[R/mbd_sim.R:162:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L162) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:163:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check <- (multiple_births_rec_tree >= minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:322:8:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L322) *style:* **Commented code should be removed.**
```r
    #  multi_births_full_tree <- sum(duplicated(births_full_tree))
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:324:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L324) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:332:8:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L332) *style:* **Use <-, not =, for assignment.**
```r
  brts = -sort(abs(as.numeric(time_points)), decreasing = TRUE)
       ^
```
[R/mbd_sim.R:333:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L333) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(l_matrix, dropextinct = T)
      ^
```
[R/mbd_sim.R:334:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L334) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(l_matrix, dropextinct = F)
      ^
```
[R/mbd_sim.R:335:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L335) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tas)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:336:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L336) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tes)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:393:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L393) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_sim.R:413:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L413) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_sim.R:444:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_sim.R#L444) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_utils.R:20:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:20:31:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L20) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:28:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:28:43:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L28) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                          ^
```
[R/mbd_utils.R:28:69:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L28) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                                                    ^
```
[R/mbd_utils.R:29:55:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L29) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name <- "blue"; truevalues_color_name = "red";
                                                      ^
```
[R/mbd_utils.R:35:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
  medians_string <- paste0("MLE Medians (", medians_color_name, ") = (", paste(signif(medians, 2), sep = "''", collapse = ", "), ")")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:36:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_string <- paste0("True Values (", truevalues_color_name, ") = (", paste(signif(sim_pars, 2), sep = "''", collapse = ", "), ")")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:41:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
      probs = 1 - percentage_hidden_outliers # BUG? Used to be with arrow operator
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:49:29:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L49) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (i in estimated_pars) { for (j in estimated_pars) {
                            ^
```
[R/mbd_utils.R:50:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L50) *style:* **Variable or function name should be snake_case.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
    ^~~~~~~~~~
```
[R/mbd_utils.R:50:16:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L50) *style:* **Use <-, not =, for assignment.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
               ^
```
[R/mbd_utils.R:51:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:51:33:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L51) *style:* **Variable or function name should be snake_case.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                ^~~~~~~~~~~~
```
[R/mbd_utils.R:51:72:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L51) *style:* **Variable or function name should be snake_case.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                                                       ^~~~~~~~~~~~
```
[R/mbd_utils.R:68:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
      graphics::points(x = sim_pars[j], y = sim_pars[i], col = truevalues_color, pch = 10, cex = 1.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:69:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
      graphics::points(x = medians[j], y = medians[i], col = medians_color, pch = 10, cex = 1.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:86:31:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L86) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    for (i in estimated_pars) { for (j in estimated_pars) {
                              ^
```
[R/mbd_utils.R:87:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L87) *style:* **Variable or function name should be snake_case.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
      ^~~~~~~~~~
```
[R/mbd_utils.R:87:18:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L87) *style:* **Use <-, not =, for assignment.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
                 ^
```
[R/mbd_utils.R:88:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:88:35:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L88) *style:* **Variable or function name should be snake_case.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                  ^~~~~~~~~~~~
```
[R/mbd_utils.R:88:74:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L88) *style:* **Variable or function name should be snake_case.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                                                         ^~~~~~~~~~~~
```
[R/mbd_utils.R:91:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
        graphics::hist((good.results[, i]), main = NULL, xlab = paste(par_names[i]), breaks = 15)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:132:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L132) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:132:31:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L132) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:135:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:135:27:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L135) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                          ^
```
[R/mbd_utils.R:135:104:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L135) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                                                                                ^
```
[R/mbd_utils.R:148:19:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L148) *style:* **Use <-, not =, for assignment.**
```r
heatmap2dataframe = function(
                  ^
```
[R/mbd_utils.R:154:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L154) *style:* **Variable or function name should be snake_case.**
```r
  heatmap.name="HeatMap"
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:157:46:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L157) *style:* **Commas should always have a space after.**
```r
  df <- data.frame(expand.grid(x = x, y = y),HeatMap = matrix_2)
                                             ^
```
[R/mbd_utils.R:164:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
#' Converts branching times to "time intervals between branching times" and "birth at nodes" vectors
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:174:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L174) *style:* **Lines should not be more than 80 characters.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:174:54:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L174) *style:* **Commas should always have a space after.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:174:54:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L174) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:195:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L195) *style:* **Variable or function name should be snake_case.**
```r
  create_mbd_P_matrix <- function(
  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:199:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L199) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_utils.R:200:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L200) *warning:* **local variable ‘lambda’ assigned but may not be used**
```r
    lambda <- pars[1]
    ^~~~~~
```
[R/mbd_utils.R:201:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L201) *warning:* **local variable ‘mu’ assigned but may not be used**
```r
    mu <- pars[2]
    ^~
```
[R/mbd_utils.R:202:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L202) *warning:* **local variable ‘q’ assigned but may not be used**
```r
    q <- pars[3]
    ^
```
[R/mbd_utils.R:203:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L203) *warning:* **local variable ‘nvec’ assigned but may not be used**
```r
    nvec <- 0:max_number_of_species
    ^~~~
```
[R/mbd_utils.R:210:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
    # my_matrix <- lambda * hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:210:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L210) *style:* **Commented code should be removed.**
```r
    # my_matrix <- lambda * hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:211:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L211) *style:* **Lines should not be more than 80 characters.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu * nvec[2:(max_number_of_species+1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:211:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L211) *style:* **Commented code should be removed.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu * nvec[2:(max_number_of_species+1)]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:212:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L212) *style:* **Commented code should be removed.**
```r
    # diag(my_matrix) = - mu * nvec - lambda * (1 - (1 - q) ^ nvec)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:213:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L213) *style:* **Commented code should be removed.**
```r
    # return(my_matrix)
      ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:217:15:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L217) *style:* **Commas should always have a space after.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:217:15:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L217) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:233:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L233) *style:* **Lines should not be more than 80 characters.**
```r
    print(paste("Sim pars are:", test_parameters[1], test_parameters[2], test_parameters[3], ". Average n is", nmedio, "with std:", std))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:253:16:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L253) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (logs == 1 ) {
               ^
```
[R/mbd_utils.R:281:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L281) *style:* **Variable or function name should be snake_case.**
```r
  lX <- x
  ^~
```
[R/mbd_utils.R:282:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L282) *style:* **Variable or function name should be snake_case.**
```r
  lY <- y
  ^~
```
[R/mbd_utils.R:283:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L283) *style:* **Variable or function name should be snake_case.**
```r
  pretty_X.at	<-	pretty(range(lX), n = x_splits)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:284:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L284) *style:* **Variable or function name should be snake_case.**
```r
  pretty_X.lab	<-	round(pretty_X.at, 2)
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:285:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L285) *style:* **Variable or function name should be snake_case.**
```r
  pretty_Y.at	<-	pretty(range(lY), n = y_splits)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:286:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L286) *style:* **Variable or function name should be snake_case.**
```r
  pretty_Y.lab	<-	round(pretty_Y.at, 2)
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:288:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L288) *style:* **Lines should not be more than 80 characters.**
```r
  jet.colors <- grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:288:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L288) *style:* **Variable or function name should be snake_case.**
```r
  jet.colors <- grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
  ^~~~~~~~~~
```
[R/mbd_utils.R:326:38:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L326) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (length(na_components) > 0) { cat("NA component are:", na_components)}
                                     ^
```
[R/mbd_utils.R:326:79:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L326) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      if (length(na_components) > 0) { cat("NA component are:", na_components)}
                                                                              ^
```
[R/mbd_utils.R:327:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L327) *style:* **Lines should not be more than 80 characters.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:327:39:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L327) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
                                      ^
```
[R/mbd_utils.R:327:82:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L327) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
                                                                                ^
```
[R/mbd_utils.R:332:6:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L332) *style:* **Commented code should be removed.**
```r
    #negatives <- v[v < 0]
     ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:333:6:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L333) *style:* **Commented code should be removed.**
```r
    #maximum <- max(v)
     ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:356:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L356) *style:* **Variable or function name should be snake_case.**
```r
    Atest1 <- (function1(...))
    ^~~~~~
```
[R/mbd_utils.R:359:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L359) *style:* **Variable or function name should be snake_case.**
```r
    Atest2 <- (function2(...))
    ^~~~~~
```
[R/mbd_utils.R:367:26:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L367) *style:* **Commas should always have a space after.**
```r
  print(all.equal(Atest1,Atest2))
                         ^
```
[R/mbd_utils.R:368:32:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L368) *style:* **Commas should always have a space after.**
```r
  return(invisible(list(Atest1,Atest2)))
                               ^
```
[R/mbd_utils.R:380:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L380) *style:* **Variable or function name should be snake_case.**
```r
    function.code <- deparse(get(function_name))
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:383:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
    left.brackets <- c(unlist(strsplit(function.code, split = "[[:space:]]*\\(")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:383:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L383) *style:* **Variable or function name should be snake_case.**
```r
    left.brackets <- c(unlist(strsplit(function.code, split = "[[:space:]]*\\(")))
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:385:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L385) *style:* **Variable or function name should be snake_case.**
```r
    called.functions <- unique(
    ^~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:394:15:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L394) *style:* **Variable or function name should be snake_case.**
```r
              last.word <- utils::tail(words, 1)
              ^~~~~~~~~
```
[R/mbd_utils.R:395:15:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L395) *style:* **Variable or function name should be snake_case.**
```r
              last.word.is.function <- tryCatch(
              ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:411:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
        # functs.to.check <- called.functions[!(called.functions %in% checked_functions)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:411:11:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L411) *style:* **Commented code should be removed.**
```r
        # functs.to.check <- called.functions[!(called.functions %in% checked_functions)]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:416:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L416) *style:* **Lines should not be more than 80 characters.**
```r
        #         listFunctions(x, recursive = T, checked_functions = c(checked_functions, called.functions))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:416:19:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L416) *style:* **Commented code should be removed.**
```r
        #         listFunctions(x, recursive = T, checked_functions = c(checked_functions, called.functions))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:422:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L422) *style:* **Lines should not be more than 80 characters.**
```r
#' Checks if some matrix entries are infinite, NaN, NA or (only in the lower triangle) negative
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:427:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L427) *style:* **Variable or function name should be snake_case.**
```r
  Mlist,
  ^~~~~
```
[R/mbd_utils.R:505:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L505) *style:* **Variable or function name should be snake_case.**
```r
branchLengths <- function(tr)
^~~~~~~~~~~~~
```
[R/mbd_utils.R:506:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L506) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/mbd_utils.R:508:13:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L508) *style:* **Only use double-quotes.**
```r
    type <- 'NAMED'
            ^~~~~~~
```
[R/mbd_utils.R:510:13:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L510) *style:* **Only use double-quotes.**
```r
    type <- 'UNNAMED'
            ^~~~~~~~~
```
[R/mbd_utils.R:513:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L513) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- tr$root
    ^~~~~~~~~~~
```
[R/mbd_utils.R:515:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L515) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- 0
    ^~~~~~~~~~~
```
[R/mbd_utils.R:518:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L518) *style:* **Variable or function name should be snake_case.**
```r
  node.numbers <- sort(unique(tr$edge[, 1]))
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:528:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L528) *style:* **Variable or function name should be snake_case.**
```r
  tip.numbers <- 1:length(tr$tip)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:561:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L561) *style:* **Variable or function name should be snake_case.**
```r
    subst.xml <- scan(input_xml, what = "raw")
    ^~~~~~~~~
```
[R/mbd_utils.R:562:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L562) *style:* **Variable or function name should be snake_case.**
```r
    where.starting.tree <- which(subst.xml == "id=\"startingTree\">") + 1
    ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:563:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L563) *style:* **Variable or function name should be snake_case.**
```r
    start.tr <- ape::read.tree(text = subst.xml[where.starting.tree])
    ^~~~~~~~
```
[R/mbd_utils.R:573:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L573) *style:* **Variable or function name should be snake_case.**
```r
    subst.tr <- scan(input_trees_path[t], what = "raw")
    ^~~~~~~~
```
[R/mbd_utils.R:579:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L579) *style:* **Variable or function name should be snake_case.**
```r
    tree.positions <- equals + 2
    ^~~~~~~~~~~~~~
```
[R/mbd_utils.R:580:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L580) *style:* **Commented code should be removed.**
```r
    # tree.names.pos <- equals - 2
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:596:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L596) *style:* **Variable or function name should be snake_case.**
```r
    Translate.pos <- (1:length(subst.tr))[subst.tr == "Translate"]
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:597:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L597) *style:* **Variable or function name should be snake_case.**
```r
    comma.pos <- which(subst.tr == ", ")
    ^~~~~~~~~
```
[R/mbd_utils.R:599:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L599) *style:* **Variable or function name should be snake_case.**
```r
      numbers.pos <- seq(Translate.pos + 1, Translate.pos + 2 * ntax, 2)
      ^~~~~~~~~~~
```
[R/mbd_utils.R:601:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L601) *style:* **Variable or function name should be snake_case.**
```r
      numbers.pos <- seq(Translate.pos + 1, Translate.pos + 3 * ntax, 3)
      ^~~~~~~~~~~
```
[R/mbd_utils.R:603:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L603) *style:* **Variable or function name should be snake_case.**
```r
    taxa.pos <- numbers.pos + 1
    ^~~~~~~~
```
[R/mbd_utils.R:633:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L633) *style:* **Variable or function name should be snake_case.**
```r
      croch1.pos <- (1:length(tree_sub2))[tree_sub2 == "["]
      ^~~~~~~~~~
```
[R/mbd_utils.R:634:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L634) *style:* **Variable or function name should be snake_case.**
```r
      croch2.pos <- (1:length(tree_sub2))[tree_sub2 == "]"]
      ^~~~~~~~~~
```
[R/mbd_utils.R:666:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L666) *style:* **Variable or function name should be snake_case.**
```r
      tree.text <- paste(tree_sub2[-remove], collapse = "")
      ^~~~~~~~~
```
[R/mbd_utils.R:669:10:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L669) *style:* **Variable or function name should be snake_case.**
```r
      tr$tip.label <- taxa[as.numeric(tr$tip.label)]
         ^~~~~~~~~
```
[R/mbd_utils.R:671:8:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L671) *style:* **Commented code should be removed.**
```r
      #trees[[i]]=tr
       ^~~~~~~~~~~~~
```
[R/mbd_utils.R:672:22:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L672) *warning:* **no visible global function definition for ‘branchLengths’**
```r
      branch_info <- branchLengths(tr)[-1, ]
                     ^~~~~~~~~~~~~
```
[R/mbd_utils.R:683:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L683) *style:* **Lines should not be more than 80 characters.**
```r
        dimnames(branch_infos) <- list(NULL, dimnames(branch_info)[[2]], 1:length(samp))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:686:21:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L686) *style:* **Commas should always have a space after.**
```r
      branch_infos[,, i] <- as.matrix(branch_info)
                    ^
```
[R/mbd_utils.R:696:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L696) *style:* **Commented code should be removed.**
```r
  # branch_info_out <- abind::abind(branch_info_tot, along = 3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:718:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L718) *style:* **Lines should not be more than 80 characters.**
```r
  # beast_posterior$branch_info # a list of branch lengths and associated information
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:739:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L739) *style:* **Commented code should be removed.**
```r
#   parnames = get_mbd_param_names()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:741:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L741) *style:* **Commented code should be removed.**
```r
#   parnames <<- parnames
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:742:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L742) *style:* **Commented code should be removed.**
```r
#   n_pars <<- length(parnames);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:743:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L743) *style:* **Commented code should be removed.**
```r
#   base_path=dirname(dirname(getwd()))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:745:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L745) *style:* **Lines should not be more than 80 characters.**
```r
#     path<<-choose.dir(paste(base_path, "/Progress /RQ1 - Multiple Births /Results + Reports / 4_parameters /", sep = ''), "Choose a suitable folder")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:745:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L745) *style:* **Commented code should be removed.**
```r
#     path<<-choose.dir(paste(base_path, "/Progress /RQ1 - Multiple Births /Results + Reports / 4_parameters /", sep = ''), "Choose a suitable folder")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:747:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L747) *style:* **Lines should not be more than 80 characters.**
```r
#   res_files = list.files(pattern=paste('[.]txt', sep = ''), path=path, full.names=TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:747:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L747) *style:* **Commented code should be removed.**
```r
#   res_files = list.files(pattern=paste('[.]txt', sep = ''), path=path, full.names=TRUE)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:749:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L749) *style:* **Commented code should be removed.**
```r
#     fileData <- utils::read.table(file=res_files[i], header=FALSE, sep=", ")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:750:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L750) *style:* **Lines should not be more than 80 characters.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:750:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L750) *style:* **Commented code should be removed.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:752:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L752) *style:* **Commented code should be removed.**
```r
#   all_results = targetTable
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:754:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L754) *style:* **Commented code should be removed.**
```r
#   tidy_results=all_results[order(all_results[, dim(all_results)[2]]), ]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:755:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L755) *style:* **Lines should not be more than 80 characters.**
```r
#   dimnames(tidy_results)[[2]]<-(c(parnames, "LL", "multiple_born", "number_of_tips", "percentage_multiple_species", "tree_id"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:755:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L755) *style:* **Commented code should be removed.**
```r
#   dimnames(tidy_results)[[2]]<-(c(parnames, "LL", "multiple_born", "number_of_tips", "percentage_multiple_species", "tree_id"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:756:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L756) *style:* **Lines should not be more than 80 characters.**
```r
#   bad_results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))==(n_pars+1), ];#print(Nbad<-dim(bad_results)[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:756:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L756) *style:* **Commented code should be removed.**
```r
#   bad_results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))==(n_pars+1), ];#print(Nbad<-dim(bad_results)[1])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:757:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L757) *style:* **Lines should not be more than 80 characters.**
```r
#   results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))!=(n_pars+1), ];#print(N<-dim(results)[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:757:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L757) *style:* **Commented code should be removed.**
```r
#   results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))!=(n_pars+1), ];#print(N<-dim(results)[1])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:758:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L758) *style:* **Lines should not be more than 80 characters.**
```r
#   print(paste("There are ",Nbad<-dim(bad_results)[1], " bad results.", sep = ''))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:758:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L758) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",Nbad<-dim(bad_results)[1], " bad results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:759:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L759) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",N<<-dim(results)[1], " good results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:761:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L761) *style:* **Lines should not be more than 80 characters.**
```r
#   load(as.character(paste(path, "/ data / general_settings", sep = '')), envir = e <- globalenv())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:761:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L761) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / general_settings", sep = '')), envir = e <- globalenv())
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:762:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L762) *style:* **Lines should not be more than 80 characters.**
```r
#   load(as.character(paste(path, "/ data / sim_data", sep = '')), envir = e <- globalenv()  )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:762:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L762) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / sim_data", sep = '')), envir = e <- globalenv()  )
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:763:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L763) *style:* **Commented code should be removed.**
```r
#   suppressWarnings(rm(targetTable, all_results, fileData, i))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:764:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/R/mbd_utils.R#L764) *style:* **Commented code should be removed.**
```r
#   return(results)
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_expo_vs_lsoda.R:16:3:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_expo_vs_lsoda.R#L16) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[tests/testthat/test-mbd_expo_vs_lsoda.R:19:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_expo_vs_lsoda.R#L19) *style:* **Lines should not be more than 80 characters.**
```r
    testpars <- c(lambda[test_size + j], mu[test_size + j], nu[test_size + j], q[test_size + j])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_expo_vs_lsoda.R:20:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_expo_vs_lsoda.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
    test_expo[j]  <- mbd::mbd_loglik(pars = testpars, brts = brts, soc = soc, cond = cond, methode = "expo")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_expo_vs_lsoda.R:21:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_expo_vs_lsoda.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    test_lsoda[j] <- mbd::mbd_loglik(pars = testpars, brts = brts, soc = soc, cond = cond, methode = "lsoda")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:4:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:5:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L5) *style:* **Commented code should be removed.**
```r
#   skip("Fix @Giappo: cannot find function 'mbd_loglik0'")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:6:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L6) *style:* **Commented code should be removed.**
```r
#   test_size <- 10
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:7:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L7) *style:* **Commented code should be removed.**
```r
#   soc <- 2
    ^~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:8:5:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L8) *style:* **Commented code should be removed.**
```r
#   cond <- 0
    ^~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:9:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:11:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L11) *style:* **Commented code should be removed.**
```r
#     #this works only for mu=0
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:12:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L12) *style:* **Commented code should be removed.**
```r
#     lambda <- pars[1]
      ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:13:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L13) *style:* **Commented code should be removed.**
```r
#     mu <- pars[2]
      ^~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:14:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L14) *style:* **Commented code should be removed.**
```r
#     q <- pars[3]
      ^~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:16:9:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L16) *style:* **Commented code should be removed.**
```r
#       return(-Inf)
        ^~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:19:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L19) *style:* **Commented code should be removed.**
```r
#     #     data=brts2time_intervals_and_births(brts)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:20:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L20) *style:* **Commented code should be removed.**
```r
#     #     time_intervals=data$time_intervals
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:21:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L21) *style:* **Commented code should be removed.**
```r
#     #     births=data$births
      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:23:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L23) *style:* **Commented code should be removed.**
```r
#     time_intervals <- data$time_intervals
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:24:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L24) *style:* **Commented code should be removed.**
```r
#     births <- data$births
      ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:25:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L25) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:27:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L27) *style:* **Commented code should be removed.**
```r
#     init_n_lineages <- soc
      ^~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:28:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L28) *style:* **Commented code should be removed.**
```r
#     k <- init_n_lineages + cumsum(c(0, births))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:29:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L29) *style:* **Commented code should be removed.**
```r
#     a_term <- 1
      ^~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:30:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L30) *style:* **Commented code should be removed.**
```r
#     i <- 0:1e6
      ^~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:32:9:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L32) *style:* **Commented code should be removed.**
```r
#       poisson_term <- stats::dpois(i, lambda*time_intervals[t], log = FALSE)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:33:9:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L33) *style:* **Commented code should be removed.**
```r
#       ii <- i[poisson_term != 0]
        ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:34:9:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L34) *style:* **Commented code should be removed.**
```r
#       pois_not_zero <- which(poisson_term != 0)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:35:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
#       a_term <- a_term * sum(((1 - q) ^ (ii * k[t])) * poisson_term[pois_not_zero] )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:35:9:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L35) *style:* **Commented code should be removed.**
```r
#       a_term <- a_term * sum(((1 - q) ^ (ii * k[t])) * poisson_term[pois_not_zero] )
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:37:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L37) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:40:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L40) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:41:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L41) *style:* **Commented code should be removed.**
```r
#     loglik <- log(a_term*b_term)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:42:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L42) *style:* **Commented code should be removed.**
```r
#     # loglik=-loglik #Rampal's optimizer uses loglik rather than -loglik
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:45:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L45) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:50:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L50) *style:* **Commented code should be removed.**
```r
#     cond = 0
      ^~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:53:9:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L53) *style:* **Commented code should be removed.**
```r
#       print("This is meant to work only for mu=0")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:56:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L56) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:57:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
#     theo_log_lik <- mbd_theoretical_loglik(pars = pars, brts = brts, soc = soc)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:57:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L57) *style:* **Commented code should be removed.**
```r
#     theo_log_lik <- mbd_theoretical_loglik(pars = pars, brts = brts, soc = soc)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:67:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L67) *style:* **Commented code should be removed.**
```r
#     ctrl_pars <- pars / 2
      ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:68:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L68) *style:* **Commented code should be removed.**
```r
#     ctrl_brts <- brts
      ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:69:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L69) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:70:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
#     ctrl_theorethical=mbd_theoretical_loglik(pars=ctrl_pars, brts = ctrl_brts, soc = soc)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:70:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L70) *style:* **Commented code should be removed.**
```r
#     ctrl_theorethical=mbd_theoretical_loglik(pars=ctrl_pars, brts = ctrl_brts, soc = soc)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:71:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
#     ctrl_lsoda=mbd_loglik0(pars=ctrl_pars, brts = ctrl_brts, soc=soc, cond=cond, missnumspec=0, methode="lsoda")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:71:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L71) *style:* **Commented code should be removed.**
```r
#     ctrl_lsoda=mbd_loglik0(pars=ctrl_pars, brts = ctrl_brts, soc=soc, cond=cond, missnumspec=0, methode="lsoda")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:72:1:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L72) *style:* **Lines should not be more than 80 characters.**
```r
#     ctrl_expo=mbd_loglik0(pars=ctrl_pars, brts = ctrl_brts, soc=soc, cond=cond, missnumspec=0, methode="expo")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:72:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L72) *style:* **Commented code should be removed.**
```r
#     ctrl_expo=mbd_loglik0(pars=ctrl_pars, brts = ctrl_brts, soc=soc, cond=cond, missnumspec=0, methode="expo")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:73:2:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L73) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:74:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L74) *style:* **Commented code should be removed.**
```r
#     theo_log_lik  =  theo_log_lik  - ctrl_theorethical
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:75:7:](https://github.com/Giappo/mbd/blob/e5306ef5d112662cc8071700a443f3b623c2963c/tests/testthat/test-mbd_pure_birth_small_trees.R#L75) *style:* **Commented code should be removed.**
```r
#     lsoda_log_lik =  lsoda_log_lik - ctrl_lsoda
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


You wrote in the commit message:

> All these extra lines are absolutely useless, if you remove them it takes the computer less power to process them, and it makes your code look more elegant.

But you missed the fact that it is a framework used by the auto batch test program: https://github.com/rrlkwt/Project-Euler-solutions/blob/master/python/eulertest.py

The tester calls the `compute()` function of each problem solution. The `if __name__ == "___main__"` ensures that the solution program will print the solution if run as a standalone application, but will not print if called as a library.

> All these extra lines are absolutely useless

Unnecessary harsh tone without understanding my work.

> if you remove them it takes the computer less power to process

If you don't use Python, it takes the computer less power to process. Worrying over the microseconds to process a few statements is folly. My Java solutions are 10 to 100× faster than Python. https://www.nayuki.io/page/project-euler-solutions#benchmark-timings

> it makes your code look more elegant

I strive to make my code elegant and functional. These goals necessitate tradeoffs, but I lean more towards elegance than the average programmer.

The way you wrote your code is definitely how I would write a standalone, one-off script to solve this Project Euler problem. But again, I have the auto tester program which calls hundreds of solution programs, and the framework is necessary.


changed: https://github.com/axkr/symja_android_library/commit/b62397f77ad0550312f532cb480c79970df94e9f


git push -u origin master


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