[R/create_mbd_params_selector.R:11:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/create_mbd_params_selector.R#L11) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/create_mbd_params_selector.R:26:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/create_mbd_params_selector.R#L26) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_calc_max_lik.R:49:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_calc_max_lik.R#L49) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:48:59:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(my_matrix) <= (-lambda) * (1 - (1 - q) ^ (k + nvec) ) - mu * (nvec + k)
                                                          ^
```
[R/mbd_loglik_utils.R:50:58:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
  my_matrix[row(my_matrix) == col(my_matrix) - 1] <- mu *
                                                         ^
```
[R/mbd_loglik_utils.R:166:3:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L166) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
  ^
```
[R/mbd_loglik_utils.R:240:26:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L240) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:307:46:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L307) *style:* **Put spaces around all infix operators.**
```r
  soc + max(mvec[(mvec %in% which((cumsum(p_m/sum(p_m))) <= 0.95))])
                                            ~^~
```
[R/mbd_loglik_utils.R:315:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L315) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:329:31:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L329) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:329:32:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L329) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:363:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L363) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:377:31:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L377) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:377:32:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L377) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:394:54:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L394) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:407:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L407) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:407:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L407) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:421:12:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L421) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:425:31:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L425) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:425:32:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L425) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:449:54:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L449) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:475:18:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L475) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:477:32:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L477) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:553:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L553) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:563:9:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L563) *warning:* **no visible global function definition for ‘find_best_lx_for_pc’**
```r
  lx <- find_best_lx_for_pc(brts = brts, pars = pars, soc = soc)
        ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:597:18:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L597) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- c(0, brts2time_intervals_and_births(brts)$births)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:640:16:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L640) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:731:35:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik_utils.R#L731) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1)/pc_1;
                                 ~^~
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_loglik.R#L236) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * q_t[t, (missnumspec + 1)]
    ^
```
[R/mbd_ml.R:74:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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:214:3:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_ml.R#L214) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml.R:216:60:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_ml.R#L216) *style:* **Commas should always have a space after.**
```r
      tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii]
                                                           ^
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L47) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:82:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
  condition1 <- (any(is.nan(test_pars)) != 0 | any(is.infinite(test_pars)) != 0 )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:82:80:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L82) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  condition1 <- (any(is.nan(test_pars)) != 0 | any(is.infinite(test_pars)) != 0 )
                                                                               ^
```
[R/mbd_pure_multiple_birth.R:87:13:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L87) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    data <- brts2time_intervals_and_births(test_brts)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:91:47:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L91) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    a_term <- rep(1, length(time_intervals)    ) #branches
                                              ^
```
[R/mbd_pure_multiple_birth.R:96:5:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L96) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_pure_multiple_birth.R:102:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
      # (1) nu contribution: (1-q)^(k*i) * (nu*(t_k-t_k-1))^i*exp(-nu*(t_k-t_k-1))/i!
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:104:24:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:104:61:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:112:17:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L112) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (1 - q)^(k[-length(k)] - births)                 # (1)
                ^
```
[R/mbd_pure_multiple_birth.R:151:33:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (min(trpars1[1:n_pars]) < 0 ) {
                                ^
```
[R/mbd_pure_multiple_birth.R:163:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:173:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L173) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML <- function(
^~~~~~
```
[R/mbd_pure_multiple_birth.R:187:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L187) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:189:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L189) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:190:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L190) *style:* **Lines should not be more than 80 characters.**
```r
  # - optimmethod = "simplex" (current default) or 'subplex' (default of previous versions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:195:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L195) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(namepars); #if you add more parameters to your model just change this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:196:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars; #those are the parameters that you get if something goes sideways
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:224:33:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L224) *style:* **Put spaces around all infix operators.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                               ~^~
```
[R/mbd_pure_multiple_birth.R:224:34:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L224) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                                 ^
```
[R/mbd_pure_multiple_birth.R:226:29:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L226) *style:* **Put spaces around all infix operators.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                           ~^~
```
[R/mbd_pure_multiple_birth.R:226:30:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L226) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                             ^
```
[R/mbd_pure_multiple_birth.R:239:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
      cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:242:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L242) *style:* **Lines should not be more than 80 characters.**
```r
        cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:246:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L246) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:251:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L251) *style:* **Lines should not be more than 80 characters.**
```r
          cat("Optimization has not converged. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:256:32:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L256) *style:* **Put spaces around all infix operators.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                              ~^~
```
[R/mbd_pure_multiple_birth.R:256:33:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L256) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            ml_pars <- mltrpars/(1 - mltrpars)
                                ^
```
[R/mbd_pure_multiple_birth.R:266:11:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L266) *style:* **Variable or function name should be snake_case.**
```r
          ML <- as.numeric(unlist(out$fvalues))
          ^~
```
[R/mbd_pure_multiple_birth.R:276:11:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L276) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_pure_multiple_birth.R:278:68:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L278) *style:* **Commas should always have a space after.**
```r
              tobeprint, paste(names(ml_pars1[ii]), ":", sep = ""),ml_pars1[ii]
                                                                   ^
```
[R/mbd_pure_multiple_birth.R:294:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_pure_multiple_birth.R#L294) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/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/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[,4]==-1,]
        ~^~
```
[R/mbd_sim.R:275:16:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L275) *style:* **Commas should always have a space after.**
```r
    alive=L[L[,4]==-1,]
               ^
```
[R/mbd_sim.R:275:18:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[,4]==-1,]
                ~^~~
```
[R/mbd_sim.R:275:23:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L275) *style:* **Commas should always have a space after.**
```r
    alive=L[L[,4]==-1,]
                      ^
```
[R/mbd_sim.R:276:10:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L276) *style:* **Use <-, not =, for assignment.**
```r
    alive=matrix(alive, ncol=4)
         ^
```
[R/mbd_sim.R:276:10:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L276) *style:* **Put spaces around all infix operators.**
```r
    alive=matrix(alive, ncol=4)
        ~^~
```
[R/mbd_sim.R:276:29:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L276) *style:* **Put spaces around all infix operators.**
```r
    alive=matrix(alive, ncol=4)
                           ~^~
```
[R/mbd_sim.R:277:30:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Use <-, not =, for assignment.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                             ^
```
[R/mbd_sim.R:277:33:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                                ^
```
[R/mbd_sim.R:277:41:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                                        ^
```
[R/mbd_sim.R:277:66:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                                                                 ^
```
[R/mbd_sim.R:277:68:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                                                                  ~^~~
```
[R/mbd_sim.R:277:71:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                                                                      ^
```
[R/mbd_sim.R:277:73:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L277) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])) )!=2 )*cond
                                                                       ~^~
```
[R/mbd_sim.R:280:1:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L280) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L280) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)) )
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:30:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L280) *style:* **Use <-, not =, for assignment.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)) )
                             ^
```
[R/mbd_sim.R:280:30:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L280) *style:* **Put spaces around all infix operators.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)) )
                            ~^~
```
[R/mbd_sim.R:280:99:](https://github.com/Giappo/mbd/blob/50d39bbb1079ff1037a6adec17f5f1fd40c993b6/R/mbd_sim.R#L280) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)) )
                                                                                ^
```


Now cannot deploy because all the allocated instances are in use.
You can either [upgrade](https://zeit.co/account/plan) your plan or [down scale](https://zeit.co/docs/getting-started/scaling) existing [deployments](https://zeit.co/dashboard/deployments).


That regexp is different. It leaves the `<pre>` block as is, it doesn't add `hljs` class to it.

So, do we really need PR to add `txt` as an alias to `plaintext`? I'm not sure. Adding meaningful aliases to _real_ languages definitely makes sense. But here we get a lot of almost, but not exactly, identical names that work almost, but not exactly, identical. Can you remember what is what after a couple of months without looking into the documentation?


the column class m-6 cause the div to look weird
fixed by correcting to "m6"


@budait , Nice tutorial! :+1:


The following doc(s) have been deployed to the [tinefinpat](https://tinefinpat-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/platform-considerations](https://tinefinpat-static-docs.pantheonsite.io/docs/platform-considerations)


Successfully aliased the URL <https://confluenza-mepzkjydqs.now.sh> to the following alias.

* https://confluenza.now.sh


Why don't you use PHP_EOL ?


i ran testlang for c++ and it gives me this:
```
 ./bin/langtest
2018/09/27 10:30:48 sandbox launching sandbox...
Language: C++
Stdin:
*-BRK-*
Code: Hidden
2018/09/27 10:30:48 writing inputfile:
*-BRK-*
2018/09/27 10:30:53 timed out
2018/09/27 10:30:53 sandbox run error: Timed out
panic: runtime error: index out of range

goroutine 1 [running]:
panic(0x532b60, 0xc82000a090)
        /usr/lib/go-1.6/src/runtime/panic.go:481 +0x3e6
main.main()
        /home/compilebox-old/API/src/langtest/main.go:40 +0xde3

```


can you help me please?


Yes it says karthik siddharth because I am using his mechine


delete me


I do not see how could this rule be useful for the majority of users. It is triggered on any bulk mail or free mail that doesn't have display name (and it is very common) regardless spam it or not.


good idea！


Why does the `ctrl` banner load the `var` styles?


My point was why do you have `web3.fromAscii(` above, see on line 52, when you test `.call`, but not here when you do it for real?
So I was saying you should prepare the parameters so that you can use twice.


this should probably be here?


PHP Coding Standard for WordPress: https://make.wordpress.org/core/handbook/best-practices/coding-standards/php/


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.


低级缺陷
这里可以用解构吧


Klaida Zodyje


Text Domain should match plugin's slug.


`load_plugin_textdomain()` should be added for `init` action.


thanks for moving those around, now it's more ordered. :nerd_face:


Sorry for the the inconvenience, but I still have messed the command up to cause a non zero exit code.

`find $WORKSPACE/tools/depends/xbmc-depends/aarch64-linux-android-*-*/ -name 'game.*' ! -name game.libretro ! -name game.libretro.2048 ! -name game.libretro.mrboom -type d -prune -exec rm -rf {} \;`

The important change is adding `-prune` others are just little improvements (remove game.netplay too).


Correct path, remove tailing slash.


建议
给0加个注释吧