[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_calc_max_lik.R:78:4:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_calc_max_lik.R#L78) *style:* **Commented code should be removed.**
```r
  #idparsopt <- which(estimated_params %in% get_mbd_param_names())
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_calc_max_lik.R:79:4:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_calc_max_lik.R#L79) *style:* **Commented code should be removed.**
```r
  #idparsfix <- which(fixed_params %in% get_mbd_param_names())
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_calc_max_lik.R:83:19:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_calc_max_lik.R#L83) *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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L174) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_utils.R:191:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L191) *style:* **Commented code should be removed.**
```r
    # exp_matrix <- rsexpm:::sexpm(transition_matrix * time_interval)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:192:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L192) *style:* **Commented code should be removed.**
```r
    # result     <- exp_matrix %*% Q
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:196:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L196) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:196:19:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L196) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:211:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L211) *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:215:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L215) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:241:26:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L241) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:286:4:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L286) *style:* **Commented code should be removed.**
```r
  #mu <- pars[2]
   ^~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:290:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L290) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx))
  ^~
```
[R/mbd_loglik_utils.R:292:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L292) *style:* **Variable or function name should be snake_case.**
```r
  T0 <- create_a(
  ^~
```
[R/mbd_loglik_utils.R:300:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L300) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- a_operator(
  ^~
```
[R/mbd_loglik_utils.R:309:45:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L309) *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:317:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L317) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:331:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L331) *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:331:31:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L331) *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:331:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L331) *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:334:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L334) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- rep(0, lx + 1);  Qi[3] <- 1
  ^~
```
[R/mbd_loglik_utils.R:336:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L336) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_a(
  ^~
```
[R/mbd_loglik_utils.R:365:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L365) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:379:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L379) *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:379:31:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L379) *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:379:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L379) *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:381:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L381) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:383:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L383) *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:396:54:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L396) *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:409:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L409) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:409:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L409) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:422:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L422) *style:* **Only use double-quotes.**
```r
    cat('mu is supposed to be equal zero to use this function')
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:423:12:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L423) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:427:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L427) *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:427:31:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L427) *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:427:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L427) *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:429:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L429) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:431:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L431) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_a(
  ^~
```
[R/mbd_loglik_utils.R:451:54:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L451) *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:455:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L455) *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:475:18:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L475) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:477:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L477) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:553:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L553) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:563:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L563) *warning:* **no visible global function definition for ‘find_best_lx_for_pc’**
```r
  lx <- find_best_lx_for_pc(brts = brts, pars = pars, soc = soc)
        ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:585:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L585) *style:* **Commented code should be removed.**
```r
    #   reltol = reltol
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:611:18:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L611) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- c(0, brts2time_intervals_and_births(brts)$births)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:623:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L623) *style:* **Variable or function name should be snake_case.**
```r
    one_over_Cm <- (3 * (m + 1)) / (m + 3)
    ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:633:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L633) *style:* **Variable or function name should be snake_case.**
```r
    Qi <- c(1, rep(0, max_number_of_species))
    ^~
```
[R/mbd_loglik_utils.R:654:16:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L654) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      a2_v1 <- negatives_correction(a2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:659:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L659) *style:* **Variable or function name should be snake_case.**
```r
      mk_n_zero.no_mbd <- create_a.no_mbd(
      ^~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:668:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L668) *style:* **Variable or function name should be snake_case.**
```r
      a2_v1.no_mbd <- a_operator(
      ^~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:722:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L722) *style:* **Commented code should be removed.**
```r
    # pc_1 <- calculate_conditional_probability(alpha = alpha, ...)$pc
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:746:35:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L746) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1)/pc_1;
                                 ~^~
```
[R/mbd_loglik_utils.R:753:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L753) *style:* **Commented code should be removed.**
```r
    # print(alpha)
      ^~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:781:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L781) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik_utils.R:782:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik_utils.R#L782) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik.R:79:15:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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:133:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L133) *style:* **Commented code should be removed.**
```r
      # lx <- 10 * alpha; #bonus line to simplify
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:134:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L134) *style:* **Commented code should be removed.**
```r
      # nvec <- 0:lx
        ^~~~~~~~~~~~
```
[R/mbd_loglik.R:137:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L137) *style:* **Variable or function name should be snake_case.**
```r
      Qi <- c(1, rep(0, lx))
      ^~
```
[R/mbd_loglik.R:140:13:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L140) *style:* **Commas should always have a space after.**
```r
      q_t[1,] <- Qi
            ^
```
[R/mbd_loglik.R:160:15:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L160) *style:* **Commas should always have a space after.**
```r
        q_t[t,] <- a_operator(
              ^
```
[R/mbd_loglik.R:161:27:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L161) *style:* **Commas should always have a space after.**
```r
          Q = q_t[(t - 1),],
                          ^
```
[R/mbd_loglik.R:172:17:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L172) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- negatives_correction(q_t[t,], pars)
                ^
```
[R/mbd_loglik.R:172:22:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L172) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
          q_t[t,] <- negatives_correction(q_t[t,], pars)
                     ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:172:49:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L172) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- negatives_correction(q_t[t,], pars)
                                                ^
```
[R/mbd_loglik.R:174:30:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L174) *style:* **Commas should always have a space after.**
```r
        if (any(is.nan(q_t[t,])))
                             ^
```
[R/mbd_loglik.R:175:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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:176:27:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L176) *style:* **Only use double-quotes.**
```r
          if (Sys.info()[['sysname']] == "Windows")
                          ^~~~~~~~~
```
[R/mbd_loglik.R:177:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L177) *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:178:38:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L178) *style:* **Commas should always have a space after.**
```r
            print(pars); print(q_t[t,])
                                     ^
```
[R/mbd_loglik.R:182:23:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L182) *style:* **Commas should always have a space after.**
```r
        if (any(q_t[t,] < 0)) {
                      ^
```
[R/mbd_loglik.R:188:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L188) *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:188:43:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L188) *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:188:54:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L188) *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:191:9:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L191) *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:193:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L193) *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:195:17:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L195) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- (B %*% q_t[t,])
                ^
```
[R/mbd_loglik.R:195:35:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L195) *style:* **Commas should always have a space after.**
```r
          q_t[t,] <- (B %*% q_t[t,])
                                  ^
```
[R/mbd_loglik.R:197:19:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L197) *style:* **Commas should always have a space after.**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                  ^
```
[R/mbd_loglik.R:197:24:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L197) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                       ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:197:51:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L197) *style:* **Commas should always have a space after.**
```r
            q_t[t,] <- negatives_correction(q_t[t,], pars)
                                                  ^
```
[R/mbd_loglik.R:199:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L199) *style:* **Commas should always have a space after.**
```r
          if (any(is.nan(q_t[t,])))
                               ^
```
[R/mbd_loglik.R:200:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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:201:29:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L201) *style:* **Only use double-quotes.**
```r
            if (Sys.info()[['sysname']] == "Windows")
                            ^~~~~~~~~
```
[R/mbd_loglik.R:202:13:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L202) *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:203:40:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L203) *style:* **Commas should always have a space after.**
```r
              print(pars); print(q_t[t,])
                                       ^
```
[R/mbd_loglik.R:207:25:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L207) *style:* **Commas should always have a space after.**
```r
          if (any(q_t[t,] < 0)) {
                        ^
```
[R/mbd_loglik.R:213:34:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L213) *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:213:45:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L213) *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:213:56:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L213) *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:237:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_loglik.R#L237) *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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L194) *style:* **Variable or function name should be snake_case.**
```r
  MLtrpars <- as.numeric(unlist(out$par))
  ^~~~~~~~
```
[R/mbd_ml.R:197:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L197) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars / (1 - MLtrpars)
    ^~~~~~
```
[R/mbd_ml.R:199:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L199) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars
    ^~~~~~
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  MLpars1 <- rep(0, n_pars); names(MLpars1) <- namepars
  ^~~~~~~
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L203) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:203:61:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L203) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                                                            ^
```
[R/mbd_ml.R:204:3:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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:13:24:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L13) *style:* **Commented code should be removed.**
```r
  test_pars <- pars  # test_pars=c(0.4,0,0.1,0.2)
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:14:24:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L14) *style:* **Commented code should be removed.**
```r
  test_brts <- brts  # test_brts=c(-10,-5,-5,-3,-3,-3,-2,-1,-1,-1)
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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:71:24:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L71) *style:* **Commented code should be removed.**
```r
  test_pars <- pars  # test_pars=c(0.4,0,0.1,0.2)
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:72:24:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L72) *style:* **Commented code should be removed.**
```r
  test_brts <- brts  # test_brts=c(-10,-5,-5,-3,-3,-3,-2,-1,-1,-1)
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:74:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
  # loglik=mbd_loglik(pars = test_pars, brts = test_brts, soc = soc, cond = 0, tips_interval = c(0,Inf))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:74:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L74) *style:* **Commented code should be removed.**
```r
  # loglik=mbd_loglik(pars = test_pars, brts = test_brts, soc = soc, cond = 0, tips_interval = c(0,Inf))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:82:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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:141:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L141) *style:* **Commented code should be removed.**
```r
  # cond <- 0
    ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:147:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
  # idparsopt=(1:3)[-c(idparsfix)] #this argument is useless but I let the user specify it because Rampal also did it (for some reason)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:147:5:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L147) *style:* **Commented code should be removed.**
```r
  # idparsopt=(1:3)[-c(idparsfix)] #this argument is useless but I let the user specify it because Rampal also did it (for some reason)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:153:33:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L153) *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:162:15:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L162) *warning:* **no visible global function definition for ‘pmb_loglik’**
```r
    loglik <- pmb_loglik(pars = pars1, brts = brts)
              ^~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:165:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L165) *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:175:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L175) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML <- function(
^~~~~~
```
[R/mbd_pure_multiple_birth.R:184:17:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L184) *style:* **Only use double-quotes.**
```r
  optimmethod = 'simplex',
                ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:189:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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:191:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L191) *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:192:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L192) *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:197:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L197) *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:198:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L198) *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:226:33:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L226) *style:* **Put spaces around all infix operators.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                               ~^~
```
[R/mbd_pure_multiple_birth.R:226:34:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L226) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt <- initparsopt/(1 + initparsopt)
                                 ^
```
[R/mbd_pure_multiple_birth.R:228:29:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L228) *style:* **Put spaces around all infix operators.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                           ~^~
```
[R/mbd_pure_multiple_birth.R:228:30:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L228) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix <- parsfix/(1 + parsfix)
                             ^
```
[R/mbd_pure_multiple_birth.R:240:8:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L240) *style:* **Trailing whitespace is superfluous.**
```r
      )
       ^
```
[R/mbd_pure_multiple_birth.R:241:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L241) *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:244:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L244) *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:248:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L248) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:253:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L253) *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:256:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L256) *style:* **Variable or function name should be snake_case.**
```r
          MLtrpars <- as.numeric(unlist(out$par))
          ^~~~~~~~
```
[R/mbd_pure_multiple_birth.R:258:13:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L258) *style:* **Variable or function name should be snake_case.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
            ^~~~~~
```
[R/mbd_pure_multiple_birth.R:258:31:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L258) *style:* **Put spaces around all infix operators.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
                             ~^~
```
[R/mbd_pure_multiple_birth.R:258:32:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L258) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
                               ^
```
[R/mbd_pure_multiple_birth.R:260:13:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L260) *style:* **Variable or function name should be snake_case.**
```r
            MLpars <- MLtrpars
            ^~~~~~
```
[R/mbd_pure_multiple_birth.R:262:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L262) *style:* **Variable or function name should be snake_case.**
```r
          MLpars1 <- rep(0, n_pars)
          ^~~~~~~
```
[R/mbd_pure_multiple_birth.R:268:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L268) *style:* **Variable or function name should be snake_case.**
```r
          ML <- as.numeric(unlist(out$fvalues))
          ^~
```
[R/mbd_pure_multiple_birth.R:269:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L269) *style:* **Lines should not be more than 80 characters.**
```r
          out2 <- data.frame(t(MLpars1), loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:273:11:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L273) *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:274:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L274) *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:274:84:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L274) *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:281:25:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L281) *style:* **Only use double-quotes.**
```r
          s2 <- sprintf('Maximum loglikelihood: %f',ML)
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:281:53:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L281) *style:* **Commas should always have a space after.**
```r
          s2 <- sprintf('Maximum loglikelihood: %f',ML)
                                                    ^
```
[R/mbd_pure_multiple_birth.R:289:1:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/R/mbd_pure_multiple_birth.R#L289) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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/1865a83257d2b2585464d4c235f5dbc13e68f270/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) )


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

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

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


Maybe you have to follow the guide in https://voodooi2c.github.io. Pin value is related to IOInterrupt.


+ space


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

* https://paul.kinlan.me


Overall great! The last few lines of code was something i created. From that example do something similar for more practice.


Interesting. I was not aware of the array version of the ``WsaPoll`` function. I also was not aware of the subtleties of decorating with ``[In, Out]`` versus language level ``ref``.


Checkmarx scan results 26 Sep 2018 15:31 UTC +03:00

High
Medium
Low
Info

New
0
0
0
0

Recurrent
0
0
0
0

Fixed
0
0
0
0

 Open Viewer
Included commits

Commit ID	Owner

a23cad998261c81bf63aa21ac681a2e8b5303e7c	@web-flow


ReUpload dhcpd.file


add braces


Good catch. @JacksonIsaac Please fix this.


the line 71 should delete the last ')'
In my case, I switch the diffX and diffY to make it work.
Thank you


yeah we could maybe work this into a code sample in the examples/ directory also at some point


Seriously, we should just kill the alphabets we don't use.