[R/mbd_sim.R:103:35:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L103) *style:* **Trailing whitespace is superfluous.**
```r
            c(-1, 1, 2), size = 1,
                                  ^
```
[R/mbd_sim.R:106:65:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L106) *style:* **Trailing whitespace is superfluous.**
```r
          delta_n <- -1 * (outcome == -1) + 1 * (outcome == 1) +
                                                                ^
```
[R/mbd_sim.R:118:43:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
            l_matrix[new_interval, 1] <- t
                                          ^
```
[R/mbd_sim.R:147:65:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L147) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    crown_species_dead <- (length(unique(sign(alive[, 3]))) != 2 ) * cond
                                                                ^
```
[R/mbd_sim.R:149:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
    births_rec_tree <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:150:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
    births_full_tree <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = FALSE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:154:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L154) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:155:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L155) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check <- (multiple_births_rec_tree >= minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:157:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
    keep_the_sim <- (!crown_species_dead) & (tips >= tips_interval[1] & tips <= tips_interval[2]) #should i keep this simulation?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:159:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
  time_points <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:177:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L177) *style:* **Lines should not be more than 80 characters.**
```r
#' @description mbd_sim0 produces simulated trees including multiple speciations at the same time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:184:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L184) *style:* **Lines should not be more than 80 characters.**
```r
#' @return The function returns a list of L table, branching times and number of extinct species.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:187:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L187) *style:* **Lines should not be more than 80 characters.**
```r
#'   \item tes is a tree-object corresponding to the reconstructed phylogenetic tree;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:189:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L189) *style:* **Lines should not be more than 80 characters.**
```r
#'   \item extinct_species is the number of species gone extinct before the present time;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:193:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L193) *style:* **Lines should not be more than 80 characters.**
```r
#'      \item second is the label of the parent of the species; positive and negative values only indicate whether the species belongs to the left or right crown lineage;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:194:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L194) *style:* **Lines should not be more than 80 characters.**
```r
#'      \item third is the label of the daughter species itself; positive and negative values only indicate whether the species belongs to the left or right crown lineage;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:195:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L195) *style:* **Lines should not be more than 80 characters.**
```r
#'      \item fourth is the time of extinction of the species. If this is equal to -1, then the species is still extant.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:200:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L200) *style:* **Lines should not be more than 80 characters.**
```r
#' out = mbd_sim0(pars=c(2.5, 0.1, 0.1), soc=2, age=10, cond=1, tips_interval=c(0,Inf))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:255:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L255) *style:* **Lines should not be more than 80 characters.**
```r
          l_matrix[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:285:56:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L285) *style:* **Trailing whitespace is superfluous.**
```r
        sort(DDD::L2brts(l_matrix, dropextinct = TRUE),
                                                       ^
```
[R/mbd_sim.R:291:59:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L291) *style:* **Trailing whitespace is superfluous.**
```r
    #     sort(DDD::L2brts(l_matrix, dropextinct = FALSE),
                                                          ^
```
[R/mbd_sim.R:296:8:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L296) *style:* **Commented code should be removed.**
```r
    #  multi_births_full_tree <- sum(duplicated(births_full_tree))
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:298:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L298) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:299:58:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L299) *style:* **Trailing whitespace is superfluous.**
```r
    multiple_births_check <- (multiple_births_rec_tree >=
                                                         ^
```
[R/mbd_sim.R:303:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L303) *style:* **Lines should not be more than 80 characters.**
```r
  time_points <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:304:8:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L304) *style:* **Use <-, not =, for assignment.**
```r
  brts = -sort(abs(as.numeric(time_points)), decreasing = TRUE)
       ^
```
[R/mbd_sim.R:305:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L305) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(l_matrix, dropextinct = T)
      ^
```
[R/mbd_sim.R:306:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L306) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(l_matrix, dropextinct = F)
      ^
```
[R/mbd_sim.R:307:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L307) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tas)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:308:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L308) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tes)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:321:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L321) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Creates a full simulated dataset of trees under the multiple birth death process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:322:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L322) *style:* **Lines should not be more than 80 characters.**
```r
#' @description mbd_sim_dataset produces a full dataset of max_sims simulated trees including multiple speciations at the same time. This second version takes into account the possibility both of allopatric and sympatric speciation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:324:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L324) *style:* **Lines should not be more than 80 characters.**
```r
#' @param edge the program automatically detects the (estimated) average number of tips. "edge" defines the width of the spread around the mean.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:325:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L325) *style:* **Lines should not be more than 80 characters.**
```r
#' @return The function returns a list of brts vectors, one for each of the max_sims simulations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:326:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L326) *style:* **Lines should not be more than 80 characters.**
```r
#' It also saves those in a file called "sim_data" and saves all the settings in a "general_settings" file.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:331:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
#' # out <- mbd_sim_dataset(pars=c(0.4, 0.1, 0.2, 0.15), soc=2, age=10, cond=1, edge=Inf )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:345:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
  #"edge" gives the extent of fluctuations around the mean that i want to consider
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:355:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L355) *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:366:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L366) *style:* **Lines should not be more than 80 characters.**
```r
    tips_interval <- c(min_tips, max_tips) #c(10, 45) #setting the upper limit over 50 may be a problem #min and max number of tips for simulated trees
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:366:45:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L366) *style:* **Commented code should be removed.**
```r
    tips_interval <- c(min_tips, max_tips) #c(10, 45) #setting the upper limit over 50 may be a problem #min and max number of tips for simulated trees
                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:373:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L373) *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:376:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L376) *style:* **Lines should not be more than 80 characters.**
```r
                                tips_interval = tips_interval, minimum_multiple_births = minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:383:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
  max_k <- (init_n_lineages - 1) + (is.list(sim_data)) * max(sapply(sim_data, length)) + (1 - is.list(sim_data)) * length(sim_data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:385:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L385) *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:398:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L398) *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:403:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L403) *style:* **Lines should not be more than 80 characters.**
```r
  # simpath=paste("sims /", sim_pars[1], "-", sim_pars[2], "-", sim_pars[3], "-", sim_pars[4], "/", sep = '')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:403:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L403) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims /", sim_pars[1], "-", sim_pars[2], "-", sim_pars[3], "-", sim_pars[4], "/", sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:417:62:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L417) *style:* **Trailing whitespace is superfluous.**
```r
    sim_pars, soc, age, cond, max_sims, tips_interval, max_k,
                                                             ^
```
[R/mbd_sim.R:418:50:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L418) *style:* **Trailing whitespace is superfluous.**
```r
    max_b, ext_species, additional_species, tips,
                                                 ^
```
[R/mbd_sim.R:421:36:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L421) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (file.exists(sim_trees_name)) {
                                   ^
```
[R/mbd_sim.R:421:37:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_sim.R#L421) *style:* **Trailing whitespace is superfluous.**
```r
  if (file.exists(sim_trees_name)) {
                                    ^
```
[R/mbd_utils.R:20:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:20:31:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L20) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:21:27:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (missing(idparsopt)) {
                          ^
```
[R/mbd_utils.R:21:28:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
  if (missing(idparsopt)) {
                           ^
```
[R/mbd_utils.R:28:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:28:43:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L28) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                          ^
```
[R/mbd_utils.R:28:69:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L28) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                                                    ^
```
[R/mbd_utils.R:29:55:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L29) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name <- "blue"; truevalues_color_name = "red";
                                                      ^
```
[R/mbd_utils.R:35:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
  medians_string <- paste0("MLE Medians (", medians_color_name, ") = (", paste(signif(medians, 2), sep = "''", collapse = ", "), ")")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:36:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_string <- paste0("True Values (", truevalues_color_name, ") = (", paste(signif(sim_pars, 2), sep = "''", collapse = ", "), ")")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:41:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
      probs = 1 - percentage_hidden_outliers # BUG? Used to be with arrow operator
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:49:29:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L49) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (i in estimated_pars) { for (j in estimated_pars) {
                            ^
```
[R/mbd_utils.R:50:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L50) *style:* **Variable or function name should be snake_case.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
    ^~~~~~~~~~
```
[R/mbd_utils.R:50:16:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L50) *style:* **Use <-, not =, for assignment.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
               ^
```
[R/mbd_utils.R:51:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:51:33:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L51) *style:* **Variable or function name should be snake_case.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                ^~~~~~~~~~~~
```
[R/mbd_utils.R:51:72:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L51) *style:* **Variable or function name should be snake_case.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                                                       ^~~~~~~~~~~~
```
[R/mbd_utils.R:68:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
      graphics::points(x = sim_pars[j], y = sim_pars[i], col = truevalues_color, pch = 10, cex = 1.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:69:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
      graphics::points(x = medians[j], y = medians[i], col = medians_color, pch = 10, cex = 1.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:86:31:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L86) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    for (i in estimated_pars) { for (j in estimated_pars) {
                              ^
```
[R/mbd_utils.R:87:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L87) *style:* **Variable or function name should be snake_case.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
      ^~~~~~~~~~
```
[R/mbd_utils.R:87:18:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L87) *style:* **Use <-, not =, for assignment.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
                 ^
```
[R/mbd_utils.R:88:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:88:35:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L88) *style:* **Variable or function name should be snake_case.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                  ^~~~~~~~~~~~
```
[R/mbd_utils.R:88:74:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L88) *style:* **Variable or function name should be snake_case.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                                                         ^~~~~~~~~~~~
```
[R/mbd_utils.R:91:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
        graphics::hist((good.results[, i]), main = NULL, xlab = paste(par_names[i]), breaks = 15)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:132:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L132) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:132:31:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L132) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:135:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:135:27:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L135) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                          ^
```
[R/mbd_utils.R:135:104:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L135) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                                                                                ^
```
[R/mbd_utils.R:148:19:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L148) *style:* **Use <-, not =, for assignment.**
```r
heatmap2dataframe = function(
                  ^
```
[R/mbd_utils.R:154:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L154) *style:* **Variable or function name should be snake_case.**
```r
  heatmap.name="HeatMap"
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:157:46:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L157) *style:* **Commas should always have a space after.**
```r
  df <- data.frame(expand.grid(x = x, y = y),HeatMap = matrix_2)
                                             ^
```
[R/mbd_utils.R:164:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
#' Converts branching times to "time intervals between branching times" and "birth at nodes" vectors
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:174:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L174) *style:* **Lines should not be more than 80 characters.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:174:54:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L174) *style:* **Commas should always have a space after.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:174:54:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L174) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:195:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L195) *style:* **Variable or function name should be snake_case.**
```r
  create_mbd_P_matrix <- function(
  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:199:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L199) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_utils.R:200:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L200) *warning:* **local variable ‘lambda’ assigned but may not be used**
```r
    lambda <- pars[1]
    ^~~~~~
```
[R/mbd_utils.R:201:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L201) *warning:* **local variable ‘mu’ assigned but may not be used**
```r
    mu <- pars[2]
    ^~
```
[R/mbd_utils.R:202:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L202) *warning:* **local variable ‘q’ assigned but may not be used**
```r
    q <- pars[3]
    ^
```
[R/mbd_utils.R:203:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L203) *warning:* **local variable ‘nvec’ assigned but may not be used**
```r
    nvec <- 0:max_number_of_species
    ^~~~
```
[R/mbd_utils.R:210:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
    # my_matrix <- lambda * hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:210:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L210) *style:* **Commented code should be removed.**
```r
    # my_matrix <- lambda * hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:211:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L211) *style:* **Lines should not be more than 80 characters.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu * nvec[2:(max_number_of_species+1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:211:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L211) *style:* **Commented code should be removed.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu * nvec[2:(max_number_of_species+1)]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:212:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L212) *style:* **Commented code should be removed.**
```r
    # diag(my_matrix) = - mu * nvec - lambda * (1 - (1 - q) ^ nvec)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:213:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L213) *style:* **Commented code should be removed.**
```r
    # return(my_matrix)
      ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:217:15:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L217) *style:* **Commas should always have a space after.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:217:15:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L217) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:233:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L233) *style:* **Lines should not be more than 80 characters.**
```r
    print(paste("Sim pars are:", test_parameters[1], test_parameters[2], test_parameters[3], ". Average n is", nmedio, "with std:", std))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:253:16:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L253) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (logs == 1 ) {
               ^
```
[R/mbd_utils.R:281:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L281) *style:* **Variable or function name should be snake_case.**
```r
  lX <- x
  ^~
```
[R/mbd_utils.R:282:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L282) *style:* **Variable or function name should be snake_case.**
```r
  lY <- y
  ^~
```
[R/mbd_utils.R:283:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L283) *style:* **Variable or function name should be snake_case.**
```r
  pretty_X.at	<-	pretty(range(lX), n = x_splits)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:284:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L284) *style:* **Variable or function name should be snake_case.**
```r
  pretty_X.lab	<-	round(pretty_X.at, 2)
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:285:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L285) *style:* **Variable or function name should be snake_case.**
```r
  pretty_Y.at	<-	pretty(range(lY), n = y_splits)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:286:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L286) *style:* **Variable or function name should be snake_case.**
```r
  pretty_Y.lab	<-	round(pretty_Y.at, 2)
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:288:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L288) *style:* **Lines should not be more than 80 characters.**
```r
  jet.colors <- grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:288:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L288) *style:* **Variable or function name should be snake_case.**
```r
  jet.colors <- grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
  ^~~~~~~~~~
```
[R/mbd_utils.R:326:38:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L326) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (length(na_components) > 0) { cat("NA component are:", na_components)}
                                     ^
```
[R/mbd_utils.R:326:79:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L326) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      if (length(na_components) > 0) { cat("NA component are:", na_components)}
                                                                              ^
```
[R/mbd_utils.R:327:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L327) *style:* **Lines should not be more than 80 characters.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:327:39:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L327) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
                                      ^
```
[R/mbd_utils.R:327:82:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L327) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
                                                                                ^
```
[R/mbd_utils.R:332:6:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L332) *style:* **Commented code should be removed.**
```r
    #negatives <- v[v < 0]
     ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:333:6:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L333) *style:* **Commented code should be removed.**
```r
    #maximum <- max(v)
     ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:356:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L356) *style:* **Variable or function name should be snake_case.**
```r
    Atest1 <- (function1(...))
    ^~~~~~
```
[R/mbd_utils.R:359:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L359) *style:* **Variable or function name should be snake_case.**
```r
    Atest2 <- (function2(...))
    ^~~~~~
```
[R/mbd_utils.R:367:26:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L367) *style:* **Commas should always have a space after.**
```r
  print(all.equal(Atest1,Atest2))
                         ^
```
[R/mbd_utils.R:368:32:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L368) *style:* **Commas should always have a space after.**
```r
  return(invisible(list(Atest1,Atest2)))
                               ^
```
[R/mbd_utils.R:380:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L380) *style:* **Variable or function name should be snake_case.**
```r
    function.code <- deparse(get(function_name))
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:383:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
    left.brackets <- c(unlist(strsplit(function.code, split = "[[:space:]]*\\(")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:383:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L383) *style:* **Variable or function name should be snake_case.**
```r
    left.brackets <- c(unlist(strsplit(function.code, split = "[[:space:]]*\\(")))
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:385:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L385) *style:* **Variable or function name should be snake_case.**
```r
    called.functions <- unique(
    ^~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:393:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L393) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/mbd_utils.R:394:15:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L394) *style:* **Variable or function name should be snake_case.**
```r
              last.word <- utils::tail(words, 1)
              ^~~~~~~~~
```
[R/mbd_utils.R:395:15:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L395) *style:* **Variable or function name should be snake_case.**
```r
              last.word.is.function <- tryCatch(
              ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:411:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L411) *style:* **Lines should not be more than 80 characters.**
```r
        # functs.to.check <- called.functions[!(called.functions %in% checked_functions)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:411:11:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L411) *style:* **Commented code should be removed.**
```r
        # functs.to.check <- called.functions[!(called.functions %in% checked_functions)]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:416:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L416) *style:* **Lines should not be more than 80 characters.**
```r
        #         listFunctions(x, recursive = T, checked_functions = c(checked_functions, called.functions))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:416:19:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L416) *style:* **Commented code should be removed.**
```r
        #         listFunctions(x, recursive = T, checked_functions = c(checked_functions, called.functions))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:422:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L422) *style:* **Lines should not be more than 80 characters.**
```r
#' Checks if some matrix entries are infinite, NaN, NA or (only in the lower triangle) negative
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:427:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L427) *style:* **Variable or function name should be snake_case.**
```r
  Mlist,
  ^~~~~
```
[R/mbd_utils.R:435:41:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L435) *style:* **Trailing whitespace is superfluous.**
```r
    if ((max(is.infinite(matrix)) > 0) |
                                        ^
```
[R/mbd_utils.R:438:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L438) *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:438:8:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L438) *style:* **Trailing whitespace is superfluous.**
```r
    ) {
       ^
```
[R/mbd_utils.R:465:36:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L465) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (min(lower_triangle) < 0) {
                                   ^
```
[R/mbd_utils.R:465:37:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L465) *style:* **Trailing whitespace is superfluous.**
```r
      if (min(lower_triangle) < 0) {
                                    ^
```
[R/mbd_utils.R:473:45:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L473) *style:* **Trailing whitespace is superfluous.**
```r
          "There is a negative entry on k=",
                                            ^
```
[R/mbd_utils.R:505:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L505) *style:* **Variable or function name should be snake_case.**
```r
branchLengths <- function(tr)
^~~~~~~~~~~~~
```
[R/mbd_utils.R:506:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L506) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/mbd_utils.R:508:13:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L508) *style:* **Only use double-quotes.**
```r
    type <- 'NAMED'
            ^~~~~~~
```
[R/mbd_utils.R:510:13:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L510) *style:* **Only use double-quotes.**
```r
    type <- 'UNNAMED'
            ^~~~~~~~~
```
[R/mbd_utils.R:513:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L513) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- tr$root
    ^~~~~~~~~~~
```
[R/mbd_utils.R:515:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L515) *style:* **Variable or function name should be snake_case.**
```r
    root.length <- 0
    ^~~~~~~~~~~
```
[R/mbd_utils.R:518:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L518) *style:* **Variable or function name should be snake_case.**
```r
  node.numbers <- sort(unique(tr$edge[, 1]))
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:528:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L528) *style:* **Variable or function name should be snake_case.**
```r
  tip.numbers <- 1:length(tr$tip)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:561:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L561) *style:* **Variable or function name should be snake_case.**
```r
    subst.xml <- scan(input_xml, what = "raw")
    ^~~~~~~~~
```
[R/mbd_utils.R:562:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L562) *style:* **Variable or function name should be snake_case.**
```r
    where.starting.tree <- which(subst.xml == "id=\"startingTree\">") + 1
    ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:563:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L563) *style:* **Variable or function name should be snake_case.**
```r
    start.tr <- ape::read.tree(text = subst.xml[where.starting.tree])
    ^~~~~~~~
```
[R/mbd_utils.R:573:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L573) *style:* **Variable or function name should be snake_case.**
```r
    subst.tr <- scan(input_trees_path[t], what = "raw")
    ^~~~~~~~
```
[R/mbd_utils.R:579:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L579) *style:* **Variable or function name should be snake_case.**
```r
    tree.positions <- equals + 2
    ^~~~~~~~~~~~~~
```
[R/mbd_utils.R:580:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L580) *style:* **Commented code should be removed.**
```r
    # tree.names.pos <- equals - 2
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:586:58:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L586) *style:* **Trailing whitespace is superfluous.**
```r
      n_trees, round(subsamp / length(input_trees_path)),
                                                         ^
```
[R/mbd_utils.R:596:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L596) *style:* **Variable or function name should be snake_case.**
```r
    Translate.pos <- (1:length(subst.tr))[subst.tr == "Translate"]
    ^~~~~~~~~~~~~
```
[R/mbd_utils.R:597:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L597) *style:* **Variable or function name should be snake_case.**
```r
    comma.pos <- which(subst.tr == ", ")
    ^~~~~~~~~
```
[R/mbd_utils.R:599:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L599) *style:* **Variable or function name should be snake_case.**
```r
      numbers.pos <- seq(Translate.pos + 1, Translate.pos + 2 * ntax, 2)
      ^~~~~~~~~~~
```
[R/mbd_utils.R:601:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L601) *style:* **Variable or function name should be snake_case.**
```r
      numbers.pos <- seq(Translate.pos + 1, Translate.pos + 3 * ntax, 3)
      ^~~~~~~~~~~
```
[R/mbd_utils.R:603:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L603) *style:* **Variable or function name should be snake_case.**
```r
    taxa.pos <- numbers.pos + 1
    ^~~~~~~~
```
[R/mbd_utils.R:633:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L633) *style:* **Variable or function name should be snake_case.**
```r
      croch1.pos <- (1:length(tree_sub2))[tree_sub2 == "["]
      ^~~~~~~~~~
```
[R/mbd_utils.R:634:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L634) *style:* **Variable or function name should be snake_case.**
```r
      croch2.pos <- (1:length(tree_sub2))[tree_sub2 == "]"]
      ^~~~~~~~~~
```
[R/mbd_utils.R:666:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L666) *style:* **Variable or function name should be snake_case.**
```r
      tree.text <- paste(tree_sub2[-remove], collapse = "")
      ^~~~~~~~~
```
[R/mbd_utils.R:669:10:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L669) *style:* **Variable or function name should be snake_case.**
```r
      tr$tip.label <- taxa[as.numeric(tr$tip.label)]
         ^~~~~~~~~
```
[R/mbd_utils.R:671:8:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L671) *style:* **Commented code should be removed.**
```r
      #trees[[i]]=tr
       ^~~~~~~~~~~~~
```
[R/mbd_utils.R:672:22:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L672) *warning:* **no visible global function definition for ‘branchLengths’**
```r
      branch_info <- branchLengths(tr)[-1, ]
                     ^~~~~~~~~~~~~
```
[R/mbd_utils.R:683:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L683) *style:* **Lines should not be more than 80 characters.**
```r
        dimnames(branch_infos) <- list(NULL, dimnames(branch_info)[[2]], 1:length(samp))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:686:21:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L686) *style:* **Commas should always have a space after.**
```r
      branch_infos[,, i] <- as.matrix(branch_info)
                    ^
```
[R/mbd_utils.R:696:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L696) *style:* **Commented code should be removed.**
```r
  # branch_info_out <- abind::abind(branch_info_tot, along = 3)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:718:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L718) *style:* **Lines should not be more than 80 characters.**
```r
  # beast_posterior$branch_info # a list of branch lengths and associated information
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:739:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L739) *style:* **Commented code should be removed.**
```r
#   parnames = get_mbd_param_names()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:741:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L741) *style:* **Commented code should be removed.**
```r
#   parnames <<- parnames
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:742:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L742) *style:* **Commented code should be removed.**
```r
#   n_pars <<- length(parnames);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:743:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L743) *style:* **Commented code should be removed.**
```r
#   base_path=dirname(dirname(getwd()))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:745:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L745) *style:* **Lines should not be more than 80 characters.**
```r
#     path<<-choose.dir(paste(base_path, "/Progress /RQ1 - Multiple Births /Results + Reports / 4_parameters /", sep = ''), "Choose a suitable folder")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:745:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L745) *style:* **Commented code should be removed.**
```r
#     path<<-choose.dir(paste(base_path, "/Progress /RQ1 - Multiple Births /Results + Reports / 4_parameters /", sep = ''), "Choose a suitable folder")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:747:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L747) *style:* **Lines should not be more than 80 characters.**
```r
#   res_files = list.files(pattern=paste('[.]txt', sep = ''), path=path, full.names=TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:747:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L747) *style:* **Commented code should be removed.**
```r
#   res_files = list.files(pattern=paste('[.]txt', sep = ''), path=path, full.names=TRUE)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:749:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L749) *style:* **Commented code should be removed.**
```r
#     fileData <- utils::read.table(file=res_files[i], header=FALSE, sep=", ")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:750:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L750) *style:* **Lines should not be more than 80 characters.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:750:7:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L750) *style:* **Commented code should be removed.**
```r
#     ifelse(exists("targetTable"), targetTable<-rbind(targetTable, fileData), targetTable<-fileData)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:752:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L752) *style:* **Commented code should be removed.**
```r
#   all_results = targetTable
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:754:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L754) *style:* **Commented code should be removed.**
```r
#   tidy_results=all_results[order(all_results[, dim(all_results)[2]]), ]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:755:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L755) *style:* **Lines should not be more than 80 characters.**
```r
#   dimnames(tidy_results)[[2]]<-(c(parnames, "LL", "multiple_born", "number_of_tips", "percentage_multiple_species", "tree_id"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:755:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L755) *style:* **Commented code should be removed.**
```r
#   dimnames(tidy_results)[[2]]<-(c(parnames, "LL", "multiple_born", "number_of_tips", "percentage_multiple_species", "tree_id"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:756:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L756) *style:* **Lines should not be more than 80 characters.**
```r
#   bad_results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))==(n_pars+1), ];#print(Nbad<-dim(bad_results)[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:756:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L756) *style:* **Commented code should be removed.**
```r
#   bad_results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))==(n_pars+1), ];#print(Nbad<-dim(bad_results)[1])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:757:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L757) *style:* **Lines should not be more than 80 characters.**
```r
#   results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))!=(n_pars+1), ];#print(N<-dim(results)[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:757:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L757) *style:* **Commented code should be removed.**
```r
#   results=tidy_results[rowSums(tidy_results[, 1:(n_pars+1)]==rep(-1,(n_pars+1)))!=(n_pars+1), ];#print(N<-dim(results)[1])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:758:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L758) *style:* **Lines should not be more than 80 characters.**
```r
#   print(paste("There are ",Nbad<-dim(bad_results)[1], " bad results.", sep = ''))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:758:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L758) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",Nbad<-dim(bad_results)[1], " bad results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:759:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L759) *style:* **Commented code should be removed.**
```r
#   print(paste("There are ",N<<-dim(results)[1], " good results.", sep = ''))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:761:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L761) *style:* **Lines should not be more than 80 characters.**
```r
#   load(as.character(paste(path, "/ data / general_settings", sep = '')), envir = e <- globalenv())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:761:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L761) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / general_settings", sep = '')), envir = e <- globalenv())
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:762:1:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L762) *style:* **Lines should not be more than 80 characters.**
```r
#   load(as.character(paste(path, "/ data / sim_data", sep = '')), envir = e <- globalenv()  )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:762:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L762) *style:* **Commented code should be removed.**
```r
#   load(as.character(paste(path, "/ data / sim_data", sep = '')), envir = e <- globalenv()  )
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:763:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L763) *style:* **Commented code should be removed.**
```r
#   suppressWarnings(rm(targetTable, all_results, fileData, i))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:764:5:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/R/mbd_utils.R#L764) *style:* **Commented code should be removed.**
```r
#   return(results)
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-mbd_expo_vs_lsoda.R:16:3:](https://github.com/Giappo/mbd/blob/af3aafd81d9496624cd177de59976cb7f15e0e5a/tests/testthat/test-mbd_expo_vs_lsoda.R#L16) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```


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Successfully aliased the URL <https://jsheroesio-ywfzigzgqv.now.sh> to the following alias.

* https://jsheroes.io


@herpaderp I can't get the difference in the process with the upper composer file. It has pinned the version too?

More efficient fix could be to report this and ask for a fix to the mainteners. I know they properly implement it on their latest version.


@Fishwaldo I'm finding that quite a lot of Values are now returning an empty string for values, but the HelpString is returned correctly. Looks like anything not declared in the Localization.xml file is not returning a label in `Value->GetLabel`. The GetHelp strings do however return the help string from the various device xmls, but stepping through code I don't see an obvious problem anywhere


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Download and test one or both of these:
- https://github.com/MarlinFirmware/Marlin/archive/bugfix-1.1.x.zip
- https://github.com/MarlinFirmware/Marlin/archive/bugfix-2.0.x.zip


LGTM. Do we need a separate PR for this? Either way, let's merge this version and close PR gearman#169.


The Developers ask to install version 2 for laravel 5. Something in the install process of docker-compose-dev is installing version 3.
Pretty sure the issue is still on our side but i can't put my finger on it


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* https://jsheroes.io


What you will do in the project?
Typically, you need to run three multi-threading applications and evaluate the tool. Reproduce the similar results as shown in paper and explain in the working on the tool in detail in your own words.