[R/mbd_loglik_utils.R:24:69:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L24) *style:* **Trailing whitespace is superfluous.**
```r
  matrix_a[n_species, n_species] <- matrix_a[n_species, n_species] *
                                                                    ^
```
[R/mbd_loglik_utils.R:43:3:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L43) *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:46:51:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L46) *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:122:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L122) *style:* **Variable or function name should be snake_case.**
```r
create_a.no_mbd <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:150:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L150) *style:* **Variable or function name should be snake_case.**
```r
create_b.no_mbd <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:163:3:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L163) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
  ^
```
[R/mbd_loglik_utils.R:192:5:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L192) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:192:19:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L192) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:207:7:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L207) *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:211:9:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L211) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:237:26:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L237) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:295:3:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L295) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- a_operator(
  ^~
```
[R/mbd_loglik_utils.R:304:45:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L304) *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:312:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L312) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:326:31:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L326) *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:326:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L326) *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:360:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L360) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:374:31:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L374) *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:374:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L374) *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:391:54:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L391) *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:404:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L404) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:404:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L404) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:418:12:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L418) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:422:31:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L422) *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:422:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L422) *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:446:54:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L446) *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:472:18:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L472) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:474:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L474) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:550:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L550) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:560:9:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L560) *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:594:18:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L594) *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:637:16:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L637) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:728:35:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik_utils.R#L728) *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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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:175:11:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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:200:13:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_loglik.R#L236) *style:* **Trailing whitespace is superfluous.**
```r
    P  <- vm * q_t[t, (missnumspec + 1)]
                                        ^
```
[R/mbd_ml.R:74:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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:206:17:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_ml.R#L206) *style:* **Trailing whitespace is superfluous.**
```r
    t(ml_pars1),
                ^
```
[R/mbd_ml.R:207:17:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_ml.R#L207) *style:* **Trailing whitespace is superfluous.**
```r
    loglik = ML,
                ^
```
[R/mbd_ml.R:208:30:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_ml.R#L208) *style:* **Trailing whitespace is superfluous.**
```r
    df = length(initparsopt),
                             ^
```
[R/mbd_ml.R:214:3:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_ml.R#L214) *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:216:60:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_ml.R#L216) *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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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:82:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L82) *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:82:80:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L82) *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:87:13:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L87) *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:91:47:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L91) *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:96:5:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L96) *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:102:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L102) *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:104:24:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L104) *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:104:61:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L104) *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:112:17:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L112) *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:151:33:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L151) *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:163:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L163) *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:173:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L173) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML <- function(
^~~~~~
```
[R/mbd_pure_multiple_birth.R:187:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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:189:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L189) *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:190:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L190) *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:195:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L195) *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:196:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L196) *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:224:33:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L224) *style:* **Put spaces around all infix operators.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                               ~^~
```
[R/mbd_pure_multiple_birth.R:224:34:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L224) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                                 ^
```
[R/mbd_pure_multiple_birth.R:226:29:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L226) *style:* **Put spaces around all infix operators.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                           ~^~
```
[R/mbd_pure_multiple_birth.R:226:30:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L226) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                             ^
```
[R/mbd_pure_multiple_birth.R:238:8:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L238) *style:* **Trailing whitespace is superfluous.**
```r
      )
       ^
```
[R/mbd_pure_multiple_birth.R:239:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L239) *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:242:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L242) *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:246:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L246) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:251:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L251) *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:256:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L256) *style:* **Put spaces around all infix operators.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                              ~^~
```
[R/mbd_pure_multiple_birth.R:256:33:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L256) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                                ^
```
[R/mbd_pure_multiple_birth.R:266:11:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L266) *style:* **Variable or function name should be snake_case.**
```r
          ML <- as.numeric(unlist(out$fvalues))
          ^~
```
[R/mbd_pure_multiple_birth.R:268:25:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L268) *style:* **Trailing whitespace is superfluous.**
```r
            t(ml_pars1),
                        ^
```
[R/mbd_pure_multiple_birth.R:269:25:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L269) *style:* **Trailing whitespace is superfluous.**
```r
            loglik = ML,
                        ^
```
[R/mbd_pure_multiple_birth.R:270:38:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L270) *style:* **Trailing whitespace is superfluous.**
```r
            df = length(initparsopt),
                                     ^
```
[R/mbd_pure_multiple_birth.R:276:11:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L276) *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:278:68:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L278) *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:294:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_pure_multiple_birth.R#L294) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim_checked.R:2:37:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#' @param mbd_params MBD parameters,
                                    ^
```
[R/mbd_sim_checked.R:4:35:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#' @param crown_age the crown age.
                                  ^
```
[R/mbd_sim_checked.R:5:72:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#'   Either \code{crown_age} or \code{stem_age} must be exclusively set
                                                                       ^~~~
```
[R/mbd_sim_checked.R:6:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#' @param stem_age the stem age
                               ^~~~
```
[R/mbd_sim_checked.R:14:14:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L14) *style:* **Trailing whitespace is superfluous.**
```r
  mbd_params,
             ^
```
[R/mbd_sim_checked.R:38:41:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L38) *style:* **Trailing whitespace is superfluous.**
```r
  pars <- as.numeric(unlist(mbd_params))
                                        ^
```
[R/mbd_sim_checked.R:43:21:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L43) *style:* **Trailing whitespace is superfluous.**
```r
    age <- crown_age
                    ^
```
[R/mbd_sim_checked.R:50:17:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
    pars = pars,
                ^
```
[R/mbd_sim_checked.R:51:15:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
    soc = soc,
              ^
```
[R/mbd_sim_checked.R:52:15:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
    age = age,
              ^
```
[R/mbd_sim_checked.R:55:1:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim_checked.R#L55) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/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/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L270) *style:* **Put spaces around all infix operators.**
```r
    L=L[(1:total_count),]
    ~^~
```
[R/mbd_sim.R:270:25:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L270) *style:* **Commas should always have a space after.**
```r
    L=L[(1:total_count),]
                        ^
```
[R/mbd_sim.R:271:21:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L271) *style:* **Use <-, not =, for assignment.**
```r
    extinct_species = sum(L[,4]!=-1)
                    ^
```
[R/mbd_sim.R:271:30:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L271) *style:* **Commas should always have a space after.**
```r
    extinct_species = sum(L[,4]!=-1)
                             ^
```
[R/mbd_sim.R:271:32:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    extinct_species = sum(L[,4]!=-1)
                              ~^~~
```
[R/mbd_sim.R:273:9:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L273) *style:* **Use <-, not =, for assignment.**
```r
    tips=length(L[,4][L[,4]==-1])
        ^
```
[R/mbd_sim.R:273:9:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[,4][L[,4]==-1])
       ~^~
```
[R/mbd_sim.R:273:20:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L273) *style:* **Commas should always have a space after.**
```r
    tips=length(L[,4][L[,4]==-1])
                   ^
```
[R/mbd_sim.R:273:26:](https://github.com/Giappo/mbd/blob/83ab1e920bdb38c61974124c5056af9a5e1d1c89/R/mbd_sim.R#L273) *style:* **Commas should always have a space after.**
```r
    tips=length(L[,4][L[,4]==-1])
                         ^
```


:+1: Conservation of hyphens.


I like the concept behind your try, however i think the changes are too high, if this test fails, maybe try with +/-10


Nie mieszaj obliczania funkcji całki ze zmianami współczynników. To powinieneś zrobić gdzieś bliżej przyjmowania parametrów wejściowych.


@moisseev : I did not get why this rule is removed. Too many false positives?

Thank you.


👍😉

If there was a CHIP-8 emoji, I would use it here.


No, in this very `readme.md` file, you should write `1. 2. 3. 4.` instead of `1. 1. 1. 1.`. :)