[R/mbd_pure_multiple_birth.R:46:60:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:100:65:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
      # (1) nu contribution: (1-q)^(k * i) * (nu *(t_k-t_k-1))^i
                                                                ^
```
[R/mbd_pure_multiple_birth.R:103:60:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L103) *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:111:17:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L111) *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:163:73:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L163) *style:* **Trailing whitespace is superfluous.**
```r
      "There are parameter values used which cause numerical problems:",
                                                                        ^
```
[R/mbd_pure_multiple_birth.R:189:57:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L189) *style:* **Trailing whitespace is superfluous.**
```r
  # - changeloglikifnoconv = if T the loglik will be set
                                                        ^
```
[R/mbd_pure_multiple_birth.R:192:57:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L192) *style:* **Trailing whitespace is superfluous.**
```r
  # - changeloglikifnoconv = if T the loglik will be set
                                                        ^
```
[R/mbd_pure_multiple_birth.R:194:61:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L194) *style:* **Trailing whitespace is superfluous.**
```r
  # - optimmethod = "simplex" (current default) or 'subplex'
                                                            ^
```
[R/mbd_pure_multiple_birth.R:202:59:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L202) *style:* **Trailing whitespace is superfluous.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars
                                                          ^
```
[R/mbd_pure_multiple_birth.R:246:65:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L246) *style:* **Trailing whitespace is superfluous.**
```r
        "The loglikelihood for the initial parameter values is",
                                                                ^
```
[R/mbd_pure_multiple_birth.R:247:20:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L247) *style:* **Trailing whitespace is superfluous.**
```r
        initloglik,
                   ^
```
[R/mbd_pure_multiple_birth.R:271:50:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_pure_multiple_birth.R#L271) *style:* **Trailing whitespace is superfluous.**
```r
              "Optimization has not converged. ",
                                                 ^
```
[R/mbd_sim.R:101:11:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
            l_matrix[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:142:65:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L144) *style:* **Lines should not be more than 80 characters.**
```r
    births_rec_tree <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L145) *style:* **Lines should not be more than 80 characters.**
```r
    births_full_tree <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = FALSE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:149:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check <- (multiple_births_rec_tree >= minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:152:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
  time_points <- unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:172:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L227) *style:* **Put spaces around all infix operators.**
```r
      total_count=init_n_lineages
                ~^~
```
[R/mbd_sim.R:231:33:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L231) *style:* **Put spaces around all infix operators.**
```r
      l_matrix <- matrix(0, nrow=1e6, 4)
                               ~^~
```
[R/mbd_sim.R:238:9:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
          l_matrix[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:252:57:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L252) *style:* **Put spaces around all infix operators.**
```r
          l_matrix[new_interval, 3] <- abs(new_interval)* sign(parents)
                                                       ~^
```
[R/mbd_sim.R:254:44:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L264) *style:* **Put spaces around all infix operators.**
```r
          pool <- pool[pool!=dead]
                          ~^~~
```
[R/mbd_sim.R:268:13:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L268) *style:* **Use <-, not =, for assignment.**
```r
    l_matrix=l_matrix[(1:total_count), ]
            ^
```
[R/mbd_sim.R:268:13:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L268) *style:* **Put spaces around all infix operators.**
```r
    l_matrix=l_matrix[(1:total_count), ]
           ~^~
```
[R/mbd_sim.R:269:21:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L269) *style:* **Use <-, not =, for assignment.**
```r
    extinct_species = sum(l_matrix[, 4]!=-1)
                    ^
```
[R/mbd_sim.R:269:40:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L269) *style:* **Put spaces around all infix operators.**
```r
    extinct_species = sum(l_matrix[, 4]!=-1)
                                      ~^~~
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L271) *style:* **Use <-, not =, for assignment.**
```r
    tips=length(l_matrix[, 4][l_matrix[, 4]==-1])
        ^
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(l_matrix[, 4][l_matrix[, 4]==-1])
       ~^~
```
[R/mbd_sim.R:271:44:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(l_matrix[, 4][l_matrix[, 4]==-1])
                                          ~^~~
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L273) *style:* **Use <-, not =, for assignment.**
```r
    alive=l_matrix[l_matrix[, 4]==-1, ]
         ^
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=l_matrix[l_matrix[, 4]==-1, ]
        ~^~
```
[R/mbd_sim.R:273:33:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=l_matrix[l_matrix[, 4]==-1, ]
                               ~^~~
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:275:65:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:275:68:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:275:70:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L278) *style:* **Lines should not be more than 80 characters.**
```r
    births_rec_tree=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:20:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L278) *style:* **Use <-, not =, for assignment.**
```r
    births_rec_tree=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
                   ^
```
[R/mbd_sim.R:278:20:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L278) *style:* **Put spaces around all infix operators.**
```r
    births_rec_tree=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
                  ~^~
```
[R/mbd_sim.R:279:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
    births_full_tree=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = F), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L279) *style:* **Use <-, not =, for assignment.**
```r
    births_full_tree=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = F), decreasing = T)))
                    ^
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L279) *style:* **Put spaces around all infix operators.**
```r
    births_full_tree=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = F), decreasing = T)))
                   ~^~
```
[R/mbd_sim.R:280:30:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L280) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births_rec_tree = sum(duplicated(births_rec_tree))
                             ^
```
[R/mbd_sim.R:281:5:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L281) *style:* **Use <-, not =, for assignment.**
```r
    multi_births_full_tree = sum(duplicated(births_full_tree))
                           ^
```
[R/mbd_sim.R:283:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:284:27:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L284) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births_check = (multiple_births_rec_tree>=minimum_multiple_births)
                          ^
```
[R/mbd_sim.R:284:54:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L284) *style:* **Put spaces around all infix operators.**
```r
    multiple_births_check = (multiple_births_rec_tree>=minimum_multiple_births)
                                                    ~^~~
```
[R/mbd_sim.R:286:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L286) *style:* **Lines should not be more than 80 characters.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L286) *style:* **Use <-, not =, for assignment.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
             ^
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L286) *style:* **Put spaces around all infix operators.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(l_matrix, dropextinct = T), decreasing = T)))
            ~^~
```
[R/mbd_sim.R:287:8:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L288) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(l_matrix, dropextinct = T)
      ^
```
[R/mbd_sim.R:289:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_sim.R#L289) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(l_matrix, dropextinct = F)
      ^
```
[R/mbd_sim.R:290:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:392:79:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:394:95:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:396:81:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L25) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name <- "blue"; truevalues_color_name = "red";
                                                      ^
```
[R/mbd_utils.R:31:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:32:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:45:29:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:64:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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/a1788814c4829ab6a83a81c50850ef29bd1e7318/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:125:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/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)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:125:31:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L125) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:128:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:128:27:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L128) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                          ^
```
[R/mbd_utils.R:128:104:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L128) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                                                                                ^
```
[R/mbd_utils.R:134:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L134) *warning:* **local variable ‘out’ assigned but may not be used**
```r
  out <- percentiles
  ^~~
```
[R/mbd_utils.R:141:19:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L141) *style:* **Use <-, not =, for assignment.**
```r
heatmap2dataframe = function(
                  ^
```
[R/mbd_utils.R:147:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L147) *style:* **Variable or function name should be snake_case.**
```r
  heatmap.name="HeatMap"
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:150:46:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L150) *style:* **Commas should always have a space after.**
```r
  df <- data.frame(expand.grid(x = x, y = y),HeatMap = matrix_2)
                                             ^
```
[R/mbd_utils.R:157:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
#' Converts branching times to "time intervals between branching times" and "birth at nodes" vectors
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:167:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L167) *style:* **Lines should not be more than 80 characters.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:167:54:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L167) *style:* **Commas should always have a space after.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:167:54:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L167) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:169:29:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L169) *style:* **Put spaces around all infix operators.**
```r
  out <- list(time_intervals=time_intervals, births=births)
                           ~^~
```
[R/mbd_utils.R:169:52:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L169) *style:* **Put spaces around all infix operators.**
```r
  out <- list(time_intervals=time_intervals, births=births)
                                                  ~^~
```
[R/mbd_utils.R:189:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L189) *style:* **Variable or function name should be snake_case.**
```r
  create_mbd_P_matrix <- function(
  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:193:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L193) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_utils.R:194:5:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L194) *warning:* **local variable ‘lambda’ assigned but may not be used**
```r
    lambda <- pars[1]
    ^~~~~~
```
[R/mbd_utils.R:195:5:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L195) *warning:* **local variable ‘mu’ assigned but may not be used**
```r
    mu <- pars[2]
    ^~
```
[R/mbd_utils.R:196:5:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L196) *warning:* **local variable ‘q’ assigned but may not be used**
```r
    q <- pars[3]
    ^
```
[R/mbd_utils.R:197:5:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L197) *warning:* **local variable ‘nvec’ assigned but may not be used**
```r
    nvec <- 0:max_number_of_species
    ^~~~
```
[R/mbd_utils.R:204:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L204) *style:* **Lines should not be more than 80 characters.**
```r
    # my_matrix <- lambda * hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:204:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L204) *style:* **Commented code should be removed.**
```r
    # my_matrix <- lambda * hyperA::hyperA(N = max_number_of_species, k = 0, q = q)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:205:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L205) *style:* **Lines should not be more than 80 characters.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu * nvec[2:(max_number_of_species+1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:205:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L205) *style:* **Commented code should be removed.**
```r
    # my_matrix[row(my_matrix) == col(my_matrix) - 1] = mu * nvec[2:(max_number_of_species+1)]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:206:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L206) *style:* **Commented code should be removed.**
```r
    # diag(my_matrix) = - mu * nvec - lambda * (1 - (1 - q) ^ nvec)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:207:7:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L207) *style:* **Commented code should be removed.**
```r
    # return(my_matrix)
      ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:211:15:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L211) *style:* **Commas should always have a space after.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:211:15:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  v0 <- rep(0,(max_number_of_species + 1))
              ^
```
[R/mbd_utils.R:227:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L227) *style:* **Lines should not be more than 80 characters.**
```r
    print(paste("Sim pars are:", test_parameters[1], test_parameters[2], test_parameters[3], ". Average n is", nmedio, "with std:", std))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:246:11:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L246) *style:* **Use <-, not =, for assignment.**
```r
  matrix_t=t(matrix[nrow(matrix):1, 1:ncol(matrix)])
          ^
```
[R/mbd_utils.R:246:11:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L246) *style:* **Put spaces around all infix operators.**
```r
  matrix_t=t(matrix[nrow(matrix):1, 1:ncol(matrix)])
         ~^~
```
[R/mbd_utils.R:247:12:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L247) *style:* **Put spaces around all infix operators.**
```r
  if (logs ==1 ) {
           ^~~
```
[R/mbd_utils.R:247:15:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L247) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (logs ==1 ) {
              ^
```
[R/mbd_utils.R:248:5:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L248) *style:* **Commented code should be removed.**
```r
  # image(log(matrix_t))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:249:39:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L249) *style:* **Put spaces around all infix operators.**
```r
    graphics::image(log(matrix_t), col=rev(colormap),...)
                                     ~^~
```
[R/mbd_utils.R:249:54:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L249) *style:* **Commas should always have a space after.**
```r
    graphics::image(log(matrix_t), col=rev(colormap),...)
                                                     ^
```
[R/mbd_utils.R:250:8:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L250) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  }else{graphics::image(matrix_t)}
       ^
```
[R/mbd_utils.R:250:34:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L250) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  }else{graphics::image(matrix_t)}
                                 ^
```
[R/mbd_utils.R:274:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L274) *style:* **Variable or function name should be snake_case.**
```r
  lX <- x
  ^~
```
[R/mbd_utils.R:275:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L275) *style:* **Variable or function name should be snake_case.**
```r
  lY <- y
  ^~
```
[R/mbd_utils.R:276:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L276) *style:* **Variable or function name should be snake_case.**
```r
  pretty_X.at	<-	pretty(range(lX), n = x_splits)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:277:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L277) *style:* **Variable or function name should be snake_case.**
```r
  pretty_X.lab	<-	round(pretty_X.at, 2)
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:278:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L278) *style:* **Variable or function name should be snake_case.**
```r
  pretty_Y.at	<-	pretty(range(lY), n = y_splits)
  ^~~~~~~~~~~
```
[R/mbd_utils.R:279:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L279) *style:* **Variable or function name should be snake_case.**
```r
  pretty_Y.lab	<-	round(pretty_Y.at, 2)
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:281:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L281) *style:* **Lines should not be more than 80 characters.**
```r
  jet.colors <- grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:281:3:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L281) *style:* **Variable or function name should be snake_case.**
```r
  jet.colors <- grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
  ^~~~~~~~~~
```
[R/mbd_utils.R:319:38:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L319) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (length(na_components) > 0) { cat("NA component are:", na_components)}
                                     ^
```
[R/mbd_utils.R:319:79:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L319) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      if (length(na_components) > 0) { cat("NA component are:", na_components)}
                                                                              ^
```
[R/mbd_utils.R:320:1:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L320) *style:* **Lines should not be more than 80 characters.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:320:39:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L320) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
                                      ^
```
[R/mbd_utils.R:320:82:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L320) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      if (length(nan_components) > 0) { cat("NaN component are:", nan_components)}
                                                                                ^
```
[R/mbd_utils.R:325:6:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L325) *style:* **Commented code should be removed.**
```r
    #negatives <- v[v < 0]
     ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:326:6:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L326) *style:* **Commented code should be removed.**
```r
    #maximum <- max(v)
     ^~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:345:9:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L345) *style:* **Use <-, not =, for assignment.**
```r
  Atime1=0;Atime2=0;
        ^
```
[R/mbd_utils.R:345:9:](https://github.com/Giappo/mbd/blob/a1788814c4829ab6a83a81c50850ef29bd1e7318/R/mbd_utils.R#L345) *style:* **Put spaces around all infix operators.**
```r
  Atime1=0;Atime2=0;
       ~^~
```


Successfully aliased the URL <https://lingonsaft-hacktober-hrlxngnyua.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Successfully aliased the URL <https://lingonsaft-hacktober-yeohsoabry.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


@nebilsolomon1  what do you think about that


Aliasing was ignored due to a new commit existing for this branch, which will be aliased instead.


Aprobado


i didnt like this  2cb1f91


Successfully aliased the URL <https://lingonsaft-hacktober-pzskkczbii.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


merging the master


Thanks for pointing that out. Fixed it in https://github.com/adhintz/openpilot/commit/e7f4a94f0aee07ce46cc1dc595af79bebe60b9eb

I think I still have some status message and/or fingerprint to improve.


@eharkins Nice breakdown into style functions here :thumbsup:


Yeh, don't worry too much about the heli specific stuff. This is part of the "what the F" has he done here. I am initially going through to make things consistent. Then I will look at what doesn't work for heli code. If we can deal with the heli requirements we can remove the heli file completly. if not then we can customize the heli file as we see fit.


Successfully aliased the URL <https://hersonhn-iwlcjjwjpg.now.sh> to the following aliases.

* https://www.herson.hn
* https://herson.hn


Task #31: Added upload button to upload image is included in this commit.


bien


I have a question.
`scroll in verticalDirection`
Is this code works? (or just sudo code?)

For example, I try to below code in chrome inspector and always return false.
`'a' in ['a', 'b', 'c']`

Or you mean below method?
`['a', 'b', 'c'].indexOf('a') > -1 && 'vertical'`


Successfully aliased the URL <https://lingonsaft-hacktober-jttvtsnink.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Bangumi url can be used at ANY type, not only in the Anime category.


Very short scope.
You should add similar features as provided by the windows task manager such as information shown in processes tab, performance tab in the form of graphs.
Also, your task manager should provide the detailed information of the selected process including the data section size, stack size, current heap size, list of open files, and etc.


Ok... what's the reference repository for .info files?

https://github.com/libretro/libretro-super/tree/master/dist/info

Ubuntu & Debian have a package for .info files, what repo should I follow?

Shouldn't one be a submodule to another?


It seems that

```ruby
# Get fluentd tag
tag = chunk.metadata.tag
```

needs to tag in chunk.

Otherwise, we can change these lines:

```diff
  def format(tag, time, record)
+    [tag, time, record].to_msgpack
-    [time, record].to_msgpack
  end
  #...
  def write(chunk)
       documents = []

-      # Get fluentd tag
-      tag = chunk.metadata.tag
```


Successfully aliased the URL <https://lingonsaft-hacktober-pywtlafcji.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


# Koutsie was here


Successfully aliased the URL <https://lingonsaft-hacktober-pljhaxbmhv.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Successfully aliased the URL <https://lingonsaft-hacktober-hsmmcwyxym.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


OMG, this takes forever 👎


@eharkins For commented out code like this which might be useful for debugging, I like to add a comment line like "debug width signal" (e.g.)


Successfully aliased the URL <https://lingonsaft-hacktober-ppjjkantan.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Checkmarx scan results 02 Oct 2018 08:46 UTC +03:00

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0
0
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0
0
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0
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0
0

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Commit ID	Owner

a23cad998261c81bf63aa21ac681a2e8b5303e7c	@web-flow


Successfully aliased the URL <https://lingonsaft-hacktober-bhwscskqvd.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


@rafeca I noticed you did not include the change that removes the global regenerator polyfill. I think this might cause it to get included it twice in the bundle when using regenerator runtime. I think the ideal solution would be to remove it from InitializeCore.js and include it as a polyfill at fb (in the internal rn-get-polyfills.js that has the babelHelpers polyfill).

Would that work?


Successfully aliased the URL <https://lingonsaft-hacktober-lgserqgqib.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


merge


Moved to #197.


Sorry for the inconvenience. The right expression is..
```
verticalDirection.includes(scroll),
['a', 'b', 'c'].includes('a')
```
I updated my branch. Please check https://github.com/enactjs/enact/commit/d23a6839837e3dc4570504a44574371fa6ea6858 commit.


Copy of this build can be found at
https://www.mewbuilds.com/build/b82be1bbd28013a0d2019a51e8df044d89af1758/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmcovKMwToHxSr8KWwtrmcv3KYdNH2vJryiCLjtc9tJamS


Copy of this build can be found at
https://www.mewbuilds.com/build/ee2e2c37ce58822d5ea68a436669318c59903c00/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmaFbtfk9gxwX4wv8RfPSPZHThSAdkRs8fzEFw76doarg2


@eharkins Great to see all the red in visualization.js!


The full comparison between your branch and my branch is...
https://github.com/enactjs/enact/compare/ENYO-5614-changgi2...ENYO-5614-ybsung


Criação das Operações de Arquivos


![](https://github.trello.services/images/mini-trello-icon.png) [As User (all) i can click notification to go that's page](https://trello.com/c/ieu5sz0d/105-as-user-all-i-can-click-notification-to-go-thats-page)


Oh, I got it. Thanks~


Successfully aliased the URL <https://lingonsaft-hacktober-bnfjgrdfwy.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Makes sense. :)


가운데글자가져오기/가운데글자가져오기.html

For문이 필요한가?


오케이 여기 이 부분 수정했음 컴펌 바람


Just noticed the builder is called with the withMasterSecretRequirement twice. I guess it's a copy paste issue.


split 함수 제거하고 substring 함수로 변경해보기
https://www.w3schools.com/jsref/jsref_substring.asp