[R/mbd_loglik_utils.R:394:54:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik_utils.R#L394) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:421:12:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik_utils.R#L421) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:449:54:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik_utils.R#L449) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:563:9:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik_utils.R#L563) *warning:* **no visible global function definition for ‘find_best_lx_for_pc’**
```r
  lx <- find_best_lx_for_pc(brts = brts, pars = pars, soc = soc)
        ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:597:18:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik_utils.R#L597) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- c(0, brts2time_intervals_and_births(brts)$births)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:640:16:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik_utils.R#L640) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik.R#L84) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    data <- brts2time_intervals_and_births(brts)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:110:11:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik.R#L110) *warning:* **local variable ‘max_number_of_species’ assigned but may not be used**
```r
    lx <- max_number_of_species <- alpha * max_k;
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:170:23:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik.R#L170) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
          q_t[t, ] <- negatives_correction(q_t[t, ], pars)
                      ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:188:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
          matrix_b <- create_b(lambda = lambda, nu = nu, q = q, k = k, b = births[t],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:192:25:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik.R#L192) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
            q_t[t, ] <- negatives_correction(q_t[t, ], pars)
                        ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:231:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_loglik.R#L231) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * q_t[t, (missnumspec + 1)]
    ^
```
[R/mbd_ml.R:85:31:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L85) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) == 0) {idparsfix <- NULL}
                              ^
```
[R/mbd_ml.R:85:49:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L85) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) == 0) {idparsfix <- NULL}
                                                ^
```
[R/mbd_ml.R:131:15:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L131) *style:* **Use <-, not =, for assignment.**
```r
    trparsopt = initparsopt / (1 + initparsopt)
              ^
```
[R/mbd_ml.R:132:42:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L132) *style:* **Use <-, not =, for assignment.**
```r
    trparsopt[which(initparsopt == Inf)] = 1
                                         ^
```
[R/mbd_ml.R:133:15:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L133) *style:* **Use <-, not =, for assignment.**
```r
    trparsfix = parsfix / (1 + parsfix)
              ^
```
[R/mbd_ml.R:134:38:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L134) *style:* **Use <-, not =, for assignment.**
```r
    trparsfix[which(parsfix == Inf)] = 1
                                     ^
```
[R/mbd_ml.R:200:31:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L200) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {ml_pars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:200:62:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L200) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {ml_pars1[idparsfix] <- parsfix}
                                                             ^
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L30) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    data <- brts2time_intervals_and_births(test_brts)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:40:41:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L40) *style:* **Put spaces around all infix operators.**
```r
      poisson_term <- stats::dpois(i, nu*time_intervals[t], log = FALSE)[
                                       ~^~
```
[R/mbd_pure_multiple_birth.R:41:27:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L41) *style:* **Put spaces around all infix operators.**
```r
        stats::dpois(i, nu*time_intervals[t], log = FALSE) != 0]
                         ~^~
```
[R/mbd_pure_multiple_birth.R:42:33:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L42) *style:* **Put spaces around all infix operators.**
```r
      ii <- i[stats::dpois(i, nu*time_intervals[t], log = FALSE) != 0 ]
                               ~^~
```
[R/mbd_pure_multiple_birth.R:42:70:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      ii <- i[stats::dpois(i, nu*time_intervals[t], log = FALSE) != 0 ]
                                                                     ^
```
[R/mbd_pure_multiple_birth.R:46:24:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L46) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:46:61:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:81:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L81) *style:* **Lines should not be more than 80 characters.**
```r
  condition1 <- (any(is.nan(test_pars)) != 0 | any(is.infinite(test_pars)) != 0 )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:81:80:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  condition1 <- (any(is.nan(test_pars)) != 0 | any(is.infinite(test_pars)) != 0 )
                                                                               ^
```
[R/mbd_pure_multiple_birth.R:86:13:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L86) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    data <- brts2time_intervals_and_births(test_brts)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:90:47:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L90) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    a_term <- rep(1, length(time_intervals)    ) #branches
                                              ^
```
[R/mbd_pure_multiple_birth.R:100:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
      # (1) nu contribution: (1-q)^(k*i) * (nu*(t_k-t_k-1))^i*exp(-nu*(t_k-t_k-1)) / i!
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:102:24:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:102:61:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:110:17:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L110) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (1 - q)^(k[-length(k)] - births)                 # (1)
                ^
```
[R/mbd_pure_multiple_birth.R:149:33:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L149) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (min(trpars1[1:n_pars]) < 0 ) {
                                ^
```
[R/mbd_pure_multiple_birth.R:161:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:185:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L185) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:187:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L187) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:188:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
  # - optimmethod = "simplex" (current default) or 'subplex' (default of previous versions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:193:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L193) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(namepars); #if you add more parameters to your model just change this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:194:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L194) *style:* **Lines should not be more than 80 characters.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars; #those are the parameters that you get if something goes sideways
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L237) *style:* **Lines should not be more than 80 characters.**
```r
      cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:240:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
        cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:244:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L244) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:249:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L249) *style:* **Lines should not be more than 80 characters.**
```r
          cat("Optimization has not converged. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:264:11:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_pure_multiple_birth.R#L264) *style:* **Variable or function name should be snake_case.**
```r
          ML <- as.numeric(unlist(out$fvalues))
          ^~
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L92) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow = 1e6, 4)
      ^
```
[R/mbd_sim.R:101:11:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
            L[new_interval, 1] <- t#-(delta_n:1)*1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:134:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L134) *style:* **Variable or function name should be snake_case.**
```r
    L <- L[(1:total_count), ]
    ^
```
[R/mbd_sim.R:142:35:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L142) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    crown_species_dead <- (length( unique(sign(alive[, 3]))) != 2 ) * cond
                                  ^
```
[R/mbd_sim.R:142:66:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L144) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:144:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L144) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L145) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = FALSE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L145) *style:* **Variable or function name should be snake_case.**
```r
    births.full_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = FALSE), decreasing = TRUE)))
    ^~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L146) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L146) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:47:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L146) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
                                              ^
```
[R/mbd_sim.R:147:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L147) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.full_tree <- sum( duplicated(births.full_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:147:38:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L147) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.full_tree <- sum( duplicated(births.full_tree))
                                     ^
```
[R/mbd_sim.R:149:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
    # multiple_births_check = (multiple_births.full_tree>=minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:149:7:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L149) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multiple_births.full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:150:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check <- (multiple_births.reconstructed_tree >= minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:152:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
  time_points <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:172:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L227) *style:* **Put spaces around all infix operators.**
```r
      total_count=init_n_lineages
                ~^~
```
[R/mbd_sim.R:231:7:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L231) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow=1e6, 4)
      ^
```
[R/mbd_sim.R:231:26:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L231) *style:* **Put spaces around all infix operators.**
```r
      L <- matrix(0, nrow=1e6, 4)
                        ~^~
```
[R/mbd_sim.R:238:9:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
          L[new_interval, 1] <- t#-(delta_n:1)*1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:252:50:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L252) *style:* **Put spaces around all infix operators.**
```r
          L[new_interval, 3] <- abs(new_interval)*sign(parents)
                                                ~^~
```
[R/mbd_sim.R:254:44:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L264) *style:* **Put spaces around all infix operators.**
```r
          pool <- pool[pool!=dead]
                          ~^~~
```
[R/mbd_sim.R:268:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L268) *style:* **Variable or function name should be snake_case.**
```r
    L=L[(1:total_count), ]
    ^
```
[R/mbd_sim.R:268:6:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L268) *style:* **Use <-, not =, for assignment.**
```r
    L=L[(1:total_count), ]
     ^
```
[R/mbd_sim.R:268:6:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L268) *style:* **Put spaces around all infix operators.**
```r
    L=L[(1:total_count), ]
    ~^~
```
[R/mbd_sim.R:269:21:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L269) *style:* **Use <-, not =, for assignment.**
```r
    extinct_species = sum(L[, 4]!=-1)
                    ^
```
[R/mbd_sim.R:269:33:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L269) *style:* **Put spaces around all infix operators.**
```r
    extinct_species = sum(L[, 4]!=-1)
                               ~^~~
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L271) *style:* **Use <-, not =, for assignment.**
```r
    tips=length(L[, 4][L[, 4]==-1])
        ^
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[, 4][L[, 4]==-1])
       ~^~
```
[R/mbd_sim.R:271:30:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[, 4][L[, 4]==-1])
                            ~^~~
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L273) *style:* **Use <-, not =, for assignment.**
```r
    alive=L[L[, 4]==-1, ]
         ^
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[, 4]==-1, ]
        ~^~
```
[R/mbd_sim.R:273:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[, 4]==-1, ]
                 ~^~~
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L275) *style:* **Use <-, not =, for assignment.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )*cond
                             ^
```
[R/mbd_sim.R:275:33:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )*cond
                                ^
```
[R/mbd_sim.R:275:41:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )*cond
                                        ^
```
[R/mbd_sim.R:275:67:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )*cond
                                                                 ~^~~
```
[R/mbd_sim.R:275:70:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )*cond
                                                                     ^
```
[R/mbd_sim.R:275:72:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L278) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L278) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:30:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L278) *style:* **Use <-, not =, for assignment.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
                             ^
```
[R/mbd_sim.R:278:30:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L278) *style:* **Put spaces around all infix operators.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
                            ~^~
```
[R/mbd_sim.R:279:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L279) *style:* **Variable or function name should be snake_case.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
    ^~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L279) *style:* **Use <-, not =, for assignment.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
                    ^
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L279) *style:* **Put spaces around all infix operators.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
                   ~^~
```
[R/mbd_sim.R:280:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L280) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L280) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L280) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:40:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L280) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
                                       ^
```
[R/mbd_sim.R:280:46:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L280) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
                                             ^
```
[R/mbd_sim.R:281:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L281) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.full_tree = sum( duplicated(births.full_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:281:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L281) *warning:* **local variable ‘multiple_births.full_tree’ assigned but may not be used**
```r
    multiple_births.full_tree = sum( duplicated(births.full_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:281:31:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L281) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births.full_tree = sum( duplicated(births.full_tree))
                              ^
```
[R/mbd_sim.R:281:37:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L281) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.full_tree = sum( duplicated(births.full_tree))
                                    ^
```
[R/mbd_sim.R:283:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
    # multiple_births_check = (multiple_births.full_tree>=minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:283:7:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L283) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multiple_births.full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:284:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L284) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:284:27:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L284) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
                          ^
```
[R/mbd_sim.R:284:64:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L284) *style:* **Put spaces around all infix operators.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
                                                              ~^~~
```
[R/mbd_sim.R:286:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L286) *style:* **Lines should not be more than 80 characters.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L286) *style:* **Use <-, not =, for assignment.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
             ^
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L286) *style:* **Put spaces around all infix operators.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
            ~^~
```
[R/mbd_sim.R:287:8:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L288) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(L, dropextinct = T)
      ^
```
[R/mbd_sim.R:289:7:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L289) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(L, dropextinct = F)
      ^
```
[R/mbd_sim.R:290:7:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:369:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L369) *style:* **Lines should not be more than 80 characters.**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:369:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L369) *style:* **Use <-, not =, for assignment.**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
                  ^
```
[R/mbd_sim.R:369:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L369) *style:* **Put spaces around all infix operators.**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
                 ~^~
```
[R/mbd_sim.R:369:57:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L369) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
                                                        ^
```
[R/mbd_sim.R:369:65:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L369) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:371:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L371) *style:* **Use <-, not =, for assignment.**
```r
    all_the_births=brts2time_intervals_and_births(sim_data)$births
                  ^
```
[R/mbd_sim.R:371:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L371) *style:* **Put spaces around all infix operators.**
```r
    all_the_births=brts2time_intervals_and_births(sim_data)$births
                 ~^~
```
[R/mbd_sim.R:371:20:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L371) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    all_the_births=brts2time_intervals_and_births(sim_data)$births
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:377:3:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L377) *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:382:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L382) *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:382:5:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L382) *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:388:34:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L388) *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:388:52:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L388) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(sim_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                                   ^
```
[R/mbd_sim.R:388:80:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L388) *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:390:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L390) *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:390:42:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L390) *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:390:60:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L390) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                                           ^
```
[R/mbd_sim.R:390:96:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L390) *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:391:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L391) *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:391:141:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L391) *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:392:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L392) *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:392:35:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                  ^
```
[R/mbd_sim.R:392:53:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_sim.R#L392) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                                    ^
```
[R/mbd_sim.R:392:82:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                                                                ^
```
[R/mbd_utils.R:20:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:20:9:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_utils.R#L20) *style:* **Use <-, not =, for assignment.**
```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:20:9:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_utils.R#L20) *style:* **Put spaces around all infix operators.**
```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:20:28:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:22:13:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_utils.R#L22) *style:* **Use <-, not =, for assignment.**
```r
  par_names = colnames(results)[1:n_pars]
            ^
```
[R/mbd_utils.R:24:1:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:24:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:24:19:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_utils.R#L24) *style:* **Put spaces around all infix operators.**
```r
  truevalues_color="red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                 ~^~
```
[R/mbd_utils.R:24:40:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:24:66:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/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:25:22:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_utils.R#L25) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name = "blue"; truevalues_color_name = "red";
                     ^
```
[R/mbd_utils.R:25:54:](https://github.com/Giappo/mbd/blob/173664a3a822a0a32bb13d537a1b8cdef4e35be5/R/mbd_utils.R#L25) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name = "blue"; truevalues_color_name = "red";
                                                     ^
```


Ты по-разному хранишь номера телефонов
В этой строчке у тебя номера сохраняются в строке через пробел
А в строчках 75, 83 через запятую


Don't be too general in exceptions.


just as a suggestion: `shape` -> `look`?


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//test

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Collecting queries from all tables in one class is not comfortable. Why not utilize the DAO or repository pattern?


Если размер нулевой, то ф-ия вернёт undefined вместо массива


would suggest to refrain from pronouns like `we` - as an alternative:

> Once the component spec is solidified, ..


コメント記入者：卜部
課題の一部を誤っているようです。
出力が求められているのはname, sex, prefectureです。


수고했어요!


수고했어요!### ****


@marcov Good point! I've fixed it. Thanks!


You should choose one of the available APIs imo. The field count will grow when new collections will be added.


Не увидел, где обрабатывается, что контакты без номеров не должны добавляться


add frequency word and frequency relation to backend service


"->" means one tab, it`ll make readability of code much better.


Oh crap, where did that came from 🙄


> The spec should demonstrate how your component's API will support all the native Stardust features

frankly, even I cannot say what these 'native features' are :) I think that we shouldn't throw that much on the person who would like to contribute, it could be sufficient just to ask for an API proposal - otherwise we might protect ourselves from bright ideas of the community :)

> The spec should demonstrate how component's API you are proposing will be used by Stardust consumer


Why load users which you will never use? I would fetch users from the database when they are needed, eg. when the users is logging in, when commands are used, etc.


very important step, very helpful section 👍


При запуске ф-ии каждый раз создаётся новый массив objectList
Ты скорее всего хотела, чтобы он хранил старые результаты, для этого нужно его создать вне ф-ии


view of changes


`relate` -> `refer`


Same here. You can fetch guilds when they are needed, eg. guild user is logging in.


God damnit sasha!! Lol


`also` could be safely removed


1. Warum disabledOtherMethode und nicht sowas wie "rasenMähen"
2. Wurde die othercode.js nirgends genutzt?


It is just longer.


> push a small change so you can open a PR early.

->  push a small change, so that your PR could be reviewed quickly.


@mradamcox   This is needed when there is migrated business data. In that case, you will want to change entitytypeid from old_entitytype_id to newentitytype in the data.entities table.


do we need to specify this? it is a general React concept, what Stardust adds on top of that?


good work!


1. Weil es ja um den Button geht der disabled ist und ich mit dem Code zum Beispiel kein Rasen mähen kann.
2. Weil es nur eine andere Methode ist von dem Originalen disabled.js und wenn ich diese nutzen wollte, dies nur bei der index.php umändern müsste.


we should either suggest or not (there shouldn't be words like 'probably' in this context) :)

I would suggest to omit this phrase altogether for now - surely, we **would** suggest some pattern to follow later, but the problem with `AutoControlledComponent` is that it is seen to be reworked in the nearest future.


:cry:


This seems odd. I guess there was a mistake in resolving merge conflicts.


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

* https://confluenza.now.sh


Ah, I see it's been already fixed in 3208288. :+1:


Chaque application gére ses propres URL


Are they in Python 2.7?


yes <=1.7 and 1.8 are very different. They changed many things. An RC with <=1.5.8 and AC 1.8 dosen't work.


Необходимо в свой коммит добавлять результаты своей работы. В данном коммите не вижу никакой диаграммы. В дальнейшем исправьте это.


Gute Arbeit, Partner !!!

Klasse Idee mit dem Sicherheitsupdate !

LG


Les URL de l'application *telemeta_front* sont utilisées en priorité


Cohérence des noms d'aplications


> ### Find All Documents in a Collection
> To retrieve all the documents in the collection, we will use the `find()` method without any parameters.
To iterate through the results, chain the `iterator()` method to the `find()`.
The following example retrieves all documents in the collection and prints the returned documents (101 documents):

```java
MongoCursor<Document> cursor = collection.find().iterator();
try {
    while (cursor.hasNext()) {
        System.out.println(cursor.next().toJson());
    }
} finally {
    cursor.close();
}
```

> **Although the following idiom for iteration is permissible, avoid its use as the application can leak a cursor if the loop terminates early:**

```java
for (Document cur : collection.find()) {
    System.out.println(cur.toJson());
}
```

http://mongodb.github.io/mongo-java-driver/3.4/driver/getting-started/quick-start/#find-all-documents-in-a-collection


It doesn't, it only throws when less than zero. Not worth another check when zero, might as well just go through the logic and end up doing nothing. I added the `< 0` check because a negative additional capacity doesn't make logical sense and probably means bad application code.


Copy of this build can be found at https://www.mewbuilds.com/build/5b6058614fe177b3c280496a052aa45ded66c76e/index.html


You will ruin us all!


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{}
//test

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Copy-paste 😉 `mailalerts` => `ps_faviconnotificationbo`


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

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Aliasing failed with the following error:

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


Looks good!


This class is actually the same as MySQLStorage.


Reasoncodes

http://docs.oasis-open.org/mqtt/mqtt/v5.0/cs02/mqtt-v5.0-cs02.html#_Toc514345303

and properties:

http://docs.oasis-open.org/mqtt/mqtt/v5.0/cs02/mqtt-v5.0-cs02.html#_Toc514345299

are part of the MQTT 5.0 specification.   Different subsets of reason codes and properties are applicable to certain packet types.  Specifying the packet type on the constructors allows validation.


Oh ok.
Sorry about my confusion.


Or, better yet, use `obj ? Object.assign({}, obj) : {}` or `obj && Object.assign({}, obj) || {}`, or something similar, instead of relying on an external library.

Most projects include shims and polyfills, now anyway.


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