[R/mbd_calc_max_lik.R:81:19:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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:417:12:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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:186:1:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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:286:1:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/R/mbd_pure_multiple_birth.R#L286) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim_checked.R:2:37:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/R/mbd_sim_checked.R#L55) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/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/c896e9d31b3c5b1450d4cb0fd2a91ea8466f9b6e/R/mbd_sim.R#L270) *style:* **Use <-, not =, for assignment.**
```r
    L=L[(1:total_count),]
     ^
```


if this defaults to 1, why not set it?


These 4 first steps should be automated somehow. We need to figure this out.


Sorry, I accidentally committed this without finishing the message


A map may not be the right type of collection. You are passing in numLines as your value for each Player, which I don't think is relevant to what you need to store. The Player object already has all the information you need, so an ArrayList of Player may be all you need here.


i think i'vre read everything, but still i dont know what's wrong with `getLowestMip`


Неправильно расположение свойств http://codeguide.academy/html-css.html#css-order


тоже самое


Метод contains возвращает true если коллекция содерижит элемет равный number или false если не содержит. Коллекция tables содрежит объекты Table, а ты передаешь int в качестве параметра в метод contains. Да и ктому же подумай нужено ли тебе тут вызывать contains


и тут


Yeah, that should probably be specified


ой-ой-ой


Bad parenthesis


Looks like you're right. Let me get a fix in.


едут отступы


it's a good change


I am going to update robust so that it can accept both pr and r for goal programming.


@baselbers you saved me Thanks a lot. It worked perfectly with PHP 7.1.9 for non-numeric value.


proponuję przemyśleć nazwę zmiennej myFunction  zmienić na mniej "książkową"


s/regression/unit


Ты читала документацию по БЭМу? https://ru.bem.info/methodology/quick-start/


Section 3 with Text101 is complete at this point


В строке кода 66 у тебя есть такой код Integer.parseInt(s); этот метод выбросит NumberFormatException если в строке s есть хотя бы один символ или спец знак. Перед тем как вызывать parseInt, тебе нужно узнать а содержит ли строка s что то отличное от цийфр.


Sorry to bother you on an issue you closed more than a year ago but I can't understand the point of treating an OCI_NO_DATA exception as a success.

I have real use cases where this change is a source of malfunctioning (I can send some examples if you need them) so before reverting back this in my code I just wanted to ask you why you purposely chose to ignore OCI_NO_DATA exception at this incredible low level instead of leaving it up to the caller to decide what to do with it.

Thanks in advance if you choose to allocate some of your time to satisfy my curiosity :-)


Part fix for issue https://github.com/radondev/RektAntiCheat/issues/4#issue-363723282


Tu proponuję zapisać obliczenia w sposób funkcyjny.


coucou


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

	Click here to see the contents of `now.json`

{}
//test

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


How to compile groovy files after adding those css and js file


You mean instead alongside the shield? Probably a good idea yeah, not sure where though


o Token temporário chamado tmpToken não tinha sido criado ainda.


До этого не было вообще отступов, а тут прям что-то понесло.
Вообще для лучшей читаемости мы обычно добавляем отступ между соседними элементами. Но только 1


This is a **very** early stage of the recipe component, to test props in react native. The next step would be to implement states for add additional functionality.


fine


This should use `sys.executable` rather than a different hard-coded string, see https://github.com/SeattleTestbed/repy_v2/issues/15 .


This would be weird/missleading since corresponding loader returns ET_IMAGE and other writers writes also ET_IMAGE. IMHO it should be documented that writers other than DDS writes lowest mipmap possible.


Engine in Ashley already support listening on entities being added and removed. [addEntityListener](https://libgdx.badlogicgames.com/ci/ashley/docs/com/badlogic/ashley/core/Engine.html#addEntityListener-com.badlogic.ashley.core.EntityListener-).


see https://github.com/Crisspl/IrrlichtBAW/commit/a6ed96ab6aa9e2945883dcdaa053f7a818fce74c#commitcomment-30656439


Tu obliczenie też nie są poprawne?
Proponuję zmienic na funkcyjne programowanie.


hello


Is there any reason to make .modecard has its own special color


Zmienić application/json na stałą z jakiejś klasy typu MIMEContent albo podobnej.


ok


engine should be called em or entityManager to not confuse it with Ashleys Engine.