[R/mbd_ml.R:85:31:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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:40:42:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_pure_multiple_birth.R#L40) *style:* **Put spaces around all infix operators.**
```r
      poisson_term <- stats::dpois(i, nu *time_intervals[t], log = FALSE)[
                                         ^~
```
[R/mbd_pure_multiple_birth.R:41:28:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_pure_multiple_birth.R#L41) *style:* **Put spaces around all infix operators.**
```r
        stats::dpois(i, nu *time_intervals[t], log = FALSE) != 0]
                           ^~
```
[R/mbd_pure_multiple_birth.R:42:34:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_pure_multiple_birth.R#L42) *style:* **Put spaces around all infix operators.**
```r
      ii <- i[stats::dpois(i, nu *time_intervals[t], log = FALSE) != 0 ]
                                 ^~
```
[R/mbd_pure_multiple_birth.R:42:71:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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:42:62:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L42) *style:* **Put spaces around all infix operators.**
```r
  grDevices::pdf(file = paste(path, "/", pdfname, ".pdf", sep=''));#plot.new();
                                                            ~^~
```
[R/mbd_utils.R:42:63:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L42) *style:* **Only use double-quotes.**
```r
  grDevices::pdf(file = paste(path, "/", pdfname, ".pdf", sep=''));#plot.new();
                                                              ^~
```
[R/mbd_utils.R:42:69:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L42) *style:* **Commented code should be removed.**
```r
  grDevices::pdf(file = paste(path, "/", pdfname, ".pdf", sep=''));#plot.new();
                                                                    ^~~~~~~~~~~
```
[R/mbd_utils.R:45:29:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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/54077c0c53af007289a97cc959fa7790c31510b6/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:46:61:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L46) *style:* **Put spaces around all infix operators.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j]<axislimits[j]
                                                           ~^~
```
[R/mbd_utils.R:47:1:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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:47:27:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L47) *style:* **Put spaces around all infix operators.**
```r
    ifelse(any(good.lines)>0, good.results <- results[good.lines, ], good.results <- results)
                         ~^~
```
[R/mbd_utils.R:47:31:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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:47:70:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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:49:1:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
    if ( i== j){graphics::hist((good.results[, i]), main=NULL, xlab = paste(par_names[i]), breaks = 15)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:49:9:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L49) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( i== j){graphics::hist((good.results[, i]), main=NULL, xlab = paste(par_names[i]), breaks = 15)
        ^
```
[R/mbd_utils.R:49:11:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L49) *style:* **Put spaces around all infix operators.**
```r
    if ( i== j){graphics::hist((good.results[, i]), main=NULL, xlab = paste(par_names[i]), breaks = 15)
         ~^
```
[R/mbd_utils.R:49:16:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/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
    if ( i== j){graphics::hist((good.results[, i]), main=NULL, xlab = paste(par_names[i]), breaks = 15)
               ^
```
[R/mbd_utils.R:49:57:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L49) *style:* **Put spaces around all infix operators.**
```r
    if ( i== j){graphics::hist((good.results[, i]), main=NULL, xlab = paste(par_names[i]), breaks = 15)
                                                       ~^~
```
[R/mbd_utils.R:53:1:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
    else{graphics::plot(good.results[, i]~good.results[, j], xlab = par_names[j], ylab = par_names[i], cex=0.3, col=points_color);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:53:9:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L53) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    else{graphics::plot(good.results[, i]~good.results[, j], xlab = par_names[j], ylab = par_names[i], cex=0.3, col=points_color);
        ^
```
[R/mbd_utils.R:53:107:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L53) *style:* **Put spaces around all infix operators.**
```r
    else{graphics::plot(good.results[, i]~good.results[, j], xlab = par_names[j], ylab = par_names[i], cex=0.3, col=points_color);
                                                                                ~^~
```
[R/mbd_utils.R:53:116:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L53) *style:* **Put spaces around all infix operators.**
```r
    else{graphics::plot(good.results[, i]~good.results[, j], xlab = par_names[j], ylab = par_names[i], cex=0.3, col=points_color);
                                                                                ~^~
```
[R/mbd_utils.R:54:1:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L54) *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:55:1:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L55) *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:58:1:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:23:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:24:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:25:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:35:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:37:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:113:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:58:125:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L58) *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:61:13:](https://github.com/Giappo/mbd/blob/54077c0c53af007289a97cc959fa7790c31510b6/R/mbd_utils.R#L61) *style:* **Put spaces around all infix operators.**
```r
  if (openit==1){
           ~^~~
```


Aliasing failed with the following error:

~~~
Error! The alias nextjsorg.now.sh is a deployment URL or it's in use by a different team.
~~~


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

I updated the Github team because of this commit.

- @dbast was added to this feedstock maintenance team.

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

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

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


修正しました


hi all,
I am receiving the following error when I click the customer name.

if I write the link manually like this, there is no problem and I see the name of customer;
http://localhost:61784/Customers/Details/1

### link becomes as:
http://localhost:61784/Customers/Details?Length=9

### error message:
The parameters dictionary contains a null entry for parameter 'id' of non-nullable type 'System.Int32' for method 'System.Web.Mvc.ActionResult Details(Int32)' in 'Vidly.Controllers.CustomersController'. An optional parameter must be a reference type, a nullable type, or be declared as an optional parameter.
Parameter name: parameters


Sorry, I didn't realise this was a rustfmt-compatible code-base!

You should put a (possibly empty, if you're happy with the defaults) `rustfmt.toml` in your project root to advertise that you use auto-formatting.