[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;
       ~^~
```


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Indeed it is!


ja


editing main class


Beim Entwickeln von neuen Tests z.B. den Test "C001_04_AddNews" möchte ich nur diesen ausführen und testen. Dazu brauche ich aber einen bestehen Kurs.
"C001_02_CreateCourse" wird in diesem Fall ja nicht ausgeführt und ich habe keinen aktuellen Kurskontext.
Somit nehme ich einfach einen Fallbackkurs, den es bereits sicherlich gibt.


Теперь эту проверку можно заменить на
`if next_station` т.е если у нас есть следующая станция, то мы можем двигаться вперед. Будет более читабельно. Если нет, next_station вернет nil и условие не выполнится


> book of stories

Do we use this term anywhere else?


creating main lca code


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Fijate que en el constructor no se le asigna el tablero entonces puede que el tablero tenga null en principio y falla


Some new Functionality gets added into the code


It would be easy to add `event_to_state_groups` to the list of tables there

could you not provide the script somewhere else then?


@opoto oops, thanks for digging in to this and giving me a heads up.

I'm not using this module myself and haven't been for quite a while (which is the reason I haven't discovered this myself), so this will not end up on the top of my todo. Feel free to submit a PR, and I will happily merge it (and maybe make a new release...)


Yo pensaba en agregar una cabeza en la nueva posicion y sacar la cola de la vibora. Sin tocar todo el cuerpo de la vibora, solo las puntas.


![](https://github.trello.services/images/mini-trello-icon.png) [SplashScreen](https://trello.com/c/J8hC737K/24-splashscreen)


What do you think about this project? Do you like it?


erledigt.


Niltze, @fplanque!

In b2evo-6.10.2 dashboard(s) there is an update to 6.10.3 notice. However, **bower** does not fetch that version and b2evolution.net site has not been updated to download b2evo 6.10.3

Thanks!


This commit allows adding a walkthrough step by adding a ref to a component, and not having to wrap your component in <CopilotStep>. In the ref callback of your component you need to call the registerStep method of copilot with an additional size prop.


@aklenik A MERGE fájl minden csapatot többször is tartalmaz, elvileg csapatonként 576 sor lenne az elvárt, de jelenleg a saját csapatomat kb 5-ször ennyiszer látom.


![](https://github.trello.services/images/mini-trello-icon.png) [Rewrite AR Fragment to Kotlin](https://trello.com/c/SFMa5W38/19-rewrite-ar-fragment-to-kotlin)


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `oaktoken` (in env: `TOKEN)`
* `mongourl` (in env: `MONGO_URL)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


Hey @madssoegaard

Sorry for asking another question on such a simple topic but me & @lptn understood your request differently.

(1) Did you want the offboarding completely gone from the `handbook` repository so that the checklist is not shown publicly? ...or
(2) Did you want to keep the offboarding checklist on the `handbook` repository but now show it on the table of contents? The checklist will still be public so that anyone who wants to read it can read it but there will be no links from the table of contents.

I thought you wanted (1) and that's why I removed it completely. @lptn thought you wanted (2). @lptn  prefers (2). I prefer (2) as well -- and I believe we should even show it in our table of contents. Offboarding is a natural process of employment and the way how elegantly we are doing it adds to our value. We should not be ashamed of showing it off to outside world.

On the other hand, I understand your concerns on IDF's first impression.

Can you please briefly pick (1) or (2)?


@null warum?


![](https://github.trello.services/images/mini-trello-icon.png) [AR Functionality](https://trello.com/c/DshiDGT2/14-ar-functionality)


![](https://github.trello.services/images/mini-trello-icon.png) [Technological Demo for AR video play](https://trello.com/c/hBzcV6zJ/10-technological-demo-for-ar-video-play)


this is a commit comment


看不懂


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@critsec you might want to file an MR for this, although since the extension isn't defined yet, it's not a big deal yet.


I think the cache is written to while passivating  a stateful bean comprising an extended scoped entity manager. I think the bean is transitioning to / out of a TRANSACTION_NEW EJB method. It seems it wants to serialize some entities managed by the entities, and that it invalidly tries to initialize some uninitialized proxies or persistent collections while doing so, or stumbling upon a concurrentmodificationerror of some sort, hence I am asking whether any of these changes are relevant. It definitely seems to be a bug in Hibernate or Wildflys recent Hibernate integration. I will check  whether the issue is present under 5.3.x as well.
Thanks for your detailed comment!


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The problem was that  both $suggestionResult and $productResult are numerically indexed arrays.This mean that plus operator will always keep items from first array and ignore items from the second array (taking into account they have the same length). I think array_merge should be used in this case. Also, I've made product results appear first, because I assume this is the desired behavior (they appear first in the feed as well as in Magento configuration section).


@Ecologeeks il manque la reinitialisation de la propriete $this->currentView


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Лишние отступы


@Ecologeeks
Je suppose que cette action est amené à faire quelque chose?

Si aucune ecriture en Bdd n'est necessaire, il suffit simplement de ne pas creer d'action et le rendu de la vue sera gérée


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Ah, yes, good point. I've gone ahead and updated this statement.


Het is wel de bedoeling dat er een default is voor de `checkout_name`?


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)


Can use TAR_NAME=`basename ${URL}` to get the actual tar name. (See the changes in script-improvements branch)


Welk mechanisme wordt er gebruikt voor de authenticatie?

(Zelf zat ik me af te vragen of ssh deploy keys niet eens een goed idee zouden zijn. Maar ik weet nog niet hoe handig die zijn in het gebruik.)


check


Definitly not right, see 18d740539f16b374228716e6b009a7590a59bb6b


Strangely enough, when running scripts/checkpatch.pl against a patch file it didn't pick this up. Anyway, I updated it so that it aligns with the kernel coding style. Thanks!


1. надо выделить numeric_limits как код, вот так `std::numeric_limits`. и привести ссылку на cppreference


крутое уточнение! я бы не догадался его добавить.
-1 выделить как код `-1`


надо еще уточнить, что стандартными функциями пользоваться нельзя


This is the sample github test repo


Published the change.

P.S.
2nd latest solution[i.e. backup of server version before this change
(To rollback the change in case of failure )] is stored at
E:\DATA Daily Backup\projects\Versioning_Backup\Attachment (ERP DB)_Before_9e6e2fa


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давайте переименуем в `remove_first_negative_element`. В тестах не забыть поправить


- New constant:
```js
t.CloudSyncResultTypes = {
    PULL: null,
    PUSH: null,
    CONFLICT: null,
    NONE: null
}
```


@ph4r05 Rather than return crypto.NULL_KEY_ENC wouldn't it be better to raise an exception in `get_destination_view_key_pub` and try catch here?


simple test


тут надо уточнить, что не только из пробелов, а из символов которые указаны вторым аргументом.


it is created after installing the client with: create-react-app client


Is it wanted that the revision changed here and some other occurrences in this file


it is a  little to use Linux


по всему файлу поправить отступы. лучше всего все файлы форматировать с помощью утиллиты clang-format. https://blogs.msdn.microsoft.com/vcblog/2018/03/13/clangformat-support-in-visual-studio-2017-15-7-preview-1/


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siehe _section_courses_get_semester_default_form_configuration


Yes, we found a bug in the upgrade process. We are fixing it now.


Close #10


works on triton just not at home


The original code and this one are both incorrect, because k won't increase when there is a NPE, so the while loop will run forever (and print the message forever). The correct fix is to move C++ out of the try/catch block.


правда жизни


И давайте все же за студентов выберем прототип. и прототип будет такой:
```cpp
bool remove_first_negative_element(const std::vector<int>& vec, int& removed_element);
```
возвращает `true` если удалось удалить элемент, а `false` если не удалось. значение удаленного элемента помещать в  `removed_element`


I had this initially in fact but wanted to keep the `767` value in one place without a need of potential sync :wink:


@yrodiere I swapped Wildfly's hibernate for the 5.3 branch and I am still having the error. Interesting except from the stacktrace:

```
at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:178)
at org.hibernate.proxy.AbstractLazyInitializer.getIdentifier(AbstractLazyInitializer.java:89)
at org.hibernate.proxy.AbstractLazyInitializer.initializeWithoutLoadIfPossible(AbstractLazyInitializer.java:255)
```

The call from `initializeWithoutLoadIfPossible`  seems to cause a load? Shouldn't this never be the case?


really nice!


еще добавить тест, где начальная строка не пустая, но в ней нет вхождения строки, которая передается первым аргументом.


if you want to be _really_ picky, `journalctl -o json` and then use `jq` to pick it apart :-D


тут не корректный синтаксис. нельзя писать `char sep = ' '`


this.visible is always false, when you close the model via the close() method,
When the (X) is pressed, the onHide emitter never gets called.


добавить пример, где в роли разделителя не пробел


@roquie thank you so much!!!


аналогично, добавить тест где вторым аргументом будет не пробел и с длинной больше одного символа


надо добавить пустую строку в конце файла. это требует cpplint.py


надо помочь студентам, и указать, что надо польззоваться функцией `std::string::find`


As a quickfix it may be okay, but we need to make it generic so that it handles any dir name. (again, script_improvements branch has made some attempts)


С точки зрения стиля лучше писать константы\дефайны ALL_CAPS-ом. Так они будут легче отличимы от обычных переменных. И вообще, круто, когда запись содержит в себе немного семантики


@null sollte nun DataCreator heißen


That leads me to believe the issue is caused with the introduction of `AvailableSettings.JpaCompliance#isJpaProxyComplianceEnabled()` in 5.2.13, while the most recent version I had in production on WF11 was 5.2.12. Is this setting `true` on default in WildFly?


Need to remove this change. It was needed at that time but now it's obsolete.


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Changes in TransfersContainer are not needed, https://github.com/seredat/karbowanec/commit/025a66b53a64cc47fc68cd2793680213798a3aef if enough as if will catch double output keys and throw an error before they will hit this check.


Shouldn't this be `dummy_get_flash_id`?


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sdf fdfds


Да-да, дефайны лучше заменять функциями, когда это можно сделать (всегда).
Вот примерчики:
#define MUL(x, y) x * y
MUL(10, 4 + 5) - боль (пойми, прочувствуй)

Ну, или лучше на эти грабли как-нибудь наступить, хз...


comment test


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I did some tests with this sample, after the last commits of search modules it wont work anymore. When i created this sample it was possible to register more than one component for an entity, the method invoked would be the last one, now it's still possible to register more than one component for the same entity, but the method invoked will always be the first one, which makes this sample obsolete. I think this sample should be removed.


Add CloudWatch and SNS Notifications


This commit allows adding a walkthrough step to a component by adding a `ref` to the component, instead of having to wrap it in a `<CopilotStep>` element. To do this, the ref callback in the component needs to call the `registerStep` method from the _copilot context, with an additional `size` prop.


Настроил проект, подготовил изображения


The command needs to be `"docker"` and the rest of the arguments need to be put in `args`.


After I survived last weekend I had another look at this. My recommendation for the future still applies. But if you don't want to add other commits to this branch, let's just fast-forward `master`, drop this feature branch and pretend it was never there. Avoids having to force-push a public branch (master).


Hello, this does not seem to work on Solaris 10. When trying to install on that platform, I'm getting the following issue which ends in failure.
Any ideas on how to fix this for Solaris 10?

warning: implicit declaration of function ‘posix_memalign’ [-Wimplicit-function-declaration]
     int ret = posix_memalign(&p, alignment, size);


Did we have a discussion about lambdas and startup before?
I'd prefer if we can avoid the use of lambdas and method references to avoid slowing down startup.

`@GenerateNodeFactory` should give you a `.getFactory()` method, if that's what you need.


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good good


Really? You create a root node and everything around that for basically nothing?

What's the goal here?
What do you try to achieve?


单独增加调节内网选项 -c


I don't really understand the change. Perhaps a description of the intention as part of the commit message could have helped me?


is the dropping of the check on !state.collapsed intentional here? Is it checked elsewhere?


You are adding spurious whitespace?
Could you change your editor to automatically remove these things?


> The call from initializeWithoutLoadIfPossible seems to cause a load? Shouldn't this never be the case?

That looks odd to me. In particular I can't fathom why `getIdentifier` would call `intialize`, since the identifier should be available without initialization. But then there's often a good, historical reason... Again, you should probably ask full-time Hibernate ORM developers on HipChat, on the forums or through a JIRA ticket. I only help from time to time, and spend most of my time on another Hibernate project (Search) so I don't have the whole history of the ORM code in mind.

> That leads me to believe the issue is caused with the introduction of AvailableSettings.JpaCompliance#isJpaProxyComplianceEnabled() in 5.2.13, while the most recent version I had in production on WF11 was 5.2.12. Is this setting true on default in WildFly?

I don't know. Hey @scottmarlow, any idea where we can find that information?


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Nice work


@bussdee This only shows the changes in current commit. To see previous changes, press the link next to "parent".


Just seeing this. Why is the comment not done as JavaDoc? works much better with tools and IDE support if it is in:

```
/**
  *
  */
```


He has the device lol


This commit is really strange. I mean, this:
```c
#include "nanosleep.h"
#include <pthread.h>
```
causes forward implicit definition of `struct timespec` in `"nanosleep.h"`. And then when `<pthread.h>` gets included, the real (and conflicting) definition from *Pthreads-W32* gets pulled in. AFAIK, MSVC allows this., but the fantastic MSVC-replacement `clang-cl`, does not:
```
In file included from common/src/windows/nanosleep.c:29:
./common/include/windows\nanosleep.h(36,28):  warning: declaration of 'struct timespec' will not be visible outside of this function
      [-Wvisibility]
int nanosleep(const struct timespec *req, struct timespec *rem);
                           ^
common/src/windows/nanosleep.c(33,5):  error: conflicting types for 'nanosleep'
int nanosleep(const struct timespec *req, struct timespec *rem)
    ^
./common/include/windows\nanosleep.h(36,5):  note: previous declaration is here
int nanosleep(const struct timespec *req, struct timespec *rem);
    ^
1 warning and 1 error generated.
```

A simple fix that works with both MSVC/clang-cl is simply this:
```diff
--- a/host/common/src/windows/nanosleep.c 2018-09-30 06:48:02
+++ b/host/common/src/windows/nanosleep.c 2018-10-01 11:51:19
@@ -26,9 +26,9 @@
 #error "This file is intended for use with WIN32 systems only."
 #endif

-#include "nanosleep.h"
 #include <pthread.h>
 #include <windows.h>
+#include "nanosleep.h"

```


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these changes don't seem to be related to the memory issue -- is there another issue for them?


Hallo Alexander,

in meiner Lesart war das eine Tabelle, in der Geschwindigkeitsbegrenzungen aufgelistet
werden, wie in Europa nach dem Grenzübertritt üblich. Falls es sich um eine
Verkehrsberuhigungsmaßnahme handelt, ist mir wohl der Kontext abhanden gekommen,
verstärkt durch die Aufforderung zur Prüfung im Tool. In diesem Fall wäre die vorherige
Übersetzung in Ordnung.

Am Montag, 1. Oktober 2018, 08:54:33 CEST schrieb Alexander Heinlein:

@SantosSi[1]
Was soll "Geschwindigkeitstabelle" bedeuten? Die vorherige Übersetzung "Bodenwelle"
war korrekt. Siehe auch https://wiki.openstreetmap.org/wiki/DE:Key:traffic_calming[2],
dort ist es als "lange Bodenwelle" beschrieben.
—You are receiving this because you were mentioned.Reply to this email directly, view it
on GitHub[3], or mute the thread[4].[5]

--------
[1] https://github.com/SantosSi
[2] https://wiki.openstreetmap.org/wiki/DE:Key:traffic_calming
[3] https://github.com/osmandapp/Osmand/commit/
f42822a8d282351f6364a5d08bd70ef4a034cc4e#commitcomment-30712325
[4] https://github.com/notifications/unsubscribe-auth/
AeFRP0081LvIEom09ybLR3fzVWNI3nBEks5ugbwpgaJpZM4XBeaT
[5] https://github.com/notifications/beacon/
AeFRP0nG6Tyle6zviZ63ennTkKY5KA-6ks5ugbwpgaJpZM4XBeaT.gif


lul
https://imgur.com/a/1mSX15d


Thanks for setting this up 👍


этот коммит сломал тест:
The command "testcafe chromium qa/testcafe/testDeleteAndRecovery.js" exited with 1.


main video to gif code here :)


I was on vacation, but I'll do this asap.


We discussed about that with M. and it was intentional :)


![vue ville 2017-03-26 modifiee](https://user-images.githubusercontent.com/43671899/46287222-198ea800-c582-11e8-9f79-e331dee09c60.jpg)


I'll have to pick (1) because showing it publicly may attract people who are job hoppers or people who are not fully motivated for working for **this** particular organization (IDF) as opposed to **any** organization.

:-)


Lel kicked a stable rom maintainer with device


get in chat


Microservice working. Login and Registration done.


Я опечатался и у меня все мое приложение закрылось - не очень реакция


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why eman stays? :)


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Реагируем так
В окне конфигурации подсвечиваем красным
В главном окне делаем не активными для поиска источники битые

Программа при этом должна работать нормально всегда и не закрываться/не падать


Alles klar. Ja, es ist eine Verkehrsberuhigungsmaßnahme. Es ist bereits korrigiert.

Bei den Übersetzungen fehlt leider der Kontext bzw. eine kurze Beschreibung von Entwicklerseite. Das könnte man definitiv verbessern.


I think you had a typo here: boostrap is a deprecated package.


strlen - это функция, которая тупо проходит по строке до '\0', инкрементируя при этом счётчик. В итоге такая атомарная операция как взятие n-ого, внезапно,  Theta(sz*n). А она вызывается в цикле, и у тебя проход по строке будет занимать O(n^3).
Что делать?
Переиначь её интерфейс так, чтобы её было неудобно вызывать в цикле. Например, представь функцию, которая берёт следующий элемент и возвращает указатель на него


@stamparm possibly, let us have ```https://github.com/Hestat/minerchk/blob/master/hostslist.txt``` as a feed?


ubuntu 18.04


Was the 404 intentional?


@Bandic007 i add a new app to webvirtcloud but later than i remove it. you can remove dashboard line from settings.py


Initial commit


Pull request


fovero debug ;p


A test for GitBook sync speed.  Super slow. 🙃🙃🙃


@Rotonen Jenkins CI reporting about code analysis
See the full report here: https://jenkins.plone.org/job/package-plone.testing/93/violations
```
src/plone/testing/z2.py:98:1: C901 'uninstallProduct' is too complex (15)
src/plone/testing/z2.py:138:19: T000 Todo note found.
src/plone/testing/z2.py:414:5: C901 'Startup.setUpPatches' is too complex (11)
src/plone/testing/z2.py:829:11: T000 Todo note found.
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


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

* https://hacktoberfest.lingonsaft.com


This is better


1 modifier


Maybe it'd be better to give the developer freedom to change url from properties.


test


Some code review


Increase seq each time,


The dev_merge branch is not the newest branch. I think I have some code in local repo that haven't been pushed.


@krystian3w Zapomniałeś o scrollu :smile:


A nie wiem, miałem odblokowany - chyba sobie czymś nadpisałem lub w ciągu kilku godzin doblokowali.


Добавил Urls
Вывел на экран в таблицы из админ


Maybe we should make the test template somewhat realistic to what you might find in a `robots.txt`?
```
User-agent: gutenberg
Allow: /
```


This commit contain changes on `transactions` table migration. For existing dompet users, please update your `transactions` table with this sql script:

```sql
ALTER TABLE `transactions`
	ADD COLUMN `partner_id` INT(10) UNSIGNED NULL DEFAULT NULL AFTER `category_id`;
```

Thanks.


Oh fck forgot dtsi changes


Ahora se ve mucho mejor.

El dom., 30 de sep. de 2018 a la(s) 22:34, damianzalazar (
notifications@github.com) escribió:

> Un método si devuelve un conjunto, lo pude probar y funciona!!
> Si lo vimos no lo recordaba. Eso, sumado a un map dentro del método para
> la colección de formaciones, y evito recordar el conjunto de vagones en una
> variable. Me parece que esta forma de resolverlo es más acorde.
>
> Saludos
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/algo1unsam/trenes-damianzalazar/commit/e5040bea6e558435ba926df8a8476f50c9077ccb#commitcomment-30710096>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AEa1OUGSk-CEuWPu4a_q8VC-uYTafHGyks5ugXEqgaJpZM4XBFA0>
> .
>


Я не понимаю, что это за константы. Что это? Ты сам через год-то вспомнишь? Если это ASCII коды, то используй кавычки (типо '\0', а не 0). Если это иные константы, просто выдели их как константы куда-то в вверх файла. И чтобы было так, что если в одном месте изменишь, меняется везде - прога должна быть гибкой


If you want to count all disordered packets as lost packets, you should keep self.packets = self.seq instead of increasing it each time. Besides, the err_rate should always be the total amount of lost packets / the total amount of packets that shoud be received.


@Rotonen Jenkins CI reporting about code analysis
See the full report here: https://jenkins.plone.org/job/package-plone.testing/94/violations
```
src/plone/testing/z2.py:98:1: C901 'uninstallProduct' is too complex (15)
src/plone/testing/z2.py:138:19: T000 Todo note found.
src/plone/testing/z2.py:414:5: C901 'Startup.setUpPatches' is too complex (11)
src/plone/testing/z2.py:829:11: T000 Todo note found.
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


Бтв, для индентации используй пробелы. Сам видишь, почему
<img width="433" alt="screen shot 2018-10-01 at 15 19 42" src="https://user-images.githubusercontent.com/7346657/46288135-793e8080-c58d-11e8-8217-8e4251eceab9.png">


bhjmbhj


bhjbhj


Done with https://github.com/stamparm/maltrail/commit/1b82cdfb1ee2137d39974242ac5fe5b1df2df4e2


Tutaj raczej wystarczy tylko `sklep.krosno.com.pl###rodo`, reszta jest od popupu z newsletterem, więc do EI :smile:.


@jensens Jenkins CI reporting about code analysis
See the full report here: https://jenkins.plone.org/job/package-plone.namedfile/95/violations
```
plone/namedfile/testing.py:18:9: D001 found xmlconfig.file( replace it with self.loadZCML(
plone/namedfile/testing.py:24:36: C812 missing trailing comma
plone/namedfile/file.py:267:9: Q001 Remove bad quotes from multiline string.
plone/namedfile/file.py:308:9: Q001 Remove bad quotes from multiline string.
plone/namedfile/handler.py:11:23: C812 missing trailing comma
plone/namedfile/interfaces.py:17:25: C812 missing trailing comma
plone/namedfile/scaling.py:193:25: C815 missing trailing comma in Python 3.5+
plone/namedfile/scaling.py:196:5: C901 'DefaultImageScalingFactory.__call__' is too complex (15)
plone/namedfile/scaling.py:203:25: C816 missing trailing comma in Python 3.6+
plone/namedfile/scaling.py:243:29: C815 missing trailing comma in Python 3.5+
plone/namedfile/scaling.py:407:21: C816 missing trailing comma in Python 3.6+
plone/namedfile/scaling.py:434:25: C815 missing trailing comma in Python 3.5+
plone/namedfile/scaling.py:446:25: C815 missing trailing comma in Python 3.5+
plone/namedfile/scaling.py:460:21: C816 missing trailing comma in Python 3.6+
plone/namedfile/scaling.py:486:29: C815 missing trailing comma in Python 3.5+
plone/namedfile/scaling.py:500:17: C816 missing trailing comma in Python 3.6+
plone/namedfile/utils/__init__.py:84:66: C812 missing trailing comma
plone/namedfile/utils/__init__.py:151:15: T000 Todo note found.
plone/namedfile/utils/__init__.py:156:73: C812 missing trailing comma
plone/namedfile/utils/__init__.py:176:15: T000 Todo note found.
plone/namedfile/utils/__init__.py:183:18: C812 missing trailing comma
plone/namedfile/utils/__init__.py:188:1: C901 'rotate_image' is too complex (20)
plone/namedfile/utils/__init__.py:219:14: C812 missing trailing comma
plone/namedfile/utils/__init__.py:271:25: F821 undefined name 'StringIO'
plone/namedfile/utils/__init__.py:276:1: E302 expected 2 blank lines, found 1
plone/namedfile/utils/__init__.py:280:1: E302 expected 2 blank lines, found 1
plone/namedfile/utils/tiff_utils.py:11:1: C901 'process_tiff' is too complex (11)
plone/namedfile/utils/tiff_utils.py:20:7: T000 Todo note found.
plone/namedfile/utils/tiff_utils.py:81:7: T000 Todo note found.
plone/namedfile/utils/tiff_utils.py:82:7: T000 Todo note found.
plone/namedfile/tests/test_blobfile.py:40:31: C812 missing trailing comma
plone/namedfile/tests/test_blobfile.py:45:35: C812 missing trailing comma
plone/namedfile/tests/test_blobfile.py:50:46: C812 missing trailing comma
plone/namedfile/tests/test_blobfile.py:55:32: C812 missing trailing comma
plone/namedfile/tests/test_scaling.py:85:80: E501 line too long (86 > 79 characters)
plone/namedfile/tests/test_scaling.py:102:80: E501 line too long (81 > 79 characters)
plone/namedfile/tests/test_scaling.py:133:80: E501 line too long (86 > 79 characters)
plone/namedfile/tests/test_scaling.py:156:80: E501 line too long (86 > 79 characters)
plone/namedfile/tests/test_scaling.py:178:80: E501 line too long (86 > 79 characters)
plone/namedfile/tests/test_scaling.py:200:80: E501 line too long (86 > 79 characters)
plone/namedfile/tests/test_image.py:25:80: E501 line too long (80 > 79 characters)
plone/namedfile/tests/test_doctests.py:26:17: Q000 Remove bad quotes.
plone/namedfile/tests/test_doctests.py:26:30: Q000 Remove bad quotes.
plone/namedfile/tests/test_doctests.py:47:10: C812 missing trailing comma
plone/namedfile/tests/test_scaling_functional.py:116:28: C812 missing trailing comma
plone/namedfile/tests/test_scaling_functional.py:146:70: C812 missing trailing comma
plone/namedfile/tests/test_scaling_functional.py:153:76: C812 missing trailing comma
plone/namedfile/tests/test_scaling_functional.py:164:74: C812 missing trailing comma
plone/namedfile/tests/test_scaling_functional.py:197:75: C812 missing trailing comma
plone/namedfile/tests/test_scaling_functional.py:202:78: C812 missing trailing comma
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


I'm not sure about the OpenSSL thing, I'll look it up and try to come up with an answer. I figure the same comment might apply to asio also?

May I ask why, though?

Also, I was under the impression it was generally preferable to have 'port:' rather than 'path' dependencies. I know in some other PR I'd made I had used a similar 'path' format for autoconf/automake for example and was asked to  change it.

I'll try to address the other comments later today.


Successfully aliased the URL <https://node-inferno-cknzkhbwlo.now.sh> to the following alias.

* https://node-inferno.now.sh


Slowly updating them all...


赔我五毛钱, 呜呜呜


w


interesting...


Esse import { } from '@material-ui/core' é necessário? Se sim, teria que ver qual componente é necessário e só importar esse componente.....


This is not compatible with Nette\Utils\Image::save().
This change have to be reverted.


Didn't Realise Git didn't upload empty folders.


Leftover log?


ko có gì để xem


Please use the issue title: "Password hash disclosure to "view only" admin users" rather than more vague "Information disclosure in Django Admin".


A TCID example:
50464E2D0021E021


Very Nice documented and presented.Please review it.


Fixed


The reason for dropping the 1. is because the FML version is 13.xxx, not 1.13.xxx


This will result in `printf("%23g\n",1.353345983795837535398738e-20)` being printed as
```~0.000000000000000000013533459837958375354```
instead of much more readable
```~1.3533459837958375354e-20```


Oh heck yes.


参见[官方修复](https://github.com/odoo/odoo/commit/b3fef6a72a0742f778eb57a33aa11c55dd214db1)


@lamartire


Both upper and lower case may exist... thats why..
"([a-fA-F0-9]{2}){6,8}"


Nice!


В названии commit - component


Oui, cette action n'est pas encore finie mais elle écrira dans la base de
donnés pour rajouter des questions

Le lun. 1 oct. 2018 à 13:04, vincebru <notifications@github.com> a écrit :

> @Ecologeeks <https://github.com/Ecologeeks>
> Je suppose que cette action est amené à faire quelque chose?
>
> Si aucune ecriture en Bdd n'est necessaire, il suffit simplement de ne pas
> creer d'action et le rendu de la vue sera gérée
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/vincebru/siteTechnoWeb/commit/78a33b60e5c3aee17569bd454ffb1076aad873ba#commitcomment-30715404>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AQg75pxYtMxBoeoOIaZnABI20HsJGmUZks5ugfbGgaJpZM4XB1cc>
> .
>


the build problem is now fixed, so I reenabled SmartCash in support.json in e42214e9619dae42e99e8fae5585314ec1db4b44


![](https://github.trello.services/images/mini-trello-icon.png) [В профиле вместо даты регистрации писать число дней на сайте](https://trello.com/c/kgLmDC70/90-%D0%B2-%D0%BF%D1%80%D0%BE%D1%84%D0%B8%D0%BB%D0%B5-%D0%B2%D0%BC%D0%B5%D1%81%D1%82%D0%BE-%D0%B4%D0%B0%D1%82%D1%8B-%D1%80%D0%B5%D0%B3%D0%B8%D1%81%D1%82%D1%80%D0%B0%D1%86%D0%B8%D0%B8-%D0%BF%D0%B8%D1%81%D0%B0%D1%82%D1%8C-%D1%87%D0%B8%D1%81%D0%BB%D0%BE-%D0%B4%D0%BD%D0%B5%D0%B9-%D0%BD%D0%B0-%D1%81%D0%B0%D0%B9%D1%82%D0%B5)


Great!


die methode wird en rückgabe wert geh, zb "OK" für logged in oder "NOK" für nöd logged in. also chasch das no bruche?


ok das sollte so nicht sein muss ich schauen


in all places use "Hyper-V VM group".
do you require -Verbose in production?
'$HyperVGroupName' exists in $HyperVHost -> exists on?


It is mentioned... `^16-` in `Extension extensions<0..2^16-1>;` means, that the length is in 16bits.


@mikkelgroth Not sure what you mean. When we create the genesis block, the nonce is automatically set to 0.


@shreeesha commit is two days old and he didn't had device at that moment.


@aurelhann Thanks for confirming 😄


Why leave PHP at 5.2.4 and not abandon the 5.x branch. Especially if you'd like to take advantage of newer PHP security advancements, code brevity, greater expression.

The fact you've been playing with versioning, rather than things at the core of what calmpress.org currently claims your goals are is both confusing and probably going to cause problems down the line.


OK. I'll adjust. 👍