[R/mbd_calc_max_lik.R:81:19:](https://github.com/Giappo/mbd/blob/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/R/mbd_pure_multiple_birth.R#L286) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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/69d331bb47d1c051dda823ae6d7b40851c5a61e5/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:273:28:](https://github.com/Giappo/mbd/blob/69d331bb47d1c051dda823ae6d7b40851c5a61e5/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[,4][L[,4]==-1])
                          ~^~~
```
[R/mbd_sim.R:275:10:](https://github.com/Giappo/mbd/blob/69d331bb47d1c051dda823ae6d7b40851c5a61e5/R/mbd_sim.R#L275) *style:* **Use <-, not =, for assignment.**
```r
    alive=L[L[,4]==-1,]
         ^
```
[R/mbd_sim.R:275:10:](https://github.com/Giappo/mbd/blob/69d331bb47d1c051dda823ae6d7b40851c5a61e5/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[,4]==-1,]
        ~^~
```


Maybe you could implement these methods as staticmethods of the ensemble class ?

That way, you would call them by Ensemble.asSubImages(...) and Ensemble.fromFiles()


…no you don’t. why? what happens if it’s not there?


-44 &curl/tmp/install-marker.sh amd64 - v - u- tags


Mistake, erase


You need to check whether `getenv` returns `nullptr` because `strcpy` cannot handle that!


line 178


Fixes #3


Added two spaces for the line break.


Actually, we checked it before this commit (https://github.com/Ultimaker/CuraEngine/commit/df536dd).
Your fix to introduce `strcpy` should be done within the if-branch.


fgfg


Put your login details


Also: good catch!


Yes, because we want to show non-public workspaces you can read. The logic is awkward because the system shows public workspaces as having read access, even if it was never explicitly shared with you, so we can't distinguish.


@@ -29,7 @@ unbuntu


Successfully aliased the URL <https://sass-build-innrkbxyqd.now.sh> to the following alias.

* https://sass.henderea.com


How does this look @josevalim?


@sahitpj I get this when I run the test:
![image](https://user-images.githubusercontent.com/7507990/46082366-eb1d6100-c16c-11e8-9af5-9f36a18679b1.png)

`[no tests to run]`

What does this mean? Isn't `go test...` testing the package by running the function?
I'll look into this. Just showing some transparency into what I'm working on. Not sure if you've already figured this out.


I really have to come up with a better system for managing this certificate...


<img width="358" alt="screen shot 2018-09-26 at 9 20 09 am" src="https://user-images.githubusercontent.com/4545419/46082589-70a11100-c16d-11e8-9e3f-10c3d0ab555e.png">


明天会跟好


CC @jsnyder in case he has some time to look at this.


working on it.


Yeah I know it did. I think @ogrisel is working on it right now.


I want to use Hash() in Javascript.
I downloaded the sha256.min.js but it gives me error ArrayBuffer is undefined.
Can anybody help me understanding what is going wrong?


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.


![](https://github.trello.services/images/mini-trello-icon.png) [база данных для кэша сообщений](https://trello.com/c/rEGkXee2/6-%D0%B1%D0%B0%D0%B7%D0%B0-%D0%B4%D0%B0%D0%BD%D0%BD%D1%8B%D1%85-%D0%B4%D0%BB%D1%8F-%D0%BA%D1%8D%D1%88%D0%B0-%D1%81%D0%BE%D0%BE%D0%B1%D1%89%D0%B5%D0%BD%D0%B8%D0%B9)


You should not use the placeholder inside this function. Also you don't need to use it. `input_data.batch_shape[i]` (or `input_data.copy_as_batch_major().batch_shape[i]`) is much simpler and should be the same as `input_data....placeholder.shape[i].value`. But maybe anyway you want to do `input_data = input_data.copy_as_batch_major()` in the beginning.


Мяу


Changing 2 lines does not require an author update. If you don't wish for us to use your one edit, we can always *revert to the previous commit*


In this function, no calculations / nothing which adds anything to the computation graph should be done. Esp `size_placeholder` is expected to be set inside `__init__`.


* Span now looks at absolute difference rather than just "distance UNDER 1.0"
* Fixed issue with resistance overlap filter posting multiple hits of same entity
* Readded position stats for contigs
* Wrote a fallback section for names that cannot be resolved.


<!-- PMABOT:SPACE -->
This commit contains trailing whitespace, what is prohibited in phpMyAdmin. Please check our [Developer guidelines](https://github.com/phpmyadmin/phpmyadmin/wiki/Developer_guidelines#Indentation) for more information.

Offending files: doc/faq.rst


Pls don't let this neo-marxistic compelled speech gender feminism equality-of-outcome bullshit get even near the linux kernel.
This is not about victims or oppression. This is an attack on the kernel and its community. Once they get a foot in the door Linux will be done.
Punch-In-Da-Face-Driven-Development works. Forget about the rest.


With Switchtec hardware, the buffer used for a memory window must be
aligned to its size (the hardware only replaces the lower bits).

Maybe it should be higher bits


`OC::$server` must start with backslash, otherwise you get php error. See at line 14.


Hello @juanesarango
I am currently attempting to create a minimal working image of ensembl-vep with BigWig support. I was wondering: why is Apache2 needed? Did this end up here accidentally? It seems really odd and unnecessary to me.
If so, it would be good to be removed as it is >= 10 MB of additional bloat.


Im referring to closing the reader. Assuming there is a place in OpenFile where you et an error and also a Reader (Downloader) that needs to be closed.


this is great, but I don't like the fact that the substitutions have changed. I understand this is because the uncertainty is not 'centered' since it is in log-space. I will check what the effect is of changing the substitutions back. And also, I think that goal programming should work regardless of whether or not someone uses pr or r.


O método LerDetalheRetornoCNAB240SegmentoT não deveria ter sido alterado neste Pull Request (que trata sobre o CNAB 400)...

Após atualizar o código em um cliente, nosso sistema começou a apresentar problemas na leitura do CNAB 240... As posições anteriores (NossoNumero + CodigoOcorrencia) estavam corretas.

**Manual Caixa - Campo 13.3T - Posição 40-56 - Nosso Número (Modalidade / Identificação)**
boleto.NossoNumeroDV = registro.Substring(56, 1);

**Manual Caixa - Campo 13.3T - Posição 57 - DV do Nosso Número do Título**
boleto.NossoNumeroFormatado = Format("{0}-{1}",

**Manual Caixa - Campo 07.3T - Código de Movimento Retorno Posição 16-17**
boleto.CodigoOcorrencia = registro.Substring(15, 2);

---------------

Estou revertendo essa alteração (apenas no método **LerDetalheRetornoCNAB240SegmentoT**)


yes, and he uploaded the correct ones :-)


Great that you replied. I had already started generating keytabs with the normal style of different SPN for each service.

So I need to use same account for all services including roundcube. Thanks, this saved hours and hours of troubleshooting.


Bien joué


Please, no IMP in stable, especially v9...


Это свойство где-то испольуется в проекте?


Ты комментарии для кого пишешь?


Created multidev environment [dgreat#pr-368](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-368).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-368-dgreat.pantheonsite.io/)


ВСе свойства прекрасно читаются, не нужно дублировать комментариями


скачут оступы


you need to change the function getWindowLevelMinMax as well, `if range.min===range.max`:
```
dwv.image.View.prototype.getWindowLevelMinMax = function ()
{
    var range = this.getImage().getRescaledDataRange();
    var min = range.min;
    var max = range.max;
    var width = max - min;
    var center = min + width/2;
    return new dwv.image.WindowLevel(center, width);
};```

but here a default of 1 would be better.


Tą klasę trzeba nazwać tak, żeby nawiązywała do jej zawartości, ta klasa tak naprawdę przetrzymuje parametry specyficzne dla wielomianu.

Dodaj klasę bazową, ponieważ type, min i max się będą pojawiać zawsze.

num of steps ma sens tylko w przypadku całkowania prostokątami czy trapezami - to będzie pole niewymagane, trzeba to będzie specjalnie obsłużyć.

pole coefficients trzeba zostawić w tej klasie.


It's nice if the numbers are incremented in plain text as well and not only in the rendered Markdown. 😃


Sorry. I was actually working on cross from macOS. I was trying to split the mass rebuild and no mass rebuild components of this, and the fix for paxctl is a mass rebuild so I kept it out. I'll be more careful.

(Also while glibc still needs work musl is ready so I should go merge that work to staging soon.)


Я тебя, наверное, сейчас сильно расстрою, то свойство float применяется крайне редко. Все твои задачи легко решаться с помощь flex свойств


bvhb


This should be a `--no-ff` merge, no? Otherwise, there won't be a merge-commit that can be tagged.


I'm just now checking out a new branch of a project that uses [an IDE built on] IntelliJ; I'll delete the .iml before running it for the first time and see what happens. If it works then it's probably optional. I expect problems.