[R/mbd_ml.R:85:31:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_ml.R#L85) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) == 0) {
                              ^
```
[R/mbd_ml.R:85:32:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_ml.R#L85) *style:* **Trailing whitespace is superfluous.**
```r
  if (length(idparsfix) == 0) {
                               ^
```
[R/mbd_ml.R:205:3:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_ml.R#L205) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_pure_multiple_birth.R:42:72:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      ii <- i[stats::dpois(i, nu * time_intervals[t], log = FALSE) != 0 ]
                                                                       ^
```
[R/mbd_pure_multiple_birth.R:46:24:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L46) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:46:61:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L46) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:90:47:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L90) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    a_term <- rep(1, length(time_intervals)    ) #branches
                                              ^
```
[R/mbd_pure_multiple_birth.R:100:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
      # (1) nu contribution: (1-q)^(k * i) * (nu *(t_k-t_k-1))^i * exp(-nu *(t_k-t_k-1)) / i!
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:102:24:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:102:61:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:110:17:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L110) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (1 - q)^(k[-length(k)] - births)                 # (1)
                ^
```
[R/mbd_pure_multiple_birth.R:161:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:185:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L185) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:187:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L187) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:188:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
  # - optimmethod = "simplex" (current default) or 'subplex' (default of previous versions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:193:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L193) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(namepars); #if you add more parameters to your model just change this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:194:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L194) *style:* **Lines should not be more than 80 characters.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars; #those are the parameters that you get if something goes sideways
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L237) *style:* **Lines should not be more than 80 characters.**
```r
      cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:240:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
        cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:244:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L244) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:249:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_pure_multiple_birth.R#L249) *style:* **Lines should not be more than 80 characters.**
```r
          cat("Optimization has not converged. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L92) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow = 1e6, 4)
      ^
```
[R/mbd_sim.R:101:11:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L101) *style:* **Variable or function name should be snake_case.**
```r
          deltaT <- stats::rexp(1, rate = total_rate)
          ^~~~~~
```
[R/mbd_sim.R:102:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
          outcome <- sample(c(-1, 1, 2), size = 1, prob = c(n_species * mu, n_species * lambda, nu))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:103:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
          delta_n <- -1 * (outcome == -1) + 1 * (outcome == 1) + (outcome == 2) * stats::rbinom(n = 1, size = n_species, prob = q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:113:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
            L[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:134:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L134) *style:* **Variable or function name should be snake_case.**
```r
    L <- L[(1:total_count), ]
    ^
```
[R/mbd_sim.R:142:35:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L142) *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:142:66:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L142) *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:144:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L144) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:144:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L144) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L145) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = FALSE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L145) *style:* **Variable or function name should be snake_case.**
```r
    births.full_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = FALSE), decreasing = TRUE)))
    ^~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L146) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L146) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:47:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L146) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
                                              ^
```
[R/mbd_sim.R:147:35:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L147) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multi_births_full_tree <- sum( duplicated(births.full_tree))
                                  ^
```
[R/mbd_sim.R:149:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L149) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:150:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check <- (multiple_births.reconstructed_tree >= minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:152:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L152) *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:154:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
  time_points <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:172:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L172) *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:179:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L179) *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:182:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L182) *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:184:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L184) *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:188:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L188) *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:189:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L189) *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:190:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L190) *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:195:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L195) *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:227:18:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L227) *style:* **Use <-, not =, for assignment.**
```r
      total_count=init_n_lineages
                 ^
```
[R/mbd_sim.R:227:18:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L227) *style:* **Put spaces around all infix operators.**
```r
      total_count=init_n_lineages
                ~^~
```
[R/mbd_sim.R:231:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L231) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow=1e6, 4)
      ^
```
[R/mbd_sim.R:231:26:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L231) *style:* **Put spaces around all infix operators.**
```r
      L <- matrix(0, nrow=1e6, 4)
                        ~^~
```
[R/mbd_sim.R:238:9:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L238) *style:* **Variable or function name should be snake_case.**
```r
        deltaT <- stats::rexp(1, rate = (lambda + n_species * mu))
        ^~~~~~
```
[R/mbd_sim.R:250:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
          L[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:252:50:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L252) *style:* **Put spaces around all infix operators.**
```r
          L[new_interval, 3] <- abs(new_interval)* sign(parents)
                                                ~^
```
[R/mbd_sim.R:254:44:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L254) *style:* **Put spaces around all infix operators.**
```r
          pool <- c(pool, abs(new_interval)* sign(parents))
                                          ~^
```
[R/mbd_sim.R:255:37:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L255) *style:* **Put spaces around all infix operators.**
```r
          total_count <- total_count+delta_n
                                   ~^~
```
[R/mbd_sim.R:259:51:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L259) *style:* **Put spaces around all infix operators.**
```r
            dead <- sample(pool, replace = F, size=1)
                                                 ~^~
```
[R/mbd_sim.R:264:28:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L264) *style:* **Put spaces around all infix operators.**
```r
          pool <- pool[pool!=dead]
                          ~^~~
```
[R/mbd_sim.R:268:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L268) *style:* **Variable or function name should be snake_case.**
```r
    L=L[(1:total_count), ]
    ^
```
[R/mbd_sim.R:268:6:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L268) *style:* **Use <-, not =, for assignment.**
```r
    L=L[(1:total_count), ]
     ^
```
[R/mbd_sim.R:268:6:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L268) *style:* **Put spaces around all infix operators.**
```r
    L=L[(1:total_count), ]
    ~^~
```
[R/mbd_sim.R:269:21:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L269) *style:* **Use <-, not =, for assignment.**
```r
    extinct_species = sum(L[, 4]!=-1)
                    ^
```
[R/mbd_sim.R:269:33:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L269) *style:* **Put spaces around all infix operators.**
```r
    extinct_species = sum(L[, 4]!=-1)
                               ~^~~
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L271) *style:* **Use <-, not =, for assignment.**
```r
    tips=length(L[, 4][L[, 4]==-1])
        ^
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[, 4][L[, 4]==-1])
       ~^~
```
[R/mbd_sim.R:271:30:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[, 4][L[, 4]==-1])
                            ~^~~
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L273) *style:* **Use <-, not =, for assignment.**
```r
    alive=L[L[, 4]==-1, ]
         ^
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[, 4]==-1, ]
        ~^~
```
[R/mbd_sim.R:273:19:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[, 4]==-1, ]
                 ~^~~
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L274) *style:* **Use <-, not =, for assignment.**
```r
    alive=matrix(alive, ncol=4)
         ^
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L274) *style:* **Put spaces around all infix operators.**
```r
    alive=matrix(alive, ncol=4)
        ~^~
```
[R/mbd_sim.R:274:29:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L274) *style:* **Put spaces around all infix operators.**
```r
    alive=matrix(alive, ncol=4)
                           ~^~
```
[R/mbd_sim.R:275:30:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L275) *style:* **Use <-, not =, for assignment.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                             ^
```
[R/mbd_sim.R:275:33:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                ^
```
[R/mbd_sim.R:275:41:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                        ^
```
[R/mbd_sim.R:275:67:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                                                 ~^~~
```
[R/mbd_sim.R:275:70:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                                                     ^
```
[R/mbd_sim.R:275:72:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                                                      ~^
```
[R/mbd_sim.R:278:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L278) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L278) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:30:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L278) *style:* **Use <-, not =, for assignment.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
                             ^
```
[R/mbd_sim.R:278:30:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L278) *style:* **Put spaces around all infix operators.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
                            ~^~
```
[R/mbd_sim.R:279:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L279) *style:* **Variable or function name should be snake_case.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
    ^~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L279) *style:* **Use <-, not =, for assignment.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
                    ^
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L279) *style:* **Put spaces around all infix operators.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
                   ~^~
```
[R/mbd_sim.R:280:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L280) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L280) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L280) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:40:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L280) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
                                       ^
```
[R/mbd_sim.R:280:46:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L280) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
                                             ^
```
[R/mbd_sim.R:281:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L281) *warning:* **local variable ‘multi_births_full_tree’ assigned but may not be used**
```r
    multi_births_full_tree = sum( duplicated(births.full_tree))
    ^~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:281:28:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L281) *style:* **Use <-, not =, for assignment.**
```r
    multi_births_full_tree = sum( duplicated(births.full_tree))
                           ^
```
[R/mbd_sim.R:281:34:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L281) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multi_births_full_tree = sum( duplicated(births.full_tree))
                                 ^
```
[R/mbd_sim.R:283:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L283) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:284:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L284) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:284:27:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L284) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
                          ^
```
[R/mbd_sim.R:284:64:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L284) *style:* **Put spaces around all infix operators.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
                                                              ~^~~
```
[R/mbd_sim.R:286:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L286) *style:* **Lines should not be more than 80 characters.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L286) *style:* **Use <-, not =, for assignment.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
             ^
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L286) *style:* **Put spaces around all infix operators.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
            ~^~
```
[R/mbd_sim.R:287:8:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L287) *style:* **Use <-, not =, for assignment.**
```r
  brts = -sort(abs(as.numeric(time_points)), decreasing = TRUE)
       ^
```
[R/mbd_sim.R:288:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L288) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(L, dropextinct = T)
      ^
```
[R/mbd_sim.R:289:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L289) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(L, dropextinct = F)
      ^
```
[R/mbd_sim.R:290:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L290) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tas)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:291:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L291) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tes)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:304:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L304) *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:305:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L305) *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:307:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L307) *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:308:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L308) *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:309:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L309) *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:314:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L314) *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:328:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L328) *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:338:3:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L338) *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:349:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L349) *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:349:45:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L349) *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:356:3:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L356) *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:359:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L359) *style:* **Lines should not be more than 80 characters.**
```r
                                tips_interval = tips_interval, minimum_multiple_births = minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:366:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L366) *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:368:3:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L368) *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:381:3:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L381) *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:386:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L386) *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:386:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L386) *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:392:34:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L392) *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_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                 ^
```
[R/mbd_sim.R:392:52:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L392) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(sim_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                                   ^
```
[R/mbd_sim.R:392:80:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L392) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (file.exists(sim_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                                                               ^
```
[R/mbd_sim.R:394:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L394) *style:* **Lines should not be more than 80 characters.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:394:42:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L394) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                         ^
```
[R/mbd_sim.R:394:60:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L394) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                                           ^
```
[R/mbd_sim.R:394:96:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L394) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                                                                ^
```
[R/mbd_sim.R:395:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L395) *style:* **Lines should not be more than 80 characters.**
```r
  save(sim_pars, soc, age, cond, max_sims, tips_interval, max_k, max_b, ext_species, additional_species, tips, minimum_multiple_births, file=general_settings_name)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:395:141:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L395) *style:* **Put spaces around all infix operators.**
```r
  save(sim_pars, soc, age, cond, max_sims, tips_interval, max_k, max_b, ext_species, additional_species, tips, minimum_multiple_births, file=general_settings_name)
                                                                                ~^~
```
[R/mbd_sim.R:396:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L396) *style:* **Lines should not be more than 80 characters.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:396:35:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L396) *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)){suppressWarnings( file.remove(sim_trees_name))}
                                  ^
```
[R/mbd_sim.R:396:53:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L396) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                                    ^
```
[R/mbd_sim.R:396:82:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_sim.R#L396) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                                                                ^
```
[R/mbd_utils.R:20:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/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/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/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:21:26:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/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)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                         ^
```
[R/mbd_utils.R:21:41:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L21) *style:* **Use <-, not =, for assignment.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                        ^
```
[R/mbd_utils.R:21:41:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L21) *style:* **Put spaces around all infix operators.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                       ~^~
```
[R/mbd_utils.R:21:50:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                 ^
```
[R/mbd_utils.R:21:55:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/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)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                      ^
```
[R/mbd_utils.R:21:70:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L21) *style:* **Use <-, not =, for assignment.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                     ^
```
[R/mbd_utils.R:21:70:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L21) *style:* **Put spaces around all infix operators.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                    ~^~
```
[R/mbd_utils.R:21:80:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                               ^
```
[R/mbd_utils.R:24:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:24:43:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L24) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                          ^
```
[R/mbd_utils.R:24:69:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L24) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                                                    ^
```
[R/mbd_utils.R:25:55:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L25) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name <- "blue"; truevalues_color_name = "red";
                                                      ^
```
[R/mbd_utils.R:28:27:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L28) *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:28:28:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
  for (idpar in 1:n_pars) {
                           ^
```
[R/mbd_utils.R:31:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L31) *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:31:28:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  medians_string <- paste0( "MLE Medians (", medians_color_name, ") = (", paste(signif(medians, 2), sep = "''", collapse = ", "), ")")
                           ^
```
[R/mbd_utils.R:32:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L32) *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:32:31:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L32) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  truevalues_string <- paste0( "True Values (", truevalues_color_name, ") = (", paste(signif(sim_pars, 2), sep = "''", collapse = ", "), ")")
                              ^
```
[R/mbd_utils.R:45:29:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L45) *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:46:5:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L46) *style:* **Variable or function name should be snake_case.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
    ^~~~~~~~~~
```
[R/mbd_utils.R:46:16:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L46) *style:* **Use <-, not =, for assignment.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
               ^
```
[R/mbd_utils.R:47:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L47) *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:47:33:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L47) *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:47:72:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L47) *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:50:55:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
      graphics::hist((good.results[, i]), main = NULL,
                                                      ^
```
[R/mbd_utils.R:58:47:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L58) *style:* **Trailing whitespace is superfluous.**
```r
        good.results[, i] ~ good.results[, j],
                                              ^
```
[R/mbd_utils.R:59:29:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
        xlab = par_names[j],
                            ^
```
[R/mbd_utils.R:60:29:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L60) *style:* **Trailing whitespace is superfluous.**
```r
        ylab = par_names[i],
                            ^
```
[R/mbd_utils.R:61:19:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L61) *style:* **Trailing whitespace is superfluous.**
```r
        cex = 0.3,
                  ^
```
[R/mbd_utils.R:64:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L64) *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:65:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L65) *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:68:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:68:27:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L68) *style:* **Variable or function name should be snake_case.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                          ^~~~~~~~~~
```
[R/mbd_utils.R:68:37:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L68) *style:* **Put spaces around all infix operators.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                   ~^~~
```
[R/mbd_utils.R:68:39:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                      ^
```
[R/mbd_utils.R:68:115:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L68) *style:* **Only use double-quotes.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                                                                ^~
```
[R/mbd_utils.R:68:127:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L68) *style:* **Put spaces around all infix operators.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                                                                ~^~
```
[R/mbd_utils.R:79:31:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L79) *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:80:7:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L80) *style:* **Variable or function name should be snake_case.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
      ^~~~~~~~~~
```
[R/mbd_utils.R:80:18:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L80) *style:* **Use <-, not =, for assignment.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
                 ^
```
[R/mbd_utils.R:81:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L81) *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:81:35:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L81) *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:81:74:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L81) *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:84:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L84) *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:89:49:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
          good.results[, i] ~ good.results[, j],
                                                ^
```
[R/mbd_utils.R:90:31:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L90) *style:* **Trailing whitespace is superfluous.**
```r
          xlab = par_names[j],
                              ^
```
[R/mbd_utils.R:91:31:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
          ylab = par_names[i],
                              ^
```
[R/mbd_utils.R:92:21:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L92) *style:* **Trailing whitespace is superfluous.**
```r
          cex = 0.3,
                    ^
```
[R/mbd_utils.R:96:27:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L96) *style:* **Trailing whitespace is superfluous.**
```r
          x = sim_pars[j],
                          ^
```
[R/mbd_utils.R:97:27:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L97) *style:* **Trailing whitespace is superfluous.**
```r
          y = sim_pars[i],
                          ^
```
[R/mbd_utils.R:98:34:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
          col = truevalues_color,
                                 ^
```
[R/mbd_utils.R:99:20:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L99) *style:* **Trailing whitespace is superfluous.**
```r
          pch = 10,
                   ^
```
[R/mbd_utils.R:103:26:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L103) *style:* **Trailing whitespace is superfluous.**
```r
          x = medians[j],
                         ^
```
[R/mbd_utils.R:104:26:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L104) *style:* **Trailing whitespace is superfluous.**
```r
          y = medians[i],
                         ^
```
[R/mbd_utils.R:105:31:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L105) *style:* **Trailing whitespace is superfluous.**
```r
          col = medians_color,
                              ^
```
[R/mbd_utils.R:106:20:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L106) *style:* **Trailing whitespace is superfluous.**
```r
          pch = 10,
                   ^
```
[R/mbd_utils.R:125:1:](https://github.com/Giappo/mbd/blob/ca16ad340301b7f4a4d426c16c08d0b4bc1937bb/R/mbd_utils.R#L125) *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)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


visit https://alishaalihashim.github.io/weather-app/


I think you can also type type :so% in normal mode to "source" the file - meaning execute the commands in the file. That way you don't need to save, close and reopen the .vimrc.


Отличная работа.


Can you share your Customer model code, your Details method in customer controller, and your Customers database table? It seems like your the Customer you selected has a null value for Id, but Id can't be null, it must contain a value of type int


Now cannot deploy because all the allocated instances are in use.
You can either [upgrade](https://zeit.co/account/plan) your plan or [down scale](https://zeit.co/docs/getting-started/scaling) existing [deployments](https://zeit.co/dashboard/deployments).


# 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)|


Shouldn't this line say "Fragment implementation <implementation> does not implement <it>". Looks like the parameters are interchanged.
I am encountering this error and when I read it, it was "Fragment implementation net.vj.spring.jpa.PeopleRepository does not implement net.vj.spring.jpa.PeopleRepositoryImpl$$EnhancerBySpringCGLIB$$11459bcf!" which is weird.


@andrew-s the sooner the better tbh, since we'll need to go through the whole review cycle on the PR - appreciate its pushing the urgency down onto you but it would be very much appreciated.


update


Done, thank you for the tip.