[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_calc_max_lik.R:81:19:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_calc_max_lik.R#L81) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
    param_name <- get_mbd_param_names()[i]
                  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:24:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
  matrix_a[n_species, n_species] <- matrix_a[n_species, n_species] * (1 - q) ^ (n_species - 1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:42:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L42) *style:* **Variable or function name should be snake_case.**
```r
  M <- lambda * matrix_builder(n_species = max_number_of_species, k = k, q = q)
  ^
```
[R/mbd_loglik_utils.R:45:51:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(M) <= (-lambda) * (1 - (1 - q) ^ (k + nvec) ) - mu * (nvec + k)
                                                  ^
```
[R/mbd_loglik_utils.R:121:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L121) *style:* **Variable or function name should be snake_case.**
```r
create_a.no_mbd <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:149:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L149) *style:* **Variable or function name should be snake_case.**
```r
create_b.no_mbd <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:162:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L162) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
  ^
```
[R/mbd_loglik_utils.R:174:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L174) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_utils.R:191:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L191) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:191:19:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L191) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:206:7:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L206) *style:* **Variable or function name should be snake_case.**
```r
      result.nan <- (any(!is.numeric(result)) || any(is.nan(result)))
      ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:210:9:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L210) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:236:26:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L236) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:284:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L284) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx))
  ^~
```
[R/mbd_loglik_utils.R:286:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L286) *style:* **Variable or function name should be snake_case.**
```r
  T0 <- create_a(
  ^~
```
[R/mbd_loglik_utils.R:294:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L294) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- a_operator(
  ^~
```
[R/mbd_loglik_utils.R:303:45:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L303) *style:* **Put spaces around all infix operators.**
```r
  soc + max(mvec[(mvec %in% which((cumsum(Pm/sum(Pm))) <= 0.95))])
                                           ~^~
```
[R/mbd_loglik_utils.R:311:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L311) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:325:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L325) *style:* **Variable or function name should be snake_case.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
  ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:325:31:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L325) *style:* **Put spaces around all infix operators.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                             ~^~
```
[R/mbd_loglik_utils.R:325:32:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L325) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                               ^
```
[R/mbd_loglik_utils.R:328:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L328) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- rep(0, lx + 1);  Qi[3] <- 1
  ^~
```
[R/mbd_loglik_utils.R:330:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L330) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_a(
  ^~
```
[R/mbd_loglik_utils.R:359:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L359) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:373:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L373) *style:* **Variable or function name should be snake_case.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
  ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:373:31:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L373) *style:* **Put spaces around all infix operators.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                             ~^~
```
[R/mbd_loglik_utils.R:373:32:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L373) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                               ^
```
[R/mbd_loglik_utils.R:375:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L375) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:377:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L377) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_a(lambda = lambda, mu = mu, nu = nu, q = q, k = soc,
  ^~
```
[R/mbd_loglik_utils.R:390:54:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L390) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:403:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L403) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:403:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L403) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:416:9:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L416) *style:* **Only use double-quotes.**
```r
    cat('mu is supposed to be equal zero to use this function')
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:417:12:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L417) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:421:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L421) *style:* **Variable or function name should be snake_case.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
  ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:421:31:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L421) *style:* **Put spaces around all infix operators.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                             ~^~
```
[R/mbd_loglik_utils.R:421:32:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L421) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                               ^
```
[R/mbd_loglik_utils.R:423:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L423) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:425:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L425) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_a(
  ^~
```
[R/mbd_loglik_utils.R:445:54:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L445) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:449:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L449) *style:* **Lines should not be more than 80 characters.**
```r
  opposite_tips_components <- (m + 1)[!((m + 1) %in% (tips_components[1]:tips_components[2]))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:469:18:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L469) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:471:32:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L471) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:547:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L547) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:557:9:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L557) *warning:* **no visible global function definition for ‘find_best_lx_for_pc’**
```r
  lx <- find_best_lx_for_pc(brts = brts, pars = pars, soc = soc)
        ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:591:18:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L591) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- c(0, brts2time_intervals_and_births(brts)$births)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:603:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L603) *style:* **Variable or function name should be snake_case.**
```r
    one_over_Cm <- (3 * (m + 1)) / (m + 3)
    ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:613:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L613) *style:* **Variable or function name should be snake_case.**
```r
    Qi <- c(1, rep(0, max_number_of_species))
    ^~
```
[R/mbd_loglik_utils.R:634:16:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L634) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:639:7:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L639) *style:* **Variable or function name should be snake_case.**
```r
      mk_n_zero.no_mbd <- create_a.no_mbd(
      ^~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:648:7:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L648) *style:* **Variable or function name should be snake_case.**
```r
      a2_v1.no_mbd <- a_operator(
      ^~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:725:35:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L725) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1)/pc_1;
                                 ~^~
```
[R/mbd_loglik_utils.R:759:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L759) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik_utils.R:760:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik_utils.R#L760) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik.R:79:15:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L79) *warning:* **no visible global function definition for ‘pmb_loglik’**
```r
    loglik <- pmb_loglik(pars = pars, brts = brts, soc = soc)
              ^~~~~~~~~~
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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:135:7:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L135) *style:* **Variable or function name should be snake_case.**
```r
      Qi <- c(1, rep(0, lx))
      ^~
```
[R/mbd_loglik.R:138:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L138) *style:* **Commas should always have a space after.**
```r
      q_t[1,] <- Qi
            ^
```
[R/mbd_loglik.R:158:15:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L158) *style:* **Commas should always have a space after.**
```r
        q_t[t,] <- a_operator(
              ^
```
[R/mbd_loglik.R:159:27:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L159) *style:* **Commas should always have a space after.**
```r
          Q = q_t[(t - 1),],
                          ^
```
[R/mbd_loglik.R:170:17:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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:174:27:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L174) *style:* **Only use double-quotes.**
```r
          if (Sys.info()[['sysname']] == "Windows")
                          ^~~~~~~~~
```
[R/mbd_loglik.R:175:11:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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:199:29:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L199) *style:* **Only use double-quotes.**
```r
            if (Sys.info()[['sysname']] == "Windows")
                            ^~~~~~~~~
```
[R/mbd_loglik.R:200:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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:235:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_loglik.R#L235) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * q_t[t, (missnumspec + 1)] #I have to include +1 because of Q0
    ^
```
[R/mbd_ml.R:66:17:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L66) *style:* **Only use double-quotes.**
```r
  optimmethod = 'simplex',
                ^~~~~~~~~
```
[R/mbd_ml.R:74:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L137) *style:* **Use <-, not =, for assignment.**
```r
    trparsfix[which(parsfix == Inf)] = 1
                                     ^
```
[R/mbd_ml.R:194:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L194) *style:* **Variable or function name should be snake_case.**
```r
  MLtrpars <- as.numeric(unlist(out$par))
  ^~~~~~~~
```
[R/mbd_ml.R:197:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L197) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars / (1 - MLtrpars)
    ^~~~~~
```
[R/mbd_ml.R:199:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L199) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars
    ^~~~~~
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  MLpars1 <- rep(0, n_pars); names(MLpars1) <- namepars
  ^~~~~~~
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L203) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:203:61:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L203) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                                                            ^
```
[R/mbd_ml.R:204:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L205) *style:* **Lines should not be more than 80 characters.**
```r
  out2 <- data.frame(t(MLpars1), loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:209:3:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L209) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml.R:210:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
    tobeprint <- paste(tobeprint, paste(names(MLpars1[ii]), ":", sep = ""),MLpars1[ii])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:210:76:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L210) *style:* **Commas should always have a space after.**
```r
    tobeprint <- paste(tobeprint, paste(names(MLpars1[ii]), ":", sep = ""),MLpars1[ii])
                                                                           ^
```
[R/mbd_ml.R:219:19:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L219) *style:* **Only use double-quotes.**
```r
    s2 <- sprintf('Maximum loglikelihood: %f',ML)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:219:47:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_ml.R#L219) *style:* **Commas should always have a space after.**
```r
    s2 <- sprintf('Maximum loglikelihood: %f',ML)
                                              ^
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L47) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:55:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
    ) + lambda * k[-length(k)] * (births == 1)                                               # lambda contribution: lambda*k (only if b==1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:66:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L66) *style:* **Variable or function name should be snake_case.**
```r
pmb_loglik_Qvector <- function(pars, brts, soc = 2){
^~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:81:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L81) *style:* **Lines should not be more than 80 characters.**
```r
  condition1 <- (any(is.nan(test_pars)) != 0 | any(is.infinite(test_pars)) != 0 )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:81:80:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  condition1 <- (any(is.nan(test_pars)) != 0 | any(is.infinite(test_pars)) != 0 )
                                                                               ^
```
[R/mbd_pure_multiple_birth.R:86:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L86) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    data <- brts2time_intervals_and_births(test_brts)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:90:47:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L90) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    a_term <- rep(1, length(time_intervals)    ) #branches
                                              ^
```
[R/mbd_pure_multiple_birth.R:95:5:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L95) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_pure_multiple_birth.R:101:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
      # (1) nu contribution: (1-q)^(k*i) * (nu*(t_k-t_k-1))^i*exp(-nu*(t_k-t_k-1))/i!
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:103:24:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:103:61:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:111:17:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (1 - q)^(k[-length(k)] - births)                 # (1)
                ^
```
[R/mbd_pure_multiple_birth.R:150:33:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L150) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (min(trpars1[1:n_pars]) < 0 ) {
                                ^
```
[R/mbd_pure_multiple_birth.R:159:15:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L159) *warning:* **no visible global function definition for ‘pmb_loglik’**
```r
    loglik <- pmb_loglik(pars = pars1, brts = brts)
              ^~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:162:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L162) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:172:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L172) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML <- function(
^~~~~~
```
[R/mbd_pure_multiple_birth.R:181:17:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L181) *style:* **Only use double-quotes.**
```r
  optimmethod = 'simplex',
                ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:186:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L186) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:188:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:189:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L189) *style:* **Lines should not be more than 80 characters.**
```r
  # - optimmethod = 'simplex' (current default) or 'subplex' (default of previous versions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:194:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L194) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(namepars); #if you add more parameters to your model just change this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:195:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L195) *style:* **Lines should not be more than 80 characters.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars; #those are the parameters that you get if something goes sideways
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:223:33:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L223) *style:* **Put spaces around all infix operators.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                               ~^~
```
[R/mbd_pure_multiple_birth.R:223:34:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L223) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                                 ^
```
[R/mbd_pure_multiple_birth.R:225:29:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L225) *style:* **Put spaces around all infix operators.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                           ~^~
```
[R/mbd_pure_multiple_birth.R:225:30:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L225) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                             ^
```
[R/mbd_pure_multiple_birth.R:237:8:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L237) *style:* **Trailing whitespace is superfluous.**
```r
      )
       ^
```
[R/mbd_pure_multiple_birth.R:238:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L238) *style:* **Lines should not be more than 80 characters.**
```r
      cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:241:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L241) *style:* **Lines should not be more than 80 characters.**
```r
        cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:245:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L245) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:250:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
          cat("Optimization has not converged. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:253:11:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L253) *style:* **Variable or function name should be snake_case.**
```r
          MLtrpars <- as.numeric(unlist(out$par))
          ^~~~~~~~
```
[R/mbd_pure_multiple_birth.R:255:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L255) *style:* **Variable or function name should be snake_case.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
            ^~~~~~
```
[R/mbd_pure_multiple_birth.R:255:31:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L255) *style:* **Put spaces around all infix operators.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
                             ~^~
```
[R/mbd_pure_multiple_birth.R:255:32:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L255) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
                               ^
```
[R/mbd_pure_multiple_birth.R:257:13:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L257) *style:* **Variable or function name should be snake_case.**
```r
            MLpars <- MLtrpars
            ^~~~~~
```
[R/mbd_pure_multiple_birth.R:259:11:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L259) *style:* **Variable or function name should be snake_case.**
```r
          MLpars1 <- rep(0, n_pars)
          ^~~~~~~
```
[R/mbd_pure_multiple_birth.R:265:11:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L265) *style:* **Variable or function name should be snake_case.**
```r
          ML <- as.numeric(unlist(out$fvalues))
          ^~
```
[R/mbd_pure_multiple_birth.R:266:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L266) *style:* **Lines should not be more than 80 characters.**
```r
          out2 <- data.frame(t(MLpars1), loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:270:11:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L270) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_pure_multiple_birth.R:271:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L271) *style:* **Lines should not be more than 80 characters.**
```r
            tobeprint <- paste(tobeprint, paste(names(MLpars1[ii]), ":", sep = ""),MLpars1[ii])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:271:84:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L271) *style:* **Commas should always have a space after.**
```r
            tobeprint <- paste(tobeprint, paste(names(MLpars1[ii]), ":", sep = ""),MLpars1[ii])
                                                                                ^
```
[R/mbd_pure_multiple_birth.R:278:25:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L278) *style:* **Only use double-quotes.**
```r
          s2 <- sprintf('Maximum loglikelihood: %f',ML)
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:278:53:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L278) *style:* **Commas should always have a space after.**
```r
          s2 <- sprintf('Maximum loglikelihood: %f',ML)
                                                    ^
```
[R/mbd_pure_multiple_birth.R:286:1:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/R/mbd_pure_multiple_birth.R#L286) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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/1bc619f0e5f5e04757abc26b9a627aaa6abfbca1/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;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Considering the usage of ``PInvoke`` style callbacks, this works against ``netstandard1.6``? I'm surprised it does not require at least ``netstandard2``. At least drawn from feedback I received from other projects.

***Pull requests*** are appreciated, thank you!

PS. This includes efforts to align with the latest (breaking) NNG changes? Chiefly, I think, is in how "socket" is now considered a struct. I'm sure not that big a deal, but it is non trivial, a change from integral value to a struct value.


Fixes #3


@TribalNightOwl There was already an issue see https://github.com/de-jcup/eclipse-jenkins-editor/issues/31 which is closed now, becaus it is possible to define this in eclipse.
Also described in FAQ at https://github.com/de-jcup/eclipse-jenkins-editor/wiki/FAQ#how-can-i-open-other-files-than-jenkinsfile-with-jenkins-editor

As mentioned by @paulvi: If there is still a need of discussion please create an own issue outside commits.


[codestyle.txt](https://github.com/jakobemilandersson/voc/files/2419666/codestyle.txt)

Note that these comments are comments on all of your commits up to this commit for Task1.


Where are the `html` and `head` tags? w3 validator returned some warnings and some errors.


typo


我刚看明白你在说什么，fetch_row会使res的指针向后移动，但是不会使res变成NULL
res==NULL  表示查询的时候出错了，数据是不可用的
row==NULL 才表示结果集遍历完成


same


spaces


Probably a good call. I sometimes like to add additional, internal bits for diagnostic purposes, so ``Explicit`` is a better fit. However, in this case, since the bits are themselves well laid out to begin with, using ``Sequential`` is the better choice.


Somewhat unrelated to the original feature, I nevertheless appreciate any improvements in separate commits (esp. in this case where the semantic is changed drastically - `p_align` vs. `p_offset`).


Is this code developed using java11? If yes please let me know how you managed with JRE. Because java11 is not coming with JRE.


![](https://github.trello.services/images/mini-trello-icon.png) [new plot: density profile of added K+ and Na+ for PC:PS bilayers](https://trello.com/c/QaiZLoAc/15-new-plot-density-profile-of-added-k-and-na-for-pcps-bilayers)


This is an ``IntPtr``? Drawing from the C code, I'm not sure this was well understood. Probably correct, however.


issue #2


I think that is all well.
![captura de pantalla 2018-09-26 a las 14 40 35](https://user-images.githubusercontent.com/22727137/46080425-326e1680-c19a-11e8-892e-aad38ef6ce4c.png)


As was I (not sure about it). I drew pretty much directly from the C code and tried not to make too many CSharp style assumptions about it, and, for the most part, was having success with it, apart from internal (NNG) threaded corruption.


I observed segmentation fault error that is generated at berkeley DB library.


I have not considered platform issues (yet). My efforts are mainly focused on Windows for the moment. Again, ***PULL REQUESTS APPRECIATED***.


# Specs execution successful
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### Plans updated

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Bamboo specs have been successfully imported and the following deployment projects have been updated.

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----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


최종


Hello, how can I Subscribe a topic? There's no arguments here.


LGTM


Aliasing failed with the following error:

~~~
Error! No permission to access domain hyper.is under zeit
~~~


It's been a little while since I've been close to the *NNG API*. This is returning a ``UIntPtr`` today? You're probably correct, no doubt with regard to some of the breaking changes.


If you are casting this back to ``ulong`` here, I am suspicious that the above is not ``UIntPtr`` after all? Can you clarify?


I just made a custom socket client program which sends a network message with proper format.
Yes, RPC protocol is more suitable but I also observed some errors when I enabled RPC server with bitcoin for shadow experiments.


Ditto concerns above re: ``UIntPtr`` return versus ``ulong`` expected return.


Just out of curiosity: I've seen you have been focusing on the 88W8997 lately, but I do not know of any device supported by OpenWrt with that chipset... is that correct?


Yes, similar things.
It manually injects some transactions and a packet containing GENERATE command.


It seems my ``Invoker`` strategy is paying off, however. It took me a couple of hours considering how to best innovate where that was concerned. i.e. and with regard to the variations, ``InvokeWithResult``, and so forth.


rm newline


I appreciate the credit.


add some indent


You definitely need it in manifest; that was the whole reason why I started the hack with requires.txt and .egg in the very, very beginning... I didn't figure out how to package the file for PyPI. It's not going to be in the source distribution if you don't have it in manifest (it's going to be in the wheel without it having in manifest, though).

Just give it a try on test pypi. ;)


Oops, thank you for catching this @gully !


Awesome, thanks+++++.


![](https://github.trello.services/images/mini-trello-icon.png) [【程式】連接 Firebase Facebook 登入](https://trello.com/c/FIuWlQgB/22-%E3%80%90%E7%A8%8B%E5%BC%8F%E3%80%91%E9%80%A3%E6%8E%A5-firebase-facebook-%E7%99%BB%E5%85%A5)


Snapshot build can downloaded from: https://oss.sonatype.org/service/local/repositories/snapshots/content/org/rrd4j/rrd4j/3.3-SNAPSHOT/.

They are build from travis, using jdk 11.


add style


@AldisiRana this needs cross references


rm


Let’s only warn once. Needs a boolean check.


@datamuc please file a feature request. I'm not sure if we will be making this configurable, but a feature request with some rationale would be a good starting point.


Та делай, мне-то что, мяу. Мне вообще лень