[R/mbd_loglik_utils.R:307:46:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L307) *style:* **Put spaces around all infix operators.**
```r
  soc + max(mvec[(mvec %in% which((cumsum(p_m/sum(p_m))) <= 0.95))])
                                            ~^~
```
[R/mbd_loglik_utils.R:315:1:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L315) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:363:1:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L363) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:394:54:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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:475:19:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L475) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations /2
                  ^~
```
[R/mbd_loglik_utils.R:477:32:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L477) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/ a)
                              ~^
```
[R/mbd_loglik_utils.R:553:1:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L553) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:563:9:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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_utils.R:731:36:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_loglik_utils.R#L731) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1) /pc_1;
                                   ^~
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_ml.R#L131) *style:* **Use <-, not =, for assignment.**
```r
    trparsopt = initparsopt/ (1 + initparsopt)
              ^
```
[R/mbd_ml.R:131:28:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_ml.R#L131) *style:* **Put spaces around all infix operators.**
```r
    trparsopt = initparsopt/ (1 + initparsopt)
                          ~^
```
[R/mbd_ml.R:132:42:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_ml.R#L133) *style:* **Use <-, not =, for assignment.**
```r
    trparsfix = parsfix/ (1 + parsfix)
              ^
```
[R/mbd_ml.R:133:24:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_ml.R#L133) *style:* **Put spaces around all infix operators.**
```r
    trparsfix = parsfix/ (1 + parsfix)
                      ~^
```
[R/mbd_ml.R:134:38:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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:222:33:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_pure_multiple_birth.R#L222) *style:* **Put spaces around all infix operators.**
```r
        trparsopt <- initparsopt/ (1 + initparsopt)
                               ~^
```
[R/mbd_pure_multiple_birth.R:224:29:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_pure_multiple_birth.R#L224) *style:* **Put spaces around all infix operators.**
```r
        trparsfix <- parsfix/ (1 + parsfix)
                           ~^
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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)$births)})
                  ^
```
[R/mbd_sim.R:369:19:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_sim.R#L369) *style:* **Put spaces around all infix operators.**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
                 ~^~
```
[R/mbd_sim.R:369:57:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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)$births)})
                                                        ^
```
[R/mbd_sim.R:369:65:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_sim.R#L369) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    all_the_births=sapply(sim_data, FUN = function(brts){return(brts2time_intervals_and_births(brts)$births)})
                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:371:19:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_sim.R#L371) *style:* **Use <-, not =, for assignment.**
```r
    all_the_births=brts2time_intervals_and_births(sim_data)$births
                  ^
```
[R/mbd_sim.R:371:19:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_sim.R#L371) *style:* **Put spaces around all infix operators.**
```r
    all_the_births=brts2time_intervals_and_births(sim_data)$births
                 ~^~
```
[R/mbd_sim.R:371:20:](https://github.com/Giappo/mbd/blob/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/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/845579dd98fdacfdc358c45b8e097208b4d859e0/R/mbd_utils.R#L21) *style:* **Use <-, not =, for assignment.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                     ^
```


This conflicts with 7c0ef4d441b3833e721df58f56e2cb8c81b34df4 where you @PACKAGE_VERSION@ as the version-info.
The soversion should not be tied to the package version. If you do that, you most likely misunderstand how soversion works.
See https://autotools.io/libtool/version.html


What have you done?!


При таких проверках могут возникнуть коллизии. Вдруг неожиданно окажется пользователь, у которого имя содержит 'show')
Да и с точки зрения быстродействия тоже, быстрее проверить 1 элемент, чем всю строку


>
>
> https://twitter.com/CoralineAda/status/1029162264979546112
>
> CoralineAda is in violation of the code of conduct!
> as shes making a generalization of white people and being 'hateful' towards them

If Coraline is to embody the "one rule for thee, one rule for me" attitude, this CoC should apply equally to her all things considered.  After all, this project can be forked with the CoC commit reverted so this policy can be used instead -> https://github.com/domgetter/NCoC


---

# FILENAME : please use your OpenClassrooms's name, available in your url.
# Example: https://openclassrooms.com/membres/celinemartinet
# must be the name of your file. If file name is celinemartinet.md, title is celinemartinet.
# lowercase, no blank space, Capital case or special character.
title: Boubacar

# First name or full name
name: Boubacar Tondé
date: 2018-09-27 13:17

# One line.
# If you need more space, go to the next line and add 4 spaces on the left, as in 'description'.
objective: Apprendre comment ça marche toute cette technologie qu'on utilise tous les jours avec nos mobiles, et pourquoi pas en faire un métier.
short_description: J'aime la musiques, les voyages. la cuisine,  et je pense que je vais aimer le code, malgré les migraines qu'il me file.

# don't touch that
template: students
description:
   Je suis musicien depuis plus d'une vingtaine d'année.
   Je suis entré en formation le 6 septembre 2018 en Option développeur d'applications IOS.
Pour moi qui voudrais faire une reconversion,  cette formation OCR, me permettra de continuer à faire ma musique, tout en suivant les cours en ligne.
# image must be located in content/images/students
# name should be the same as this file. Eg: celinemartinet.png
image: Boubacar.jpg

# Change this to True when you do you pull request.
public: True

# You need to keep the exact same structure for each new project.
projects:
  - title: Présentez-vous !
    description: Une présentation de moi-même et un lien vers mon LinkedIn.
    # Create a new repository for your images. Name it the same as your nickname and profile picture.
    # Image must be here: content/students/yourrepo/project1.png
    image: Boubacar/projet_1.png
    link:vhttps://www.linkedin.com/in/boubacar-tonde-537790170/
    # 'true' makes it fully available.
    # 'false' will add a black layer on the picture. IT WILL BE PUBLIC!
    finished: true
  - title: Intégrez la communauté !
    description: Modifier un projet Open Source pour comprendre le fonctionnement de Git, de Github et des pull requests.
    image: ratus/projet_2.png
    link: https://github.com/Thiecko
    finished: true
  - title: Aidez MacGyver à sortir !
    description: Création d’un jeu développé en Python et utilisant PyGame.
    image: ratus/projet_3.png
    link: https://www.github.com
    finished: false
---


A small white bar/line has been added to the top of the sidebar, it looks bad when using the Arc Theme, maybe implement an option to turn it off?


ད་ནི་བཟོ་བཅོས་བྱས་ཚར་ཡོད།


Please remove this comment and extra lines and update description with what changes are done and why.
Code should be clean


Hi kwk,
why will it overwritten now?


"Add my Introduction file, and picture "


probably, to align with common way of how it is always expressed: `Make sure you have Node.js version v8 or later installed.`


@natnat201193 if the values are 0 that means they are just read from the DBC and not overwritten, so I just changed what I needed and left everything else as is.


This comments too are to be removed


s


Trying to delete


Successfully aliased the URL <https://next-calorie-uydfqtdltm.now.sh> to the following alias.

* https://calorie.now.sh


コメント記入者：卜部
平仄として、複数カラムを表示する場合は以下のように表記しましょう

p_name,
price


Just remove 2 and 3 from the variables names. Physical parameters as a class is a good idea, nevertheless numbers are confusing.


My mistake. At the very beginning we had a function that wasn't normalized on 1 and had additional parameters for such cases.


補足
以下も同様の指摘ありますが、冗長なため省略します。


my test


base_url.endsWith -> error on IE

https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/endsWith#Polyfill


Oh, it's on 100 now :D


We already have function `absorptivity`.


> Hi kwk,
> why will it overwritten now?

This code is almost 3 years old and I've overwritten it because the non-browse features were broken, I think.


Can you please check emails and get back to me? Thank you :)


objectList.num
objectList - массив, он вроде не содержит поле num, это разве работает?


What is the 0d28081 that is mentioned in the commit description?


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