[R/mbd_sim.R:162:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L162) *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/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L322) *style:* **Use <-, not =, for assignment.**
```r
  brts = -sort(abs(as.numeric(time_points)), decreasing = TRUE)
       ^
```
[R/mbd_sim.R:323:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L323) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(l_matrix, dropextinct = T)
      ^
```
[R/mbd_sim.R:324:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L324) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(l_matrix, dropextinct = F)
      ^
```
[R/mbd_sim.R:325:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L325) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tas)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:326:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L326) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tes)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:383:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L383) *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:403:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L403) *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:434:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_sim.R#L434) *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:39:76:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L39) *style:* **Trailing whitespace is superfluous.**
```r
    "MLE Medians (", medians_color_name, ") = (", paste(signif(medians, 2),
                                                                           ^
```
[R/mbd_utils.R:51:45:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
      probs = 1 - percentage_hidden_outliers
                                            ^
```
[R/mbd_utils.R:59:29:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L59) *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:62:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L62) *style:* **Variable or function name should be snake_case.**
```r
      good.results <- results[good_lines, ]
      ^~~~~~~~~~~~
```
[R/mbd_utils.R:64:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L64) *style:* **Variable or function name should be snake_case.**
```r
      good.results <- results
      ^~~~~~~~~~~~
```
[R/mbd_utils.R:83:76:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
        x = sim_pars[j], y = sim_pars[i], col = truevalues_color, pch = 10,
                                                                           ^
```
[R/mbd_utils.R:87:71:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
        x = medians[j], y = medians[i], col = medians_color, pch = 10,
                                                                      ^
```
[R/mbd_utils.R:106:31:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L106) *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:109:9:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L109) *style:* **Variable or function name should be snake_case.**
```r
        good.results <- results[good_lines, ]
        ^~~~~~~~~~~~
```
[R/mbd_utils.R:110:14:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L110) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      } else {
             ^
```
[R/mbd_utils.R:110:15:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L110) *style:* **Trailing whitespace is superfluous.**
```r
      } else {
              ^
```
[R/mbd_utils.R:111:9:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L111) *style:* **Variable or function name should be snake_case.**
```r
        good.results <- results
        ^~~~~~~~~~~~
```
[R/mbd_utils.R:116:29:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L116) *style:* **Trailing whitespace is superfluous.**
```r
          good.results[, i],
                            ^
```
[R/mbd_utils.R:162:27:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L162) *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) {
                          ^
```
[R/mbd_utils.R:162:28:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L162) *style:* **Trailing whitespace is superfluous.**
```r
  for (idpar in 1:n_pars) {
                           ^
```
[R/mbd_utils.R:177:19:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L177) *style:* **Use <-, not =, for assignment.**
```r
heatmap2dataframe = function(
                  ^
```
[R/mbd_utils.R:193:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L193) *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:227:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L227) *style:* **Variable or function name should be snake_case.**
```r
  create_mbd_P_matrix <- function(
  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:231:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L231) *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:232:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L232) *warning:* **local variable ‘lambda’ assigned but may not be used**
```r
    lambda <- pars[1]
    ^~~~~~
```
[R/mbd_utils.R:233:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L233) *warning:* **local variable ‘mu’ assigned but may not be used**
```r
    mu <- pars[2]
    ^~
```
[R/mbd_utils.R:234:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L234) *warning:* **local variable ‘q’ assigned but may not be used**
```r
    q <- pars[3]
    ^
```
[R/mbd_utils.R:235:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L235) *warning:* **local variable ‘nvec’ assigned but may not be used**
```r
    nvec <- 0:max_number_of_species
    ^~~~
```
[R/mbd_utils.R:242:28:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L242) *style:* **Trailing whitespace is superfluous.**
```r
    # my_matrix <- lambda *
                           ^
```
[R/mbd_utils.R:243:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L243) *style:* **Commented code should be removed.**
```r
    # hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:244:61:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L244) *style:* **Trailing whitespace is superfluous.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu *
                                                            ^
```
[R/mbd_utils.R:245:9:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L245) *style:* **Commented code should be removed.**
```r
    #   nvec[2:(max_number_of_species+1)]
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:246:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L246) *style:* **Commented code should be removed.**
```r
    # diag(my_matrix) = - mu * nvec - lambda * (1 - (1 - q) ^ nvec)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:247:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L247) *style:* **Commented code should be removed.**
```r
    # return(my_matrix)
      ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:251:15:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L251) *style:* **Commas should always have a space after.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:251:15:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L251) *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:269:25:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L269) *style:* **Trailing whitespace is superfluous.**
```r
        "Sim pars are:",
                        ^
```
[R/mbd_utils.R:270:28:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L270) *style:* **Trailing whitespace is superfluous.**
```r
        test_parameters[1],
                           ^
```
[R/mbd_utils.R:271:28:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L271) *style:* **Trailing whitespace is superfluous.**
```r
        test_parameters[2],
                           ^
```
[R/mbd_utils.R:272:28:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L272) *style:* **Trailing whitespace is superfluous.**
```r
        test_parameters[3],
                           ^
```
[R/mbd_utils.R:295:16:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L295) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (logs == 1 ) {
               ^
```
[R/mbd_utils.R:323:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L323) *style:* **Variable or function name should be snake_case.**
```r
  lX <- x
  ^~
```
[R/mbd_utils.R:324:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L324) *style:* **Variable or function name should be snake_case.**
```r
  lY <- y
  ^~
```
[R/mbd_utils.R:330:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L330) *style:* **Variable or function name should be snake_case.**
```r
  jet.colors <- grDevices::colorRampPalette(
  ^~~~~~~~~~
```
[R/mbd_utils.R:332:44:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L332) *style:* **Trailing whitespace is superfluous.**
```r
      "#00007F", "blue", "#007FFF", "cyan",
                                           ^
```
[R/mbd_utils.R:373:38:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L373) *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) {
                                     ^
```
[R/mbd_utils.R:373:39:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L373) *style:* **Trailing whitespace is superfluous.**
```r
      if (length(na_components) > 0) {
                                      ^
```
[R/mbd_utils.R:376:39:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L376) *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) {
                                      ^
```
[R/mbd_utils.R:376:40:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L376) *style:* **Trailing whitespace is superfluous.**
```r
      if (length(nan_components) > 0) {
                                       ^
```
[R/mbd_utils.R:383:6:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L383) *style:* **Commented code should be removed.**
```r
    #negatives <- v[v < 0]
     ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:384:6:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L384) *style:* **Commented code should be removed.**
```r
    #maximum <- max(v)
     ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:407:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L407) *style:* **Variable or function name should be snake_case.**
```r
    Atest1 <- (function1(...))
    ^~~~~~
```
[R/mbd_utils.R:410:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L410) *style:* **Variable or function name should be snake_case.**
```r
    Atest2 <- (function2(...))
    ^~~~~~
```
[R/mbd_utils.R:418:26:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L418) *style:* **Commas should always have a space after.**
```r
  print(all.equal(Atest1,Atest2))
                         ^
```
[R/mbd_utils.R:419:32:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L419) *style:* **Commas should always have a space after.**
```r
  return(invisible(list(Atest1,Atest2)))
                               ^
```
[R/mbd_utils.R:431:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L431) *style:* **Variable or function name should be snake_case.**
```r
    function.code <- deparse(get(function_name))
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:434:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    left.brackets <- c(
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:438:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L438) *style:* **Variable or function name should be snake_case.**
```r
    called.functions <- unique(
    ^~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:447:15:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L447) *style:* **Variable or function name should be snake_case.**
```r
              last.word <- utils::tail(words, 1)
              ^~~~~~~~~
```
[R/mbd_utils.R:448:15:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L448) *style:* **Variable or function name should be snake_case.**
```r
              last.word.is.function <- tryCatch(
              ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:465:13:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L465) *style:* **Commented code should be removed.**
```r
        #   !(called.functions %in% checked_functions)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:471:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L471) *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:471:19:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L471) *style:* **Commented code should be removed.**
```r
        #         listFunctions(x, recursive = T, checked_functions = c(checked_functions, called.functions))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:477:55:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L477) *style:* **Trailing whitespace is superfluous.**
```r
#' Checks if some matrix entries are infinite, NaN, NA
                                                      ^
```
[R/mbd_utils.R:483:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L483) *style:* **Variable or function name should be snake_case.**
```r
  Mlist,
  ^~~~~
```
[R/mbd_utils.R:561:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L561) *style:* **Variable or function name should be snake_case.**
```r
branchLengths <- function(tr)
^~~~~~~~~~~~~
```
[R/mbd_utils.R:562:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L562) *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:564:13:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L564) *style:* **Only use double-quotes.**
```r
    type <- 'NAMED'
            ^~~~~~~
```
[R/mbd_utils.R:566:13:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L566) *style:* **Only use double-quotes.**
```r
    type <- 'UNNAMED'
            ^~~~~~~~~
```
[R/mbd_utils.R:569:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L569) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- tr$root
    ^~~~~~~~~~~
```
[R/mbd_utils.R:571:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L571) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- 0
    ^~~~~~~~~~~
```
[R/mbd_utils.R:574:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L574) *style:* **Variable or function name should be snake_case.**
```r
  node.numbers <- sort(unique(tr$edge[, 1]))
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:584:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L584) *style:* **Variable or function name should be snake_case.**
```r
  tip.numbers <- 1:length(tr$tip)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:617:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L617) *style:* **Variable or function name should be snake_case.**
```r
    subst.xml <- scan(input_xml, what = "raw")
    ^~~~~~~~~
```
[R/mbd_utils.R:618:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L618) *style:* **Variable or function name should be snake_case.**
```r
    where.starting.tree <- which(subst.xml == "id=\"startingTree\">") + 1
    ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:619:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L619) *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:629:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L629) *style:* **Variable or function name should be snake_case.**
```r
    subst.tr <- scan(input_trees_path[t], what = "raw")
    ^~~~~~~~
```
[R/mbd_utils.R:635:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L635) *style:* **Variable or function name should be snake_case.**
```r
    tree.positions <- equals + 2
    ^~~~~~~~~~~~~~
```
[R/mbd_utils.R:636:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L636) *style:* **Commented code should be removed.**
```r
    # tree.names.pos <- equals - 2
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:652:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L652) *style:* **Variable or function name should be snake_case.**
```r
    Translate.pos <- (1:length(subst.tr))[subst.tr == "Translate"]
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:653:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L653) *style:* **Variable or function name should be snake_case.**
```r
    comma.pos <- which(subst.tr == ", ")
    ^~~~~~~~~
```
[R/mbd_utils.R:655:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L655) *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:657:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L657) *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:659:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L659) *style:* **Variable or function name should be snake_case.**
```r
    taxa.pos <- numbers.pos + 1
    ^~~~~~~~
```
[R/mbd_utils.R:689:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L689) *style:* **Variable or function name should be snake_case.**
```r
      croch1.pos <- (1:length(tree_sub2))[tree_sub2 == "["]
      ^~~~~~~~~~
```
[R/mbd_utils.R:690:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L690) *style:* **Variable or function name should be snake_case.**
```r
      croch2.pos <- (1:length(tree_sub2))[tree_sub2 == "]"]
      ^~~~~~~~~~
```
[R/mbd_utils.R:722:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L722) *style:* **Variable or function name should be snake_case.**
```r
      tree.text <- paste(tree_sub2[-remove], collapse = "")
      ^~~~~~~~~
```
[R/mbd_utils.R:725:10:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L725) *style:* **Variable or function name should be snake_case.**
```r
      tr$tip.label <- taxa[as.numeric(tr$tip.label)]
         ^~~~~~~~~
```
[R/mbd_utils.R:727:8:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L727) *style:* **Commented code should be removed.**
```r
      #trees[[i]]=tr
       ^~~~~~~~~~~~~
```
[R/mbd_utils.R:728:22:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L728) *warning:* **no visible global function definition for ‘branchLengths’**
```r
      branch_info <- branchLengths(tr)[-1, ]
                     ^~~~~~~~~~~~~
```
[R/mbd_utils.R:744:21:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L744) *style:* **Commas should always have a space after.**
```r
      branch_infos[,, i] <- as.matrix(branch_info)
                    ^
```
[R/mbd_utils.R:754:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L754) *style:* **Commented code should be removed.**
```r
  # branch_info_out <- abind::abind(branch_info_tot, along = 3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:776:63:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L776) *style:* **Trailing whitespace is superfluous.**
```r
  # beast_posterior$branch_info # a list of branch lengths and
                                                              ^
```
[R/mbd_utils.R:798:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L798) *style:* **Commented code should be removed.**
```r
#   parnames = get_mbd_param_names()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:800:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L800) *style:* **Commented code should be removed.**
```r
#   parnames <<- parnames
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:801:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L801) *style:* **Commented code should be removed.**
```r
#   n_pars <<- length(parnames);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:802:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L802) *style:* **Commented code should be removed.**
```r
#   base_path=dirname(dirname(getwd()))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:804:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L804) *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:804:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L804) *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:806:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L806) *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:806:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L806) *style:* **Commented code should be removed.**
```r
#   res_files = list.files(pattern=paste('[.]txt', sep = ''), path=path, full.names=TRUE)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:808:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L808) *style:* **Commented code should be removed.**
```r
#     fileData <- utils::read.table(file=res_files[i], header=FALSE, sep=", ")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:809:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L809) *style:* **Lines should not be more than 80 characters.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:809:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L809) *style:* **Commented code should be removed.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:811:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L811) *style:* **Commented code should be removed.**
```r
#   all_results = targetTable
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:813:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L813) *style:* **Commented code should be removed.**
```r
#   tidy_results=all_results[order(all_results[, dim(all_results)[2]]), ]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:814:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L814) *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:814:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L814) *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:815:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L815) *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:815:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L815) *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:816:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L816) *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:816:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L816) *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:817:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L817) *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:817:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L817) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",Nbad<-dim(bad_results)[1], " bad results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:818:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L818) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",N<<-dim(results)[1], " good results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:820:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L820) *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:820:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L820) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / general_settings", sep = '')), envir = e <- globalenv())
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:821:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L821) *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:821:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L821) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / sim_data", sep = '')), envir = e <- globalenv()  )
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:822:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L822) *style:* **Commented code should be removed.**
```r
#   suppressWarnings(rm(targetTable, all_results, fileData, i))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:823:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/R/mbd_utils.R#L823) *style:* **Commented code should be removed.**
```r
#   return(results)
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_expo_vs_lsoda.R:18:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_expo_vs_lsoda.R#L18) *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_pure_birth_small_trees.R:4:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L20) *style:* **Commented code should be removed.**
```r
#     #     time_intervals=data$time_intervals
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:21:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L21) *style:* **Commented code should be removed.**
```r
#     #     births=data$births
      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:23:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L23) *style:* **Commented code should be removed.**
```r
#     time_intervals <- data$time_intervals
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:24:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L24) *style:* **Commented code should be removed.**
```r
#     births <- data$births
      ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:25:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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/a51662d40256bf3668bf17d2929674c4eab02f47/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
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:76:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L76) *style:* **Commented code should be removed.**
```r
#     expo_log_lik = expo_log_lik - ctrl_expo
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:77:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L77) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:78:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L78) *style:* **Lines should not be more than 80 characters.**
```r
#     out=list(theo_log_lik=theo_log_lik, lsoda_log_lik=lsoda_log_lik, expo_log_lik=expo_log_lik)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:78:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L78) *style:* **Commented code should be removed.**
```r
#     out=list(theo_log_lik=theo_log_lik, lsoda_log_lik=lsoda_log_lik, expo_log_lik=expo_log_lik)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:79:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L79) *style:* **Commented code should be removed.**
```r
#     return(out)
      ^~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:81:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:82:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L82) *style:* **Commented code should be removed.**
```r
#   lambda=sample(size = test_size, x = (1:18)*0.1, replace = T)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:83:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L83) *style:* **Commented code should be removed.**
```r
#   q=sample(size = test_size, x = (1:18)*0.01, replace = T)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:84:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L84) *style:* **Commented code should be removed.**
```r
#   res_theorethical=rep(0, test_size)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:85:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L85) *style:* **Commented code should be removed.**
```r
#   res_lsoda=rep(0, test_size)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:86:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L86) *style:* **Commented code should be removed.**
```r
#   res_expo=rep(0, test_size)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:87:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:88:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L88) *style:* **Commented code should be removed.**
```r
#   brts = c(10)
    ^~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:90:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L90) *style:* **Commented code should be removed.**
```r
#     testpars=c(lambda[j],0, q[j])
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:91:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
#     test_p_b = mbd_test_pure_birth_small_trees(testpars, brts, soc=soc, cond=cond)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:91:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L91) *style:* **Commented code should be removed.**
```r
#     test_p_b = mbd_test_pure_birth_small_trees(testpars, brts, soc=soc, cond=cond)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:92:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L92) *style:* **Commented code should be removed.**
```r
#     res_theorethical[j] = test_p_b$theo_log_lik
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:93:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L93) *style:* **Commented code should be removed.**
```r
#     res_lsoda[j]        = test_p_b$lsoda_log_lik
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:94:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L94) *style:* **Commented code should be removed.**
```r
#     res_expo[j]         = test_p_b$expo_log_lik
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:96:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L96) *style:* **Commented code should be removed.**
```r
#   # all.equal(res_theorethical, res_expo)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:97:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L97) *style:* **Commented code should be removed.**
```r
#   # all.equal(res_theorethical, res_lsoda)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:98:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:99:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L99) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:100:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:102:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L102) *style:* **Commented code should be removed.**
```r
#   expect_equal(res_theorethical[i], res_expo[i])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:103:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L103) *style:* **Commented code should be removed.**
```r
#   expect_equal(res_theorethical[i], res_lsoda[i])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:107:3:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L107) *style:* **Commented code should be removed.**
```r
# warnings()
  ^~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:108:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L108) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-mbd_pure_birth_small_trees.R:109:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth_small_trees.R#L109) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-mbd_pure_birth.R:4:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L4) *style:* **Commented code should be removed.**
```r
#   skip("For @Giappo: cannot find function 'mbd_loglik0'")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:5:5:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L5) *style:* **Commented code should be removed.**
```r
#   test_size <- 10; methode = "both" #"lsoda" "expo"
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:6:1:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#   #without the new Hanno's product I can check only up to some degree of accuracy
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:8:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth.R:10:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L10) *style:* **Commented code should be removed.**
```r
#     #this works only for mu=0
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:11:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L11) *style:* **Commented code should be removed.**
```r
#     lambda=pars[1]; mu=pars[2]; q=pars[3]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:13:9:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L13) *style:* **Commented code should be removed.**
```r
#       return(-Inf)
        ^~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:16:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L16) *style:* **Commented code should be removed.**
```r
#     #     data=brts2time_intervals_and_births(brts)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:17:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L17) *style:* **Commented code should be removed.**
```r
#     #     time_intervals=data$time_intervals
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:18:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L18) *style:* **Commented code should be removed.**
```r
#     #     births=data$births
      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:19:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L19) *style:* **Commented code should be removed.**
```r
#     data <- brts2time_intervals_and_births(brts)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:20:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L20) *style:* **Commented code should be removed.**
```r
#     time_intervals=data$time_intervals
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:21:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L21) *style:* **Commented code should be removed.**
```r
#     births=data$births
      ^~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_pure_birth.R:22:2:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
#
 ^
```
[tests/testthat/test-mbd_pure_birth.R:24:7:](https://github.com/Giappo/mbd/blob/a51662d40256bf3668bf17d2929674c4eab02f47/tests/testthat/test-mbd_pure_birth.R#L24) *style:* **Commented code should be removed.**
```r
#     init_n_lineages <- soc
      ^~~~~~~~~~~~~~~~~~~~~~
```


Add the link of paper to be focused.
What tasks you will perform in this project?
Typically, you need to develop a  case study to test a system call using the defined methodology. As you are 4 members in the project, so you should test 4 different system call and explain the results.


Would it be bad at all to leak the AM messages here to logs?


Fixes #23


[R/mbd_sim.R:162:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L162) *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/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L322) *style:* **Use <-, not =, for assignment.**
```r
  brts = -sort(abs(as.numeric(time_points)), decreasing = TRUE)
       ^
```
[R/mbd_sim.R:323:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L323) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(l_matrix, dropextinct = T)
      ^
```
[R/mbd_sim.R:324:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L324) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(l_matrix, dropextinct = F)
      ^
```
[R/mbd_sim.R:325:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L325) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tas)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:326:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L326) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tes)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:383:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L383) *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:403:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L403) *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:434:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_sim.R#L434) *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:59:29:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L59) *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:62:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L62) *style:* **Variable or function name should be snake_case.**
```r
      good.results <- results[good_lines, ]
      ^~~~~~~~~~~~
```
[R/mbd_utils.R:64:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L64) *style:* **Variable or function name should be snake_case.**
```r
      good.results <- results
      ^~~~~~~~~~~~
```
[R/mbd_utils.R:106:31:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L106) *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:109:9:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L109) *style:* **Variable or function name should be snake_case.**
```r
        good.results <- results[good_lines, ]
        ^~~~~~~~~~~~
```
[R/mbd_utils.R:111:9:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L111) *style:* **Variable or function name should be snake_case.**
```r
        good.results <- results
        ^~~~~~~~~~~~
```
[R/mbd_utils.R:177:19:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L177) *style:* **Use <-, not =, for assignment.**
```r
heatmap2dataframe = function(
                  ^
```
[R/mbd_utils.R:193:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L193) *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:227:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L227) *style:* **Variable or function name should be snake_case.**
```r
  create_mbd_P_matrix <- function(
  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:231:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L231) *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:232:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L232) *warning:* **local variable ‘lambda’ assigned but may not be used**
```r
    lambda <- pars[1]
    ^~~~~~
```
[R/mbd_utils.R:233:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L233) *warning:* **local variable ‘mu’ assigned but may not be used**
```r
    mu <- pars[2]
    ^~
```
[R/mbd_utils.R:234:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L234) *warning:* **local variable ‘q’ assigned but may not be used**
```r
    q <- pars[3]
    ^
```
[R/mbd_utils.R:235:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L235) *warning:* **local variable ‘nvec’ assigned but may not be used**
```r
    nvec <- 0:max_number_of_species
    ^~~~
```
[R/mbd_utils.R:243:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L243) *style:* **Commented code should be removed.**
```r
    # hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:245:9:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L245) *style:* **Commented code should be removed.**
```r
    #   nvec[2:(max_number_of_species+1)]
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:246:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L246) *style:* **Commented code should be removed.**
```r
    # diag(my_matrix) = - mu * nvec - lambda * (1 - (1 - q) ^ nvec)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:247:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L247) *style:* **Commented code should be removed.**
```r
    # return(my_matrix)
      ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:251:15:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L251) *style:* **Commas should always have a space after.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:251:15:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L251) *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:295:16:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L295) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (logs == 1 ) {
               ^
```
[R/mbd_utils.R:323:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L323) *style:* **Variable or function name should be snake_case.**
```r
  lX <- x
  ^~
```
[R/mbd_utils.R:324:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L324) *style:* **Variable or function name should be snake_case.**
```r
  lY <- y
  ^~
```
[R/mbd_utils.R:330:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L330) *style:* **Variable or function name should be snake_case.**
```r
  jet.colors <- grDevices::colorRampPalette(
  ^~~~~~~~~~
```
[R/mbd_utils.R:383:6:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L383) *style:* **Commented code should be removed.**
```r
    #negatives <- v[v < 0]
     ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:384:6:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L384) *style:* **Commented code should be removed.**
```r
    #maximum <- max(v)
     ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:407:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L407) *style:* **Variable or function name should be snake_case.**
```r
    Atest1 <- (function1(...))
    ^~~~~~
```
[R/mbd_utils.R:410:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L410) *style:* **Variable or function name should be snake_case.**
```r
    Atest2 <- (function2(...))
    ^~~~~~
```
[R/mbd_utils.R:418:26:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L418) *style:* **Commas should always have a space after.**
```r
  print(all.equal(Atest1,Atest2))
                         ^
```
[R/mbd_utils.R:419:32:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L419) *style:* **Commas should always have a space after.**
```r
  return(invisible(list(Atest1,Atest2)))
                               ^
```
[R/mbd_utils.R:431:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L431) *style:* **Variable or function name should be snake_case.**
```r
    function.code <- deparse(get(function_name))
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:434:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    left.brackets <- c(
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:438:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L438) *style:* **Variable or function name should be snake_case.**
```r
    called.functions <- unique(
    ^~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:447:15:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L447) *style:* **Variable or function name should be snake_case.**
```r
              last.word <- utils::tail(words, 1)
              ^~~~~~~~~
```
[R/mbd_utils.R:448:15:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L448) *style:* **Variable or function name should be snake_case.**
```r
              last.word.is.function <- tryCatch(
              ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:465:13:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L465) *style:* **Commented code should be removed.**
```r
        #   !(called.functions %in% checked_functions)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:471:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L471) *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:471:19:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L471) *style:* **Commented code should be removed.**
```r
        #         listFunctions(x, recursive = T, checked_functions = c(checked_functions, called.functions))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:483:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L483) *style:* **Variable or function name should be snake_case.**
```r
  Mlist,
  ^~~~~
```
[R/mbd_utils.R:561:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L561) *style:* **Variable or function name should be snake_case.**
```r
branchLengths <- function(tr)
^~~~~~~~~~~~~
```
[R/mbd_utils.R:562:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L562) *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:564:13:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L564) *style:* **Only use double-quotes.**
```r
    type <- 'NAMED'
            ^~~~~~~
```
[R/mbd_utils.R:566:13:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L566) *style:* **Only use double-quotes.**
```r
    type <- 'UNNAMED'
            ^~~~~~~~~
```
[R/mbd_utils.R:569:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L569) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- tr$root
    ^~~~~~~~~~~
```
[R/mbd_utils.R:571:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L571) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- 0
    ^~~~~~~~~~~
```
[R/mbd_utils.R:574:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L574) *style:* **Variable or function name should be snake_case.**
```r
  node.numbers <- sort(unique(tr$edge[, 1]))
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:584:3:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L584) *style:* **Variable or function name should be snake_case.**
```r
  tip.numbers <- 1:length(tr$tip)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:617:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L617) *style:* **Variable or function name should be snake_case.**
```r
    subst.xml <- scan(input_xml, what = "raw")
    ^~~~~~~~~
```
[R/mbd_utils.R:618:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L618) *style:* **Variable or function name should be snake_case.**
```r
    where.starting.tree <- which(subst.xml == "id=\"startingTree\">") + 1
    ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:619:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L619) *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:629:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L629) *style:* **Variable or function name should be snake_case.**
```r
    subst.tr <- scan(input_trees_path[t], what = "raw")
    ^~~~~~~~
```
[R/mbd_utils.R:635:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L635) *style:* **Variable or function name should be snake_case.**
```r
    tree.positions <- equals + 2
    ^~~~~~~~~~~~~~
```
[R/mbd_utils.R:636:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L636) *style:* **Commented code should be removed.**
```r
    # tree.names.pos <- equals - 2
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:652:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L652) *style:* **Variable or function name should be snake_case.**
```r
    Translate.pos <- (1:length(subst.tr))[subst.tr == "Translate"]
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:653:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L653) *style:* **Variable or function name should be snake_case.**
```r
    comma.pos <- which(subst.tr == ", ")
    ^~~~~~~~~
```
[R/mbd_utils.R:655:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L655) *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:657:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L657) *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:659:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L659) *style:* **Variable or function name should be snake_case.**
```r
    taxa.pos <- numbers.pos + 1
    ^~~~~~~~
```
[R/mbd_utils.R:689:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L689) *style:* **Variable or function name should be snake_case.**
```r
      croch1.pos <- (1:length(tree_sub2))[tree_sub2 == "["]
      ^~~~~~~~~~
```
[R/mbd_utils.R:690:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L690) *style:* **Variable or function name should be snake_case.**
```r
      croch2.pos <- (1:length(tree_sub2))[tree_sub2 == "]"]
      ^~~~~~~~~~
```
[R/mbd_utils.R:722:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L722) *style:* **Variable or function name should be snake_case.**
```r
      tree.text <- paste(tree_sub2[-remove], collapse = "")
      ^~~~~~~~~
```
[R/mbd_utils.R:725:10:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L725) *style:* **Variable or function name should be snake_case.**
```r
      tr$tip.label <- taxa[as.numeric(tr$tip.label)]
         ^~~~~~~~~
```
[R/mbd_utils.R:727:8:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L727) *style:* **Commented code should be removed.**
```r
      #trees[[i]]=tr
       ^~~~~~~~~~~~~
```
[R/mbd_utils.R:728:22:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L728) *warning:* **no visible global function definition for ‘branchLengths’**
```r
      branch_info <- branchLengths(tr)[-1, ]
                     ^~~~~~~~~~~~~
```
[R/mbd_utils.R:744:21:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L744) *style:* **Commas should always have a space after.**
```r
      branch_infos[,, i] <- as.matrix(branch_info)
                    ^
```
[R/mbd_utils.R:754:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L754) *style:* **Commented code should be removed.**
```r
  # branch_info_out <- abind::abind(branch_info_tot, along = 3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:798:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L798) *style:* **Commented code should be removed.**
```r
#   parnames = get_mbd_param_names()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:800:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L800) *style:* **Commented code should be removed.**
```r
#   parnames <<- parnames
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:801:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L801) *style:* **Commented code should be removed.**
```r
#   n_pars <<- length(parnames);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:802:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L802) *style:* **Commented code should be removed.**
```r
#   base_path=dirname(dirname(getwd()))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:804:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L804) *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:804:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L804) *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:806:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L806) *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:806:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L806) *style:* **Commented code should be removed.**
```r
#   res_files = list.files(pattern=paste('[.]txt', sep = ''), path=path, full.names=TRUE)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:808:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L808) *style:* **Commented code should be removed.**
```r
#     fileData <- utils::read.table(file=res_files[i], header=FALSE, sep=", ")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:809:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L809) *style:* **Lines should not be more than 80 characters.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:809:7:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L809) *style:* **Commented code should be removed.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:811:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L811) *style:* **Commented code should be removed.**
```r
#   all_results = targetTable
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:813:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L813) *style:* **Commented code should be removed.**
```r
#   tidy_results=all_results[order(all_results[, dim(all_results)[2]]), ]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:814:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L814) *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:814:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L814) *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:815:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L815) *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:815:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L815) *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:816:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L816) *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:816:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L816) *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:817:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L817) *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:817:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L817) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",Nbad<-dim(bad_results)[1], " bad results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:818:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L818) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",N<<-dim(results)[1], " good results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:820:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L820) *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:820:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L820) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / general_settings", sep = '')), envir = e <- globalenv())
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:821:1:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L821) *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:821:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L821) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / sim_data", sep = '')), envir = e <- globalenv()  )
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:822:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L822) *style:* **Commented code should be removed.**
```r
#   suppressWarnings(rm(targetTable, all_results, fileData, i))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:823:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/R/mbd_utils.R#L823) *style:* **Commented code should be removed.**
```r
#   return(results)
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_sims.R:8:48:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/tests/testthat/test-mbd_sims.R#L8) *style:* **Put spaces around all infix operators.**
```r
  lambda <- sample(size = test_size, x = (1:18)*0.1, replace = T)
                                              ~^~
```
[tests/testthat/test-mbd_sims.R:9:44:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/tests/testthat/test-mbd_sims.R#L9) *style:* **Put spaces around all infix operators.**
```r
  mu <- sample(size = test_size, x = (1:18)*0.01, replace = T)
                                          ~^~
```
[tests/testthat/test-mbd_sims.R:10:43:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/tests/testthat/test-mbd_sims.R#L10) *style:* **Put spaces around all infix operators.**
```r
  q <- sample(size = test_size, x = (1:16)*0.01, replace = T)
                                         ~^~
```
[tests/testthat/test-mbd_sims.R:28:21:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/tests/testthat/test-mbd_sims.R#L28) *style:* **Use <-, not =, for assignment.**
```r
  conditioning_test = 1
                    ^
```
[tests/testthat/test-mbd_sims.R:37:5:](https://github.com/Giappo/mbd/blob/b0b042c236987676a5fba6458f2cdc3af918c185/tests/testthat/test-mbd_sims.R#L37) *style:* **Commented code should be removed.**
```r
  # warnings()
    ^~~~~~~~~~
```


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/error-when-running-likes-report/98524/3


I guess it's potentially a lot of logs.. That part is inspired by the travis ci webhook implementation which also logs all it's messages


I don't fully like what is being done here - UI should display proper descriptions like the comments on attributes, not stringified enum name


This is from codecov's documentation:
![a](https://user-images.githubusercontent.com/767959/46333792-f9162a80-c621-11e8-8b1b-91fceb714e07.png)

In theory the token is not even needed. But I guess the worse that can happen is that someone starts to upload fake coverage reports.


Why the ternary condition? Isn't `@username.blank?` enough?


Yes thanks, i'll try to improve that.


Add a project plan in the document. What you will present in the interim presentation and what will be included in the final demonstration?


No, that is not necessary. Due to NPC reordering/etc, this data is only valid for the first moment the level is loaded anyway. Lua code will make it's own copy in pnpc immediately in onStart.


Pair assignment with @abravo3641


Save it as `/etc/systemd/system/local-reverse-geocoder.service`
Run at boot
`systemctl enable local-reverse-geocoder`
Start it immediately
`systemctl start local-reverse-geocoder`
View status
`systemctl status local-reverse-geocoder`
View all logs from app stdout
`journalctl -u local-reverse-geocoder`


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


set up files for **film** endpoints not genre


kek


tag removed ...


why not override the 3 line into the function , instead of just getDomain
and return the correct attachment?


need to check that website is in registry !


generated :)


code bi sai


fix


Accepted as is.


![](https://github.trello.services/images/mini-trello-icon.png) [test commit](https://trello.com/c/EUseNEn8/1-test-commit)


I legitimately would like to know why.


Prone to race conditions - probably better to lock before assigning a new instance:

```csharp
private static readonly object _lock = new object();

public static FLogger GetInstance() {
    if (log == null) {
        lock (_lock) {
            log = log ?? new FLogger();
        }
    }
    return log;
}
```


sdgdghshf


Thank you!

Tanakiat Srisaranyakul <notifications@github.com> schrieb am Mo., 1. Okt.
2018 um 16:28 Uhr:

> The library readme is the best way to check.
>
> https://github.com/h2non/jsonpath-ng/blob/master/README.rst
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/idxn/robotframework-jsonlibrary/commit/b6d2956c8f6e2dfb03f0de1261d1c5c39792ab00#commitcomment-30718944>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AFX9hvr6SBosbe7BbeY9YS6bbK1hdeDVks5ugiZygaJpZM4XBevQ>
> .
>


Not that it makes any big difference in this specific context, but if you're going the singleton way, then at least implement some best practices. 😜


Good point :+1: