r
  name %in% get_tree_prior_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/R/mcmc_to_xml_run.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    xml <- paste0(xml, " numInitializationAttempts=\"", mcmc$n_init_attempts, "\"")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mrca_prior_to_xml_lh_distr.R:6:34:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/mrca_prior_to_xml_lh_distr.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_prior) == 1 && is_one_na(mrca_prior)) return(NULL) # nolint beautier function
                                 ^~~~~~~~~
```
[R/mrca_priors_to_xml_state.R:6:35:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/mrca_priors_to_xml_state.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_priors) == 1 && is_one_na(mrca_priors)) return(NULL) # nolint beautier function
                                  ^~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/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$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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/e99e0b52b0705674fc468724aece06959a1d16bb/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\"/>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Nice instructions added I will do the same of how to access my scene.


Deprecations and warning, I should have said. Mostly warnings.


From this point on we must split out and work in different scenes to be able to both complete our contracts.


> Fixed an issue with the graphs with.

Maybe?


Thank you! I will change it to snake case.


[R/bbt_get_paths.R:4:21:](https://github.com/ropensci/babette/blob/1055f6ac9344c4ef71e829b56bb57576b1af1bd6/R/bbt_get_paths.R#L4) *warning:* **no visible global function definition for ‘get_babette_path’**
```r
    filenames[i] <- get_babette_path(filenames[i]) # nolint internal function
                    ^~~~~~~~~~~~~~~~
```
[R/bbt_process_pkg_output.R:7:15:](https://github.com/ropensci/babette/blob/1055f6ac9344c4ef71e829b56bb57576b1af1bd6/R/bbt_process_pkg_output.R#L7) *warning:* **no visible global function definition for ‘bbt_create_ns’**
```r
    out$ns <- bbt_create_ns(out$output) # nolint internal function
              ^~~~~~~~~~~~~
```


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @xylar was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


can't amend commit message without throwing everyone else out of sync, but this should reference issue 178, not 179


[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)
  ^~
```


ahum


Successfully deployed to following URLs:

* https://scratchpay-coding-challenge-1ggbp3noa.now.sh
* https://scratchpay-coding-challenge.now.sh
* https://scratchpayusermanagementui.now.sh
* https://scratchpay-coding-challenge.kumarabhirup1.now.sh
* https://scratchpay-coding-challenge-git-master.kumarabhirup1.now.sh


Be aware that this change do not allow users to upgrade because of https://stackoverflow.com/a/28859409/1312346


@MattPD Would you mind taking a look before I merge this in?


@aasami I'm not native speaker too, so it's kind of uneasy for me to decide, but I don't find weight as much improvement. Anyway, this description is copy/pasted from knet description, so if we would decide to clarify it, then we should change it on both places.

@chrissie-c You are native speaker, would you find "weight" more understandable? Or other idea how to make description easier to understand/less prone to confusion?


Keine expressions am Anfang der variablen


Successfully deployed to following URLs:

* https://portfolio-1hzxlzoy6.now.sh
* https://takahirofujii.dev
* https://portfolio.taka.now.sh
* https://portfolio-git-master.taka.now.sh


thanks, I put it in my similar skin but not the same, when I have an error message it gives me a bound although it does not get to crash.
I missed two png¨s, imput warning and imput message.
Tonight I put it like this and I comment results.


  #bushi2019011264#
x1 <- c(25,20,6,1001,525,825,120,28,7,532,75,40,187,122,74)
x2 <- c(3547.79,896.34,750.32,2087.05,1639.31,3357.70,808.47,520.27,671.13,2863.32,1160.00,862.75,
672.99,901.76,3546.18)
y <- c(553.96,208.55,3.10,2815.40,1052.12,3427.00,442.82,70.12,122.24,1400.00,464.00,7.50,224.18,
538.94,2442.79)
a <- data.frame(x1,x2)
is.data.frame(a)
lm.eco <- lm(y~x1+x2,a);lm.eco
summary(lm.eco)
yy <- fitted(lm.eco);yy
ei <- y-yy;ei
b <- rep(1,15)
X <- cbind(b,x1,x2);X
H <- X%*%solve(t(X)%*%X)%*%t(X);H
hii <- diag(H);hii
SRE <- (ei/(475.8*sqrt(1-hii)));SRE
DRE <- ei/(1-hii);DRE
SDR <- SRE*sqrt((15-2-2)/(15-2-1-SRE^2));SDR
ch_ii <- hii-1/15;ch_ii
Di <- (hii*ei^2)/((2+1)*475.8^2*(1-hii)^2);Di
e_i <- DRE
SREi <- SDR
data <-data.frame(x1,x2,y,ei,SRE,e_i,SREi,ch_ii,Di);data


@JuliaRegistrator register


Be aware that PostgreSQL/PostGIS Docker images do not upgrade the database automatically: https://github.com/docker-library/postgres/issues/37


good


Registration pull request created: [JuliaRegistries/General/5877](https://github.com/JuliaRegistries/General/pull/5877)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.9.1 -m "<description of version>" 445b9f1135998f2da6461eccd9eea11f12d9cef8
git push origin v0.9.1
```


@Giappo: You tried to do the right thing, but adding namespace to functions of the package itself to tests is not boy scouting; that is, it is not undeniably The Right Thing,

In tests, one avoids to use the namespace of the package itself (see e.g. [ggplot2](https://github.com/tidyverse/ggplot2/tree/master/tests/testthat)), CTRL-L will load the package into the namespace.

I thinks it's fine to add namespaces while one works on code to speed up development (I may do the same in some occasions), it's just not called 'boy scouting'. It's called something like 'Fix #314'.

Keep up the good work :+1:


@Alessia998 è per te, amo.


tao mà biết tại sao req.body vs res.status của tao bị lỗi là tao không để ghê vậy đâu @hminh21 .  Nó ghi req.body không tồn tại. in ra thì lại thấy 2 req lồng nhau


possibly related to https://github.com/docker/docker-ce-packaging/pull/378


Successfully deployed to following URLs:

* https://entrepreneur-site-next-gg58pmwm2.now.sh
* https://wealthmack.com
* https://www.wealthmack.com
* https://entrepreneur-site-next.hacker-tom.now.sh
* https://entrepreneur-site-next-git-master.hacker-tom.now.sh


Successfully deployed to following URLs:

* https://site-elcyvl7to.now.sh
* https://josephluck.co.uk
* https://www.josephluck.co.uk
* https://site.josephluck.now.sh
* https://site-git-master.josephluck.now.sh


sss


teststs


Pentru aplicația asta nu contează chiar așa de mult, dar de regulă nu-i frumos să faci metode statice în layerul de servicii.

- mai greu să rezolvi dependințele.
- nu se comportă foarte OOP. De exemplu nu le poți face override.

https://medium.com/stackavenue/why-to-use-service-layer-in-spring-mvc-5f4fc52643c0


Truyền về front end nhận code rồi tự xuất ra lỗi tiếng Việt nha, không lấy lỗi từ trên server in ra


git checkout develop
git pull

remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 3 (delta 1), reused 2 (delta 1), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/thijsjanzen/nodeSub
   2e37f8e..184c3f0  richel     -> origin/richel
There is no tracking information for the current branch.
Please specify which branch you want to merge with.
See git-pull(1) for details.

    git pull <remote> <branch>

If you wish to set tracking information for this branch you can do so with:

    git branch --set-upstream-to=origin/<branch> develop

> git branch --list --all :
Temp_develop
* develop
  master
  richel
  remotes/origin/develop
  remotes/origin/master
  remotes/origin/richel


should be added to original commit


@vthinkxie wow, didn't know that


So what's the best recommendation ?
Dump and restore ?


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
check_pir_out <- function(
^
```
[R/create_alignment_with_std_site_model.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/create_alignment_with_std_site_model.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/create_all_experiments.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
create_all_experiments <- function(
^
```
[R/create_copy_twin_tree_from_true_fun.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/create_copy_twin_tree_from_true_fun.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_fun <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_sim_true_alignment_with_lns_site_model_fun.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/get_sim_true_alignment_with_lns_site_model_fun.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_lns_site_model_fun <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_std_site_model_fun.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/get_sim_true_alignment_with_std_site_model_fun.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_std_site_model_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_uns_site_model_fun.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/get_sim_true_alignment_with_uns_site_model_fun.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_uns_site_model_fun <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_fun.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/get_sim_twin_alignment_with_same_n_mutation_fun.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_std_site_model_fun.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/get_sim_twin_alignment_with_std_site_model_fun.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_std_site_model_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_alignment_with_std_site_model.R:15:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_alignment_with_std_site_model.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_lns_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_true_alignment_with_lns_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_lns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_std_site_model.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_true_alignment_with_std_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_uns_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_true_alignment_with_uns_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_uns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_lns_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_twin_alignment_with_lns_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_lns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model_raw.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_twin_alignment_with_std_site_model_raw.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_twin_alignment_with_std_site_model.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_uns_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/sim_twin_alignment_with_uns_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_uns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/update_pirouette.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/update_pirouette.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
  devtools::install_github("richelbilderbeek/babette", quiet = TRUE, dependencies = TRUE, upgrade = "always")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/update_pirouette.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/R/update_pirouette.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
  devtools::install_github("richelbilderbeek/mcbette", quiet = TRUE, dependencies = TRUE, upgrade = "always")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_fun.R:53:25:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/tests/testthat/test-check_sim_twin_tree_fun.R#L53) *style:* **Variable and function name style should be snake_case.**
```r
        true_phylogeny2$tip.label <- paste0(true_phylogeny$tip.label, "h")
                        ^~~~~~~~~
```
[tests/testthat/test-get_experiments_filenames.R:38:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/tests/testthat/test-get_experiments_filenames.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:47:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/tests/testthat/test-get_pir_params_filenames.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:71:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/tests/testthat/test-get_pir_params_filenames.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:114:1:](https://github.com/richelbilderbeek/pirouette/blob/53cb5d781bcb6218f998ad47205950a44517b8e3/tests/testthat/test-get_pir_params_filenames.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://more-lhmj7tbpp.now.sh
* https://more.617754841.now.sh
* https://more-git-master.617754841.now.sh


Do not need `null` checking?


use url_patterns_dict.setdefault twice


1. 제조사, 모델, 세부모델 내부 출력 형식 수정 (수정 완료)
ArrayList 을 이용해서 실제 index을 저장하는 것이 필요

4. 도메인 관리 (수정 필요)

8.(수정됨) UI 상, 2분법 선택 y, n으로 받기

9.(수정됨)
      int flag;

      while (true) {
         String input = sc.nextLine();
         switch (input) {
         case "Y":
         case "y":
            flag = 1;
            break;
         case "N":
         case "n":
            flag = 2;
            break;
         default:
            System.out.println("Try again.");
            continue;
         }
         break;
      }

10.(수정됨)
 연료형식, 색상 잘못 입력 받았을 때 vehicle 추가되는 문제 해결해야 함
>>> 연료 또는 색상에 대한 index 값을 잘못 입력 받았을 시,
        즉시 재입력을 요청하는 형태로 수정함


Please don't use github PRs to merge updates from storybook into your copy of the repo. It creates unnecessary changelog entries in our release process.


TeamCity Identity and Access Management / Identity - RoleManagementAPI [Build 564](https://teamcity.nice.org.uk/viewLog.html?buildId=62182&buildTypeId=IdentityandAccessManagement_RoleManagementAPI) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:20


Why was line 526: removed? (xmlConfiguration.configure(webApp);).This breaks support for using a custom context.xml-file when using jetty-maven-plugin.


You may also want to consider using a conditional="icon" in case the skin is used on other images.


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):
~~~


This is tolerable as a refactoring.


Successfully deployed to following URLs:

* https://merchant-center-application-kit-l88s8zd6l.now.sh
* https://mc-custom-applications.now.sh
* https://merchant-center-application-kit.commercetools.now.sh
* https://merchant-center-application-kit-git-master.commercetools.now.sh


why delete？


creation


Successfully deployed to following URLs:

* https://react-awesome-reveal-o1er7gpwb.now.sh
* https://react-awesome-reveal.now.sh
* https://react-awesome-reveal.dennismorello.now.sh
* https://react-awesome-reveal-git-master.dennismorello.now.sh


いいねがある$item先では、likes()はあり遷移するが、いいねがないとlikes()がnull隣404ページに遷移してしまう。


#2019011265 李鑫 应用统计#
x1 <- c(25,20,6,1001,525,825,120,28,7,532,75,40,187,122,74)
x2 <- c(3547.79,896.34,750.32,2087.05,1639.31,3357.70,808.47,520.27,671.13,2863.32,1160.00,862.75,672.99,901.76,3546.18)
y <- c(553.96,208.55,3.10,2815.40,1052.12,3427.00,442.82,70.12,122.24,1400.00,464.00,7.50,224.18,538.94,2442.79)
l <- c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)
n <- 15
p <- 2
#计算回归
x <- matrix(c(l,x1,x2),ncol=3,nrow=15,byrow=FALSE)
y <- matrix(y,ncol=1,nrow=15,byrow=FALSE)
beta <- solve(t(x) %*% x) %*% t(x) %*% y
#计算帽子矩阵
 H <- x %*% solve(t(x) %*% x) %*% t(x)

#用公式计算ei
ei <- y - (H %*% y)

#计算MSE
mse <- (t(ei)%*%ei)/(n-p-1)
mse <- c(mse)

#调用帽子矩阵的对角线元素
h <- diag(H)

#用公式计算标准化残差
SREi <-  ei/(sqrt(mse*(1-h)))

#用公式计算e（i）
ei2 <- ei/(1-h)

#用公式计算SRE（i）
SREi2 <- SREi * sqrt((n-p-2)/(n-p-1-SREi^2))

#用公式计算chii
chii <- h-1/n

#用公式计算Di
Di1 <- ei^2/((p+1)*mse)
Di2 <- (1-h)^2
Di <- Di1*(h/Di2)

#输出表格
ei <- round(ei,0)
SREi  <- round(SREi,3)
ei2 <- round(ei2,0)
SREi2 <- round(SREi2,3)
chii <- round(chii,3)
Di <- round(Di,3)

a <- c(x1,x2,y,ei ,SREi ,ei2,SREi2,chii,Di)
A <- matrix(a,ncol=9,nrow=15,byrow=FALSE)
colnames(A) <- c("x1","x2","y","ei" ,"SREi" ,"ei(i)","SREi(i)","chii","Di")
data.frame(A)


Reference: https://swagger.io/docs/specification/data-models/dictionaries/


Successfully deployed to following URLs:

* https://englishcomedyinparis-jvh88zjl6.now.sh
* https://englishcomedyinparis-three-beta.now.sh
* https://englishcomedyinparis.com
* https://englishcomedyinparis.terrencewwong.now.sh
* https://englishcomedyinparis-git-master.terrencewwong.now.sh


Deployment failed with the following error:

~~~
The property `dest` is not allowed in now.json when using Now 2.0 – please remove it.
~~~


Thank you for reporting. We'll get that fixed.


TeamCity Identity and Access Management / Identity - RoleManagementAPI [Build 565-IDAM-121-CommentsInt](https://teamcity.nice.org.uk/viewLog.html?buildId=62183&buildTypeId=IdentityandAccessManagement_RoleManagementAPI) outcome was **SUCCESS**
Summary: Tests passed: 13 Build time: 00:04:28


LGTM


hi,
correct command is:  mapshaper polygons.shp polygons3.shp combine-files -union -o out.shp