[R/mbd_calc_max_lik.R:81:19:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_calc_max_lik.R#L81) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
    param_name <- get_mbd_param_names()[i]
                  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:24:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
  matrix_a[n_species, n_species] <- matrix_a[n_species, n_species] * (1 - q) ^ (n_species - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:42:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L42) *style:* **Variable or function name should be snake_case.**
```r
  M <- lambda * matrix_builder(n_species = max_number_of_species, k = k, q = q)
  ^
```
[R/mbd_loglik_utils.R:45:51:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(M) <= (-lambda) * (1 - (1 - q) ^ (k + nvec) ) - mu * (nvec + k)
                                                  ^
```
[R/mbd_loglik_utils.R:121:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L121) *style:* **Variable or function name should be snake_case.**
```r
create_a.no_mbd <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:149:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L149) *style:* **Variable or function name should be snake_case.**
```r
create_b.no_mbd <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:162:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L162) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
  ^
```
[R/mbd_loglik_utils.R:191:5:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L191) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:191:19:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L191) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:206:7:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L206) *style:* **Variable or function name should be snake_case.**
```r
      result.nan <- (any(!is.numeric(result)) || any(is.nan(result)))
      ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:210:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L210) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:236:26:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L236) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:294:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L294) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- a_operator(
  ^~
```
[R/mbd_loglik_utils.R:303:45:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L303) *style:* **Put spaces around all infix operators.**
```r
  soc + max(mvec[(mvec %in% which((cumsum(Pm/sum(Pm))) <= 0.95))])
                                           ~^~
```
[R/mbd_loglik_utils.R:311:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L311) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:325:31:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L325) *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:325:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L325) *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:359:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L359) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:373:31:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L373) *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:373:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L373) *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:390:54:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L390) *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:403:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L403) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:403:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L403) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:416:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L416) *style:* **Only use double-quotes.**
```r
    cat('mu is supposed to be equal zero to use this function')
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:417:12:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L417) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:421:31:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L421) *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:421:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L421) *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:445:54:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L445) *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:449:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L449) *style:* **Lines should not be more than 80 characters.**
```r
  opposite_tips_components <- (m + 1)[!((m + 1) %in% (tips_components[1]:tips_components[2]))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:469:18:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L469) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:471:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L471) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:547:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L547) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:557:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L557) *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:591:18:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L591) *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:634:16:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L634) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:725:35:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik_utils.R#L725) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1)/pc_1;
                                 ~^~
```
[R/mbd_loglik.R:79:15:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L79) *warning:* **no visible global function definition for ‘pmb_loglik’**
```r
    loglik <- pmb_loglik(pars = pars, brts = brts, soc = soc)
              ^~~~~~~~~~
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:173:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L173) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        {
        ^
```
[R/mbd_loglik.R:174:27:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L174) *style:* **Only use double-quotes.**
```r
          if (Sys.info()[['sysname']] == "Windows")
                          ^~~~~~~~~
```
[R/mbd_loglik.R:175:11:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L175) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_loglik.R:176:38:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L176) *style:* **Commas should always have a space after.**
```r
            print(pars); print(q_t[t,])
                                     ^
```
[R/mbd_loglik.R:180:23:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L180) *style:* **Commas should always have a space after.**
```r
        if (any(q_t[t,] < 0)) {
                      ^
```
[R/mbd_loglik.R:186:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L186) *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:186:43:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L186) *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:186:54:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L186) *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:189:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L189) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        {
        ^
```
[R/mbd_loglik.R:191:11:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L191) *style:* **Variable or function name should be snake_case.**
```r
          B <- create_b(lambda = lambda, nu = nu, q = q, k = k, b = births[t],
          ^
```
[R/mbd_loglik.R:193:17:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L193) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- (B %*% q_t[t,])
                ^
```
[R/mbd_loglik.R:193:35:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L193) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- (B %*% q_t[t,])
                                  ^
```
[R/mbd_loglik.R:195:19:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L195) *style:* **Commas should always have a space after.**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                  ^
```
[R/mbd_loglik.R:195:24:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L195) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                       ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:195:51:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L195) *style:* **Commas should always have a space after.**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                                                  ^
```
[R/mbd_loglik.R:197:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L197) *style:* **Commas should always have a space after.**
```r
          if (any(is.nan(q_t[t,])))
                               ^
```
[R/mbd_loglik.R:198:11:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L198) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_loglik.R:199:29:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L199) *style:* **Only use double-quotes.**
```r
            if (Sys.info()[['sysname']] == "Windows")
                            ^~~~~~~~~
```
[R/mbd_loglik.R:200:13:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L200) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
            {
            ^
```
[R/mbd_loglik.R:201:40:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L201) *style:* **Commas should always have a space after.**
```r
              print(pars); print(q_t[t,])
                                       ^
```
[R/mbd_loglik.R:205:25:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L205) *style:* **Commas should always have a space after.**
```r
          if (any(q_t[t,] < 0)) {
                        ^
```
[R/mbd_loglik.R:211:34:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L211) *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:211:45:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L211) *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:211:56:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L211) *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:236:5:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L236) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * q_t[t, (missnumspec + 1)]
    ^
```
[R/mbd_loglik.R:236:41:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_loglik.R#L236) *style:* **Trailing whitespace is superfluous.**
```r
    P  <- vm * q_t[t, (missnumspec + 1)]
                                        ^
```
[R/mbd_ml.R:66:17:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L66) *style:* **Only use double-quotes.**
```r
  optimmethod = 'simplex',
                ^~~~~~~~~
```
[R/mbd_ml.R:74:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L74) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/mbd_ml.R:84:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L84) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml.R:87:31:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L87) *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:87:49:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L87) *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:99:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L99) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml.R:134:15:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L134) *style:* **Use <-, not =, for assignment.**
```r
    trparsopt = initparsopt/(1 + initparsopt)
              ^
```
[R/mbd_ml.R:134:28:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L134) *style:* **Put spaces around all infix operators.**
```r
    trparsopt = initparsopt/(1 + initparsopt)
                          ~^~
```
[R/mbd_ml.R:134:29:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L134) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    trparsopt = initparsopt/(1 + initparsopt)
                            ^
```
[R/mbd_ml.R:135:42:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L135) *style:* **Use <-, not =, for assignment.**
```r
    trparsopt[which(initparsopt == Inf)] = 1
                                         ^
```
[R/mbd_ml.R:136:15:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L136) *style:* **Use <-, not =, for assignment.**
```r
    trparsfix = parsfix/(1 + parsfix)
              ^
```
[R/mbd_ml.R:136:24:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L136) *style:* **Put spaces around all infix operators.**
```r
    trparsfix = parsfix/(1 + parsfix)
                      ~^~
```
[R/mbd_ml.R:136:25:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L136) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    trparsfix = parsfix/(1 + parsfix)
                        ^
```
[R/mbd_ml.R:137:38:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L137) *style:* **Use <-, not =, for assignment.**
```r
    trparsfix[which(parsfix == Inf)] = 1
                                     ^
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L203) *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:203:62:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L203) *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:204:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L205) *style:* **Lines should not be more than 80 characters.**
```r
  out2 <- data.frame(t(ml_pars1), loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:209:3:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L209) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml.R:210:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
    tobeprint <- paste(tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:210:77:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L210) *style:* **Commas should always have a space after.**
```r
    tobeprint <- paste(tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii])
                                                                            ^
```
[R/mbd_ml.R:219:19:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L219) *style:* **Only use double-quotes.**
```r
    s2 <- sprintf('Maximum loglikelihood: %f',ML)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:219:47:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_ml.R#L219) *style:* **Commas should always have a space after.**
```r
    s2 <- sprintf('Maximum loglikelihood: %f',ML)
                                              ^
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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:39:5:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L39) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_pure_multiple_birth.R:41:41:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L41) *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:42:27:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L42) *style:* **Put spaces around all infix operators.**
```r
        stats::dpois(i, nu*time_intervals[t], log = FALSE) != 0]
                         ~^~
```
[R/mbd_pure_multiple_birth.R:43:33:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L43) *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:43:70:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L43) *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:47:24:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L47) *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:47:61:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L47) *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:55:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
    ) + lambda * k[-length(k)] * (births == 1)                                               # lambda contribution: lambda*k (only if b==1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:81:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:95:5:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L95) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_pure_multiple_birth.R:101:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L101) *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:103:24:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:103:61:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:111:17:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (1 - q)^(k[-length(k)] - births)                 # (1)
                ^
```
[R/mbd_pure_multiple_birth.R:150:33:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L150) *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:159:15:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L159) *warning:* **no visible global function definition for ‘pmb_loglik’**
```r
    loglik <- pmb_loglik(pars = pars1, brts = brts)
              ^~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:162:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L162) *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:172:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L172) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML <- function(
^~~~~~
```
[R/mbd_pure_multiple_birth.R:181:17:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L181) *style:* **Only use double-quotes.**
```r
  optimmethod = 'simplex',
                ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:186:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L186) *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/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L188) *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:189:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L189) *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:194:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L194) *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:195:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L195) *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:223:33:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L223) *style:* **Put spaces around all infix operators.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                               ~^~
```
[R/mbd_pure_multiple_birth.R:223:34:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L223) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                                 ^
```
[R/mbd_pure_multiple_birth.R:225:29:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L225) *style:* **Put spaces around all infix operators.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                           ~^~
```
[R/mbd_pure_multiple_birth.R:225:30:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L225) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                             ^
```
[R/mbd_pure_multiple_birth.R:237:8:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L237) *style:* **Trailing whitespace is superfluous.**
```r
      )
       ^
```
[R/mbd_pure_multiple_birth.R:238:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L238) *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:241:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L241) *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:245:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L245) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:250:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L250) *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:255:32:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L255) *style:* **Put spaces around all infix operators.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                              ~^~
```
[R/mbd_pure_multiple_birth.R:255:33:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L255) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                                ^
```
[R/mbd_pure_multiple_birth.R:265:11:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L265) *style:* **Variable or function name should be snake_case.**
```r
          ML <- as.numeric(unlist(out$fvalues))
          ^~
```
[R/mbd_pure_multiple_birth.R:266:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L266) *style:* **Lines should not be more than 80 characters.**
```r
          out2 <- data.frame(t(ml_pars1), loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:270:11:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L270) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_pure_multiple_birth.R:271:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L271) *style:* **Lines should not be more than 80 characters.**
```r
            tobeprint <- paste(tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:271:85:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L271) *style:* **Commas should always have a space after.**
```r
            tobeprint <- paste(tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii])
                                                                                ^
```
[R/mbd_pure_multiple_birth.R:278:25:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L278) *style:* **Only use double-quotes.**
```r
          s2 <- sprintf('Maximum loglikelihood: %f',ML)
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:278:53:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L278) *style:* **Commas should always have a space after.**
```r
          s2 <- sprintf('Maximum loglikelihood: %f',ML)
                                                    ^
```
[R/mbd_pure_multiple_birth.R:286:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_pure_multiple_birth.R#L286) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:117:62:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L117) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            pool <- c(pool, abs(new_interval) * sign(parents) )
                                                             ^
```
[R/mbd_sim.R:126:25:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:142:60:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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:142:67:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:144:108:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L144) *style:* **Do not place spaces around code in parentheses or square brackets.**
```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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:145:100:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L145) *style:* **Do not place spaces around code in parentheses or square brackets.**
```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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:146:85:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:147:67:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:154:92:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L154) *style:* **Do not place spaces around code in parentheses or square brackets.**
```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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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/85a38d9efb4c18f6c0be29e176934090c4b14462/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:227:5:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L227) *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:228:18:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L228) *style:* **Use <-, not =, for assignment.**
```r
      total_count=init_n_lineages
                 ^
```
[R/mbd_sim.R:228:18:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L228) *style:* **Put spaces around all infix operators.**
```r
      total_count=init_n_lineages
                ~^~
```
[R/mbd_sim.R:232:7:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L232) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow=1e6,4)
      ^
```
[R/mbd_sim.R:232:26:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L232) *style:* **Put spaces around all infix operators.**
```r
      L <- matrix(0, nrow=1e6,4)
                        ~^~
```
[R/mbd_sim.R:232:31:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L232) *style:* **Commas should always have a space after.**
```r
      L <- matrix(0, nrow=1e6,4)
                              ^
```
[R/mbd_sim.R:233:10:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L233) *style:* **Commas should always have a space after.**
```r
      L[,4] <- -1
         ^
```
[R/mbd_sim.R:235:24:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L235) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t,0,-1,-1)
                       ^
```
[R/mbd_sim.R:235:26:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L235) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t,0,-1,-1)
                         ^
```
[R/mbd_sim.R:235:29:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L235) *style:* **Commas should always have a space after.**
```r
      L[1, 1:4] <- c(t,0,-1,-1)
                            ^
```
[R/mbd_sim.R:236:24:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L236) *style:* **Commas should always have a space after.**
```r
      L[2, 1:4] <- c(t,-1, 2,-1)
                       ^
```
[R/mbd_sim.R:236:30:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L236) *style:* **Commas should always have a space after.**
```r
      L[2, 1:4] <- c(t,-1, 2,-1)
                             ^
```
[R/mbd_sim.R:239:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L239) *style:* **Variable or function name should be snake_case.**
```r
        deltaT <- stats::rexp(1, rate = (lambda + n_species * mu))
        ^~~~~~
```
[R/mbd_sim.R:245:9:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L245) *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:252:1:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L252) *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:254:50:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L254) *style:* **Put spaces around all infix operators.**
```r
          L[new_interval, 3] <- abs(new_interval)*sign(parents)
                                                ~^~
```
[R/mbd_sim.R:256:44:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L256) *style:* **Put spaces around all infix operators.**
```r
          pool <- c(pool, abs(new_interval)*sign(parents) )
                                          ~^~
```
[R/mbd_sim.R:256:58:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L256) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
          pool <- c(pool, abs(new_interval)*sign(parents) )
                                                         ^
```
[R/mbd_sim.R:257:37:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L257) *style:* **Put spaces around all infix operators.**
```r
          total_count <- total_count+delta_n
                                   ~^~
```
[R/mbd_sim.R:261:51:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L261) *style:* **Put spaces around all infix operators.**
```r
            dead <- sample(pool, replace = F, size=1)
                                                 ~^~
```
[R/mbd_sim.R:265:23:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L265) *style:* **Commas should always have a space after.**
```r
          L[abs(dead),4] <- t
                      ^
```
[R/mbd_sim.R:266:28:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L266) *style:* **Put spaces around all infix operators.**
```r
          pool <- pool[pool!=dead]
                          ~^~~
```
[R/mbd_sim.R:270:5:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L270) *style:* **Variable or function name should be snake_case.**
```r
    L=L[(1:total_count),]
    ^
```
[R/mbd_sim.R:270:6:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L270) *style:* **Use <-, not =, for assignment.**
```r
    L=L[(1:total_count),]
     ^
```
[R/mbd_sim.R:270:6:](https://github.com/Giappo/mbd/blob/85a38d9efb4c18f6c0be29e176934090c4b14462/R/mbd_sim.R#L270) *style:* **Put spaces around all infix operators.**
```r
    L=L[(1:total_count),]
    ~^~
```


Anywhere you have a raw pointer like this, I think you should consider using a smart pointer, for example, std::unique_ptr or std::shared_ptr if you require shared ownership.


you could create a tiny type to replace the Integer, which makes its purpose clearer


Other projects use it.


You are overwriting the same variable. Only one of the timers will be stopped on destroy(). Which will make errors if you disable or remove the instance later on.


codea bien wachoooo :P


Jajajajajaja

El El mié, 26 sep. 2018 a las 10:04, Hernan Bessera <
notifications@github.com> escribió:

> codea bien wachoooo :P
>
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