[R/mbd_loglik_utils.R:240:26:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L240) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:307:46:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:329:31:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L329) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:329:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L329) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:363:1:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:377:31:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L377) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:377:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L377) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:394:54:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:425:31:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L425) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:425:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik_utils.R#L425) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:449:54:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:475:18:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:731:35:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:138:13:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L138) *style:* **Commas should always have a space after.**
```r
      q_t[1,] <- q_i
            ^
```
[R/mbd_loglik.R:158:15:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L158) *style:* **Commas should always have a space after.**
```r
        q_t[t,] <- a_operator(
              ^
```
[R/mbd_loglik.R:159:34:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L159) *style:* **Commas should always have a space after.**
```r
          q_matrix = q_t[(t - 1),],
                                 ^
```
[R/mbd_loglik.R:170:17:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L170) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- negatives_correction(q_t[t,], pars)
                ^
```
[R/mbd_loglik.R:170:22:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:170:49:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L170) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- negatives_correction(q_t[t,], pars)
                                                ^
```
[R/mbd_loglik.R:172:30:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L172) *style:* **Commas should always have a space after.**
```r
        if (any(is.nan(q_t[t,]))) {
                             ^
```
[R/mbd_loglik.R:174:38:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L174) *style:* **Commas should always have a space after.**
```r
            print(pars); print(q_t[t,])
                                     ^
```
[R/mbd_loglik.R:178:23:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L178) *style:* **Commas should always have a space after.**
```r
        if (any(q_t[t,] < 0)) {
                      ^
```
[R/mbd_loglik.R:184:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L184) *style:* **Commas should always have a space after.**
```r
        C[t] <- 1 / (sum(q_t[t,])); q_t[t,] <- q_t[t,] * C[t]
                               ^
```
[R/mbd_loglik.R:184:43:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L184) *style:* **Commas should always have a space after.**
```r
        C[t] <- 1 / (sum(q_t[t,])); q_t[t,] <- q_t[t,] * C[t]
                                          ^
```
[R/mbd_loglik.R:184:54:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L184) *style:* **Commas should always have a space after.**
```r
        C[t] <- 1 / (sum(q_t[t,])); q_t[t,] <- q_t[t,] * C[t]
                                                     ^
```
[R/mbd_loglik.R:188:1:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:190:17:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L190) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- (matrix_b %*% q_t[t,])
                ^
```
[R/mbd_loglik.R:190:42:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L190) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- (matrix_b %*% q_t[t,])
                                         ^
```
[R/mbd_loglik.R:192:19:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L192) *style:* **Commas should always have a space after.**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                  ^
```
[R/mbd_loglik.R:192:24:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:192:51:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L192) *style:* **Commas should always have a space after.**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                                                  ^
```
[R/mbd_loglik.R:194:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L194) *style:* **Commas should always have a space after.**
```r
          if (any(is.nan(q_t[t,]))) {
                               ^
```
[R/mbd_loglik.R:196:40:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L196) *style:* **Commas should always have a space after.**
```r
              print(pars); print(q_t[t,])
                                       ^
```
[R/mbd_loglik.R:200:25:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L200) *style:* **Commas should always have a space after.**
```r
          if (any(q_t[t,] < 0)) {
                        ^
```
[R/mbd_loglik.R:206:34:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L206) *style:* **Commas should always have a space after.**
```r
          D[t] <- 1 / (sum(q_t[t,])); q_t[t,] <- q_t[t,] * D[t]
                                 ^
```
[R/mbd_loglik.R:206:45:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L206) *style:* **Commas should always have a space after.**
```r
          D[t] <- 1 / (sum(q_t[t,])); q_t[t,] <- q_t[t,] * D[t]
                                            ^
```
[R/mbd_loglik.R:206:56:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_loglik.R#L206) *style:* **Commas should always have a space after.**
```r
          D[t] <- 1 / (sum(q_t[t,])); q_t[t,] <- q_t[t,] * D[t]
                                                       ^
```
[R/mbd_loglik.R:231:5:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_ml.R#L131) *style:* **Put spaces around all infix operators.**
```r
    trparsopt = initparsopt/(1 + initparsopt)
                          ~^~
```
[R/mbd_ml.R:131:29:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_ml.R#L131) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    trparsopt = initparsopt/(1 + initparsopt)
                            ^
```
[R/mbd_ml.R:132:42:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_ml.R#L133) *style:* **Put spaces around all infix operators.**
```r
    trparsfix = parsfix/(1 + parsfix)
                      ~^~
```
[R/mbd_ml.R:133:25:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_ml.R#L133) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    trparsfix = parsfix/(1 + parsfix)
                        ^
```
[R/mbd_ml.R:134:38:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:212:60:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_ml.R#L212) *style:* **Commas should always have a space after.**
```r
      tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii]
                                                           ^
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:222:34:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_pure_multiple_birth.R#L222) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                                 ^
```
[R/mbd_pure_multiple_birth.R:224:29:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:224:30:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_pure_multiple_birth.R#L224) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                             ^
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:254:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_pure_multiple_birth.R#L254) *style:* **Put spaces around all infix operators.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                              ~^~
```
[R/mbd_pure_multiple_birth.R:254:33:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_pure_multiple_birth.R#L254) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                                ^
```
[R/mbd_pure_multiple_birth.R:264:11:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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_pure_multiple_birth.R:275:68:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_pure_multiple_birth.R#L275) *style:* **Commas should always have a space after.**
```r
              tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii]
                                                                   ^
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:93:10:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L93) *style:* **Commas should always have a space after.**
```r
      L[,4] <- -1
         ^
```
[R/mbd_sim.R:95:27:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L95) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t, 0,-1, -1)
                          ^
```
[R/mbd_sim.R:96:24:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L96) *style:* **Commas should always have a space after.**
```r
      L[2, 1:4] <- c(t,-1, 2, -1)
                       ^
```
[R/mbd_sim.R:101:11:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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:126:25:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L126) *style:* **Commas should always have a space after.**
```r
            L[abs(dead),4] <- t
                        ^
```
[R/mbd_sim.R:134:5:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L134) *style:* **Variable or function name should be snake_case.**
```r
    L <- L[(1:total_count),]
    ^
```
[R/mbd_sim.R:134:28:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L134) *style:* **Commas should always have a space after.**
```r
    L <- L[(1:total_count),]
                           ^
```
[R/mbd_sim.R:135:31:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L135) *style:* **Commas should always have a space after.**
```r
    extinct_species <- sum(L[,4] != -1)
                              ^
```
[R/mbd_sim.R:137:23:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L137) *style:* **Commas should always have a space after.**
```r
    tips <- length(L[,4][L[,4] == -1])
                      ^
```
[R/mbd_sim.R:137:29:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L137) *style:* **Commas should always have a space after.**
```r
    tips <- length(L[,4][L[,4] == -1])
                            ^
```
[R/mbd_sim.R:139:19:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L139) *style:* **Commas should always have a space after.**
```r
    alive <- L[L[,4] == -1,]
                  ^
```
[R/mbd_sim.R:139:28:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L139) *style:* **Commas should always have a space after.**
```r
    alive <- L[L[,4] == -1,]
                           ^
```
[R/mbd_sim.R:142:35:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L231) *style:* **Put spaces around all infix operators.**
```r
      L <- matrix(0, nrow=1e6,4)
                        ~^~
```
[R/mbd_sim.R:231:31:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L231) *style:* **Commas should always have a space after.**
```r
      L <- matrix(0, nrow=1e6,4)
                              ^
```
[R/mbd_sim.R:232:10:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L232) *style:* **Commas should always have a space after.**
```r
      L[,4] <- -1
         ^
```
[R/mbd_sim.R:234:24:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L234) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t,0,-1,-1)
                       ^
```
[R/mbd_sim.R:234:26:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L234) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t,0,-1,-1)
                         ^
```
[R/mbd_sim.R:234:29:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L234) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t,0,-1,-1)
                            ^
```
[R/mbd_sim.R:235:24:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L235) *style:* **Commas should always have a space after.**
```r
      L[2, 1:4] <- c(t,-1, 2,-1)
                       ^
```
[R/mbd_sim.R:235:30:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L235) *style:* **Commas should always have a space after.**
```r
      L[2, 1:4] <- c(t,-1, 2,-1)
                             ^
```
[R/mbd_sim.R:238:9:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L259) *style:* **Put spaces around all infix operators.**
```r
            dead <- sample(pool, replace = F, size=1)
                                                 ~^~
```
[R/mbd_sim.R:263:23:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L263) *style:* **Commas should always have a space after.**
```r
          L[abs(dead),4] <- t
                      ^
```
[R/mbd_sim.R:264:28:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L268) *style:* **Put spaces around all infix operators.**
```r
    L=L[(1:total_count),]
    ~^~
```
[R/mbd_sim.R:268:25:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L268) *style:* **Commas should always have a space after.**
```r
    L=L[(1:total_count),]
                        ^
```
[R/mbd_sim.R:269:21:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L269) *style:* **Use <-, not =, for assignment.**
```r
    extinct_species = sum(L[,4]!=-1)
                    ^
```
[R/mbd_sim.R:269:30:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L269) *style:* **Commas should always have a space after.**
```r
    extinct_species = sum(L[,4]!=-1)
                             ^
```
[R/mbd_sim.R:269:32:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[,4][L[,4]==-1])
       ~^~
```
[R/mbd_sim.R:271:20:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L271) *style:* **Commas should always have a space after.**
```r
    tips=length(L[,4][L[,4]==-1])
                   ^
```
[R/mbd_sim.R:271:26:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L271) *style:* **Commas should always have a space after.**
```r
    tips=length(L[,4][L[,4]==-1])
                         ^
```
[R/mbd_sim.R:271:28:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[,4]==-1,]
        ~^~
```
[R/mbd_sim.R:273:16:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L273) *style:* **Commas should always have a space after.**
```r
    alive=L[L[,4]==-1,]
               ^
```
[R/mbd_sim.R:273:18:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[,4]==-1,]
                ~^~~
```
[R/mbd_sim.R:273:23:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/R/mbd_sim.R#L273) *style:* **Commas should always have a space after.**
```r
    alive=L[L[,4]==-1,]
                      ^
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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/216ea98fab74c31ccb5ac3bffccab5599e941e93/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.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


This error log will be confusing. Most probably one of the iscsi timeout key will be a success & others might fail. We are logging only the error.


The original error is swallowed.


done


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

I updated the Github team because of this commit.

- @carreau was added to this feedstock maintenance team.

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

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

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
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Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

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{}
//test

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


sorry doesn't work with version 1.7.60 nor 1.4.10

C:\Temp\P3X_beyond_fcc_on_air_side-v1>lightbridge_stm32_hardcod
er.py -vv -x -e P3X_FW_V01.07.0060_m0900.elf
P3X_FW_V01.07.0060_m0900.elf: Opening for extract
P3X_FW_V01.07.0060_m0900.elf: Pattern of cmd_exec_set09_cmd12-original was not f
ound; closest was 1 lines at 0x1001e9e
P3X_FW_V01.07.0060_m0900.elf: Pattern of cmd_exec_set09_cmd12-constatt was not f
ound; closest was 1 lines at 0x1001e9e
P3X_FW_V01.07.0060_m0900.elf: Pattern of tcx_config_power_zone was not found; cl
osest was 0 lines at 0x0
P3X_FW_V01.07.0060_m0900.elf: Pattern of init_fpga_config was not found; closest
 was 2 lines at 0x10062b8
Traceback (most recent call last):
  File "C:\Temp\P3X_beyond_fcc_on_air_side-v1\lightbridge_stm32
_hardcoder.py", line 1059, in <module>
    main()
  File "C:\Temp\P3X_beyond_fcc_on_air_side-v1\lightbridge_stm32
_hardcoder.py", line 1039, in main
    armfw_elf_lbstm32_extract(po, elffh)
  File "C:\Temp\P3X_beyond_fcc_on_air_side-v1\lightbridge_stm32
_hardcoder.py", line 889, in armfw_elf_lbstm32_extract
    raise ValueError("No known values found in ELF file.")
ValueError: No known values found in ELF file.


I was going to comment, but I forgot, that for it to be an easter egg it should be rare


iskyex


me


PHP_EOL does not convert the shelloutput correctly on windows, will investigate


База данных, залить в форму отчета.


klaida varde


6.GB memory might be too less, 12.15 GB memory was needed when I was testing
Required walltime  was around 15 min for such a testrun


Pulled Richmond's changes.
Added dns to the net_init to allow the application to specify a DNS server if DHCP doesn't find one or DHCP is disabled.


For testing use unit tests instead of such long main method.


Successfully aliased the URL <https://simple-now-app-nhxqgskpsq.now.sh> to the following alias.

* https://akurulk-4-simple-now-app.now.sh


Not correctly state the humidity sensor is connected BME280


Formula One Game/Team Components/Driver.cs

nuimk .Team_Components nuo visu


Using such generic exceptions as Error, RuntimeException, Throwable, and Exception prevents calling methods from handling true, system-generated exceptions differently than application-generated errors.


BRS Document


I see; I will work on compatibility with different FW versions as soon as I finish packet_received_attenuation_override.


Seems like going for chr(10) or "/n" seems to be the best option to ensure cross os compat here.


`tempname_dir` is added to export.


Guide how to connect the project


vec3 N = tangentToWorldMatrix * (2.0 * (texture2D(u_NormalMap, texNormal).xyz - 0.5));

... this is how it is done in DBS entity glsl


Assignments within sub-expressions are hard to spot and therefore make the code less readable. Ideally, sub-expressions should not have side-effects.


This method should be T[] toArray(), read task description


Type parameters that aren't used are dead code, which can only distract and possibly confuse developers during maintenance. Therefore, unused type parameters should be removed.


更新至52节


Sir, shall I change it to glog.Infof(...) to know whether the timeout setting is the default value or passed in provisioner.


No need for pointers


If they're not pointers, destructor can be empty as well


enum class SystemPriority { ... }


replace -> with . again, if removing pointers


1) Create new index2.html
2) To plug css
3) Create list and ten elements
4) Position list on center top
5) Any style for list
6) Create in center bottom form :
- name
- last name
- email
- telephone
(name and telephone be sure)

7) And create in right bottom position button "add" (style any)


@fgalan

*in our lab tests in a machine with Orion 1.13.0 running with 4 RAM.*

Is an unit of RAM **GB** ? (Is '4 GB RAM' correct?)


??? Doesn't this handle the npe?


Correct. Quick fix on the way. Thanks for noticing!


move exception to seperate cmake definition
```cmake
set(EXCEPTIONS_SRC
    exceptions/ComponentManagerNotFoundException.h
)

...
add_library(engine ${ECS_SRC} ... ${EXCEPTIONS_SRC})
```


Nice performance improvement!


margin: 10;


Very good; please can we also have an integration test for `additionalProperties: false` just to make sure it all fits together right? :-)


j'ai retire deux icones d'image pour en obtenir plus que 8


Refactored queries into queries.js

:package: demo


<img alt="clapper" height="30" width="20" src="https://lh3.googleusercontent.com/4-xBGWmF2OwFW2fJYJpVkvyGPKjOI1mhEo2SeMpNT9dk_aRw6xJud8iBFer_efE2Egj55Dfg6qWGkN5ESp7DndsxLYddxHNTOUFAdNqXO0jJFDhFPrSenXHIrSFNJmYcw2Qt8O_PA5baA7U9gmYIF1B-NWjUfBJ8eWhQ5zxIQs5YyvZLAatLPcnaVsp_hoeSOBHk2uRxaP5IHlnO2cZg1tzkmeJNWMALeYqaFcxcNZAQTOUPugNcbuQ6GjA4OScd_U0EBrcgWMHkz1Eo2meFKCXbqC7NkZhQhaD5crMxbzoBQ2L_9NxKm15oOhn-lS0K2QbHxjldjr1gFR_6wtsJ9HmrDWAhqN7AJAr0RnXl2b2t76m7FQqz0TEyxV3FlJsWJMWdkpQx9gKD2y6SFF0MuV1k8EHVQPyIdWNQjq2RmIPKSz3Q1gclcYmmEXo8_j7G_bGOk1np5Co-aMPgN6z0yhRaZl9Yn5LsQyRGiQpANBjo2OUcumhRN40eKHutjSlZ5CmJBtVoiHMWmkNfWoAW-8Fc6KNQIB_I8vIHIJpWe3V3wnaYLq6Urq3SFsCVzGNu0SfBsrQ1b1NZopinPLNy9pcXbCfZj7Gb2k6odpOuYHItkqijwxvsPhIM5I1lNzYpvBw7CeYylqTSRWS--OOZEpAQxiM8FGDwdvBpq8WqHeUdPUTjw1-zOLDM=w597-h901-no"> Refactored queries into queries.js

  :clapper: cypress test video


Checkmarx scan results 27 Sep 2018 13:59 UTC +03:00

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Commit ID	Owner

a23cad998261c81bf63aa21ac681a2e8b5303e7c	@web-flow


Do you not have to change row of order for the genesis hash and the nonce init....since your first validate hash operation will turn out false since genesis hash is calculated with out nonce=0 ?


- Pinning the overlay text chat widget feature has been reverted, all code along with it removed.
- New action type: `APPLICATION_STORE_RESET_NAVIGATION`
- New constant: `STORE_NAVIGATION_CACHE_TIME = 6e5`


spring:
  profiles:
    active:
    - dev
---
spring:
  profiles: dev
  application:
    name: microservicecloud-config-atguigu-dev
---
spring:
  profiles: test
  application:
name: microservicecloud-config-atguigu-test


No sir,
iscsi having different timeouts like replacement_timeout, login_timeout, logout_timeout e.t.c., So I named it like getISCSITimeoutvalues(...)


Sir, shall I change it to glog.Infof(...) to know whether the timeout setting is the default value or fetching from pv object.


Those 3 number should be put into an enum.


I got this error on my dinobot4k:

/etc/rc0.d/S89suspend: line 6: syntax error: unexpected "then"


Веб мут всё равно не работает. Проверил,  выдал мут игроку, он продолжал говорить.
Ведать это в самом плагине MA нужно править.


what is this


![](https://github.trello.services/images/mini-trello-icon.png) [Stop for Trivia](https://trello.com/c/aP2BbbhN/79-stop-for-trivia)


![capture d ecran 2018-09-27 a 13 01 36](https://user-images.githubusercontent.com/43266233/46141944-ade0ce00-c255-11e8-8235-b63e652ac6cd.png)


Success


@vaaski we're most likely changing name to Apollo and aleksy had his try at a logo. check discord


Ok will adapt that _ can't say whether the Travis CI testing uses that much memory though...


Glad to hear it, @mhaig; it's always nice when you can add another little efficiency to your workflow :-)


![capture d ecran 2018-09-27 a 13 01 36](https://user-images.githubusercontent.com/43266233/46142083-116afb80-c256-11e8-9d8c-1833add10b35.png)


This and `OPENSHIFT_INSTALL_SSH_PUB_KEY_PATH` aren't supported in the installer yet, but I think we want to add them as alternatives to the non-`PATH` forms.  Otherwise we'd need to involve a shell in this job instead of going straight to the installer (which isn't the end of the world ;).


![capture d ecran 2018-09-27 a 13 01 36](https://user-images.githubusercontent.com/43266233/46142105-20ea4480-c256-11e8-8f52-1d20b3ef0fe9.png)


クリックイベントを追加しました。


also sorted it


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

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{}
//test

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I'll wait for your proposal, I'm still not convinced this way is valid :(


@dmach is working on solution.


Hi how can i run instabot on server?
please help me.


A lot of my steps could have been committed separately. I'm still working on remembering to commit after each crucial change.


multiple choice形式のみ取得するように変更しました。


Please change to debug


追加した解答欄
```answer_c```
```answer_d```
に変数に代入しました


Can you please change all info to debug


You have reached the limit of Now deployments through the GitHub integration in a 5 minutes window.

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im starting to think that all this `epsilon`, `max`, `abs` etc is a bit too complicated and not flexible.

We could just do

```"isEqual": "(a, b) => Math.abs(a) === Math.abs(b)"```

Then in the code just do

```const isEqual = eval(item.isEqual);```