[R/mbd_loglik_utils.R:43:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
  my_matrix <- lambda * matrix_builder(n_species = max_number_of_species, k = k, q = q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:46:59:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L46) *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:48:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
  my_matrix[row(my_matrix) == col(my_matrix) - 1] <- mu * nvec[2:(max_number_of_species + 1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:163:3:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L163) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
  ^
```
[R/mbd_loglik_utils.R:237:26:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L237) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:304:46:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L304) *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:312:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L312) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:326:31:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L326) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:326:32:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L326) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:360:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L360) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:374:31:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L374) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:374:32:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L374) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:391:54:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L391) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:404:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L404) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:404:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L404) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:418:12:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L418) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:422:31:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L422) *style:* **Put spaces around all infix operators.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                             ~^~
```
[R/mbd_loglik_utils.R:422:32:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L422) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_cm <- (3 * (m + 1))/(m + 3); length(one_over_cm)
                               ^
```
[R/mbd_loglik_utils.R:446:54:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L446) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:472:18:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L472) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:474:32:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L474) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:550:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L550) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:560:9:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L560) *warning:* **no visible global function definition for ‘find_best_lx_for_pc’**
```r
  lx <- find_best_lx_for_pc(brts = brts, pars = pars, soc = soc)
        ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:594:18:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L594) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- c(0, brts2time_intervals_and_births(brts)$births)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:637:16:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L637) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:728:35:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_loglik_utils.R#L728) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1)/pc_1;
                                 ~^~
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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/c0f9f2922fd119035bc138d597d0c3d72691f55a/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)) )
                                                                                ^
```
[R/mbd_sim.R:281:1:](https://github.com/Giappo/mbd/blob/c0f9f2922fd119035bc138d597d0c3d72691f55a/R/mbd_sim.R#L281) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)) )


problem with this file


I'm afraid that  these method could only get the balance of address which is  only in full node wallet. Not any address.


sm


高级：
JSON.parse处理必须强制加try/catch。


This is addition of two numbers


@catborise - will make this addition in to the master branch and push it to retspen repo?


Ok


@raniesantos You're still seing this warning because libsass has not been released since April this year.


高级缺陷：
JSON.parse处理必须强制加try/catch。


Guys this was fixed upstream https://git.zx2c4.com/WireGuard/commit/?id=9a86aa8d75330436c73b1f643ec485bb66c501be


commit from intelliJ


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @mcflugen was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


this


Doesn't seem to be working correctly with HA 0.78.3 (using OZW 1.5). The device is recognized, but no scene ID is received after inserting PINs.


![](https://github.trello.services/images/mini-trello-icon.png) [Display information about current eNodeB.](https://trello.com/c/ftVUhxDk/47-display-information-about-current-enodeb)


![](https://github.trello.services/images/mini-trello-icon.png) [UE stores information about eNodeB to which is currently connected.](https://trello.com/c/48w9LKQ9/46-ue-stores-information-about-enodeb-to-which-is-currently-connected)


![](https://github.trello.services/images/mini-trello-icon.png) [As an Employee I can exchange any amount of my carrot balance for a selected reward option](https://trello.com/c/vTNp8hm2/29-as-an-employee-i-can-exchange-any-amount-of-my-carrot-balance-for-a-selected-reward-option)


![](https://github.trello.services/images/mini-trello-icon.png) [【程式】連接 Google Map](https://trello.com/c/UjquIb0F/30-%E3%80%90%E7%A8%8B%E5%BC%8F%E3%80%91%E9%80%A3%E6%8E%A5-google-map)


@mibby Build size is back down to 341kb in latest commit, accidentally shaded the entire SQLite jar


vispy


Successfully aliased the URL <https://just-another-todo-app-obprlkawzx.now.sh> to the following alias.

* https://just-another-todo-app.now.sh


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

* https://tetris.herson.hn


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.


Was genau meinst du damit?


GOOD


Hey, why do you recommend using `self` over strongSelf?
For me the strongSelf term makes it clearer to see/detect if someone accidentally used a strong self reference in a closure.


@eldy will `google+` work or should it be changed to `googleplus` ?


Checked


#6982-EngRefEquationFixPart6 (RKStrand) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-UnitTestsCoverage-Debug: OK (1773 of 1773 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-41.35%25-green.png)


第一次提交


@ovasquez Please, create this version.


Can also remove parameters while you are here.


Sends an error message.


The `let `self` = self` statement is a compile bug and should be avoided.
Maybe you should point out 2 variants of this.
Version < 4.2: `guard let strongSelf = self``
Version > 4.2: `guard let self = self`


Understand Absolute versus Relative Units


Gardenlet is fine I guess


3,700,000 bytes


Sehr gute LoginPage, idee mit der Wassermelone muss von einem Profi gekommen sein. Weiter so! Viel Glück in der fünften Klasse HTL weiterhin! 👍


Swears at  return getters.cartProducts.reduce((total, product) => total + product.price * product.quantity, 0):
TypeError: Cannot read property 'reduce' of undefined
    at cartTotal (index.js?e3b1:36)


去重、去短文本、去默认评论


@pkarw got it, thanks!


ok


Diese Datei würde ich nicht in das Repos hinzufügen


Glad you guys are keeping me honest; I was rushed and didn't pay close attention. Fixing soon (I've had to replace my wireless network today).


Yep this is great ! Nice job.
I think we need to add an indicator to show this functionality, idk how maybe an :hover on the three divs with a tooltip ? I can do that if you want, can you create a PR ? 🎉


Logdateien nicht in das Repository hinzufügen


edit on 2018


you can remove `go` from the `hostmakedepends`
it's automatically installed when you use `build_style=go`

move `fftw-devel` and `libsndfile-devel` to the `makedepends` instead.


one last try ;-) how about Gardelet or Gardlet ?


why after running` ./bin/compilebox` on port 3000 i get `404 page not found` ?


@ckoven this looks great to me. I think i'd noticed this was a bit off in the past, so it's good to figure out why!


Instead, I rewrote the part of the code that produced BEAM code to produce a list of SSA instructions.

Feel repetitive with two "Instead".


sdffd


sdfsdf


data 没有正确传入，应该是还有需要特殊处理的地方


IBM Cloud [toolchain](https://console.ng.bluemix.net/devops/toolchains/f094bbc3-fc3f-402f-b769-7d23d4d5533c?env_id=ibm%3Ayp%3Aus-south "hive764"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/8e16040c-6017-478f-90c4-f224ad9a140e?env_id=ibm%3Ayp%3Aus-south "HIVE764") deployed [hive](https://github.com/WEITAO764/hive/releases/tag/deploy-ibm-yp-us-south-wtao-deakin.edu.au_1532874841224-dev-20180927-091225 "deploy-ibm-yp-us-south-wtao-deakin.edu.au_1532874841224-dev-20180927-091225") to [dev](https://console.bluemix.net/apps/247b1604-f5f3-41a1-b4ba-3af134758235?env_id=ibm:yp:us-south "ibm:yp:us-south:wtao@deakin.edu.au_1532874841224:dev"), including this commit


All Good! 👍


aaaa


I think this dependency is automatically detected:
````
=> mpdviz-0.4.6_1: running pre-pkg hook: 04-generate-runtime-deps ...
   SONAME: libfftw3.so.3 <-> libfftw>=3.3_1
   SONAME: libc.so <-> musl>=0.9.9_1
````


Sweet, thanks.


use [SPDX](https://spdx.org/licenses/) license identifier.

`license="MIT"`


Are you sure about editing the migrations files directly ? The stale tables won't be deleted this way...

It would have been safer just to let makemigrations drop the tables (or even better to do it like this : https://stackoverflow.com/a/26472482 so that if anyone has used that feature already he doesn't loose data)


move this line right below `build_style=go`


When I try the latest build from an old style project, I get `error MSB4057: The target "RunResolvePackageDependencies" does not exist in the project.`


test Comment


another comment


This should be ultimaker_cura right? I mean, it's not the drive plugin anymore.


Can this peerDependency only be satisfied by -alpha.13 or is >alpha.13 also ok? I'm getting a warning if I use a newer alpha of date-fns


Note that the problem here was that type arguments in a qualifying type that is an intersection where being ignored. e.g. in `<Foo<X>&Bar<Y>>.Baz`, `X` and `Y` were not being substituted into supertypes of `Baz`.


testing comment on this comment


中级：
注释下0是啥


@olivierdalang right. I didn't take into account old setups. Will change it accordingly. Thanks for looking.


less then two


missing newline at end of file (on your other template, too).


我觉得，username做辅助索引还是有必要的


See comment in PR


iOS test