[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_utils.R:14:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L14) *style:* **Variable or function name should be snake_case.**
```r
  A <- diag(a_1[1], nrow = n_species + 2, ncol = n_species + 2)
  ^
```
[R/mbd_loglik_utils.R:23:27:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L23) *style:* **Use <-, not =, for assignment.**
```r
  A[n_species, n_species] = A[n_species, n_species] * (1 - q) ^ (n_species - 1);
                          ^
```
[R/mbd_loglik_utils.R:41:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L41) *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:44:51:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L44) *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:46:27:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L46) *style:* **Use <-, not =, for assignment.**
```r
  M[row(M) == col(M) - 1] = mu * nvec[2:(max_number_of_species + 1)]
                          ^
```
[R/mbd_loglik_utils.R:54:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L54) *style:* **Variable or function name should be snake_case.**
```r
create_B0 <- function(
^~~~~~~~~
```
[R/mbd_loglik_utils.R:71:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L71) *style:* **Variable or function name should be snake_case.**
```r
create_A <- function(
^~~~~~~~
```
[R/mbd_loglik_utils.R:97:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L97) *style:* **Variable or function name should be snake_case.**
```r
create_B <- function(
^~~~~~~~
```
[R/mbd_loglik_utils.R:120:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L120) *style:* **Variable or function name should be snake_case.**
```r
create_A.no_mbd = function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:120:17:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L120) *style:* **Use <-, not =, for assignment.**
```r
create_A.no_mbd = function(
                ^
```
[R/mbd_loglik_utils.R:148:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L148) *style:* **Variable or function name should be snake_case.**
```r
create_B.no_mbd = function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:148:17:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L148) *style:* **Use <-, not =, for assignment.**
```r
create_B.no_mbd = function(
                ^
```
[R/mbd_loglik_utils.R:161:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L161) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
  ^
```
[R/mbd_loglik_utils.R:172:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L172) *style:* **Variable or function name should be snake_case.**
```r
A_operator <- function(
^~~~~~~~~~
```
[R/mbd_loglik_utils.R:173:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_utils.R:190:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L190) *style:* **Commented code should be removed.**
```r
    # exp_matrix <- rsexpm:::sexpm(transition_matrix * time_interval)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:191:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L191) *style:* **Commented code should be removed.**
```r
    # result     <- exp_matrix %*% Q
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:195:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L195) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:195:19:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L195) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:210:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L210) *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:214:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L214) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:240:26:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L240) *style:* **Commas should always have a space after.**
```r
      rtol = a_reltol)[2,-1],
                         ^
```
[R/mbd_loglik_utils.R:260:21:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L260) *style:* **Use <-, not =, for assignment.**
```r
    starting_vector = x
                    ^
```
[R/mbd_loglik_utils.R:261:23:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L261) *style:* **Use <-, not =, for assignment.**
```r
    transition_matrix = pars
                      ^
```
[R/mbd_loglik_utils.R:262:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L262) *style:* **Use <-, not =, for assignment.**
```r
    dx  = rep(0, length(starting_vector))
        ^
```
[R/mbd_loglik_utils.R:263:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L263) *style:* **Use <-, not =, for assignment.**
```r
    dx  = drop(transition_matrix %*% starting_vector)
        ^
```
[R/mbd_loglik_utils.R:264:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L264) *style:* **Use <-, not =, for assignment.**
```r
    out = (dx)
        ^
```
[R/mbd_loglik_utils.R:265:16:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L265) *style:* **Use <-, not =, for assignment.**
```r
    names(out) = names(x)
               ^
```
[R/mbd_loglik_utils.R:285:4:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L285) *style:* **Commented code should be removed.**
```r
  #mu <- pars[2]
   ^~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:289:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L289) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx))
  ^~
```
[R/mbd_loglik_utils.R:291:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L291) *style:* **Variable or function name should be snake_case.**
```r
  T0 <- create_A(
  ^~
```
[R/mbd_loglik_utils.R:299:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L299) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- A_operator(
  ^~
```
[R/mbd_loglik_utils.R:308:45:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L308) *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:316:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L316) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:322:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L322) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:330:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L330) *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:330:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L330) *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:330:32:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L330) *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:333:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L333) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- rep(0, lx + 1);  Qi[3] <- 1
  ^~
```
[R/mbd_loglik_utils.R:335:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L335) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_A(
  ^~
```
[R/mbd_loglik_utils.R:340:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L340) *style:* **Variable or function name should be snake_case.**
```r
  A2_v1 <- A_operator(
  ^~~~~
```
[R/mbd_loglik_utils.R:364:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L364) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:370:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L370) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:378:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L378) *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:378:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L378) *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:378:32:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L378) *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:380:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L380) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:382:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L382) *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:385:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L385) *style:* **Variable or function name should be snake_case.**
```r
  A2_v1 <- A_operator(
  ^~~~~
```
[R/mbd_loglik_utils.R:395:54:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L395) *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:408:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L408) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:408:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L408) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:414:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L414) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:421:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L421) *style:* **Only use double-quotes.**
```r
    cat('mu is supposed to be equal zero to use this function')
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:422:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L422) *warning:* **local variable ‘pc’ assigned but may not be used**
```r
    return(pc <- NA)
           ^~
```
[R/mbd_loglik_utils.R:426:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L426) *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:426:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L426) *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:426:32:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L426) *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:428:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L428) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:430:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L430) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_A(
  ^~
```
[R/mbd_loglik_utils.R:439:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L439) *style:* **Variable or function name should be snake_case.**
```r
  A2_v1 <- A_operator(
  ^~~~~
```
[R/mbd_loglik_utils.R:450:54:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L450) *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:454:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L454) *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:467:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L467) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:474:18:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L474) *style:* **Put spaces around all infix operators.**
```r
  a <- iterations/2
                ~^~
```
[R/mbd_loglik_utils.R:476:32:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L476) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:483:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L483) *style:* **Variable or function name should be snake_case.**
```r
  right.lx_coord <- 0
  ^~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:497:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L497) *style:* **Variable or function name should be snake_case.**
```r
        right.lx_coord <- i
        ^~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:505:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L505) *style:* **Variable or function name should be snake_case.**
```r
    right.lx_coord <- which(
    ^~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:516:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L516) *style:* **Variable or function name should be snake_case.**
```r
  right.lx_coord2 <- 0
  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:530:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L530) *style:* **Variable or function name should be snake_case.**
```r
        right.lx_coord2 <- j
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:536:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L536) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  }; lx_test2
  ^
```
[R/mbd_loglik_utils.R:538:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L538) *style:* **Variable or function name should be snake_case.**
```r
    right.lx_coord2 <- which(
    ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:552:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L552) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability1 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:557:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L557) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:562:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L562) *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:584:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L584) *style:* **Commented code should be removed.**
```r
    #   reltol = reltol
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:610:18:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L610) *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:619:14:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L619) *style:* **Variable or function name should be snake_case.**
```r
    pc <- 1; A2_v1 <- c(1, rep(0, max_number_of_species))
             ^~~~~
```
[R/mbd_loglik_utils.R:622:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L622) *style:* **Variable or function name should be snake_case.**
```r
    one_over_Cm <- (3 * (m + 1)) / (m + 3)
    ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:632:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L632) *style:* **Variable or function name should be snake_case.**
```r
    Qi <- c(1, rep(0, max_number_of_species))
    ^~
```
[R/mbd_loglik_utils.R:641:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L641) *style:* **Variable or function name should be snake_case.**
```r
    A2_v1 <- A_operator(
    ^~~~~
```
[R/mbd_loglik_utils.R:653:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L653) *style:* **Variable or function name should be snake_case.**
```r
      A2_v1 <- negatives_correction(A2_v1, pars)
      ^~~~~
```
[R/mbd_loglik_utils.R:653:16:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L653) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
      A2_v1 <- negatives_correction(A2_v1, pars)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:658:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L658) *style:* **Variable or function name should be snake_case.**
```r
      mk_n_zero.no_mbd <- create_A.no_mbd(
      ^~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:667:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L667) *style:* **Variable or function name should be snake_case.**
```r
      A2_v1.no_mbd <- A_operator(
      ^~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:676:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L676) *style:* **Variable or function name should be snake_case.**
```r
      A2_v1 <- A2_v1 - A2_v1.no_mbd
      ^~~~~
```
[R/mbd_loglik_utils.R:698:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L698) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:721:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L721) *style:* **Commented code should be removed.**
```r
    # pc_1 <- calculate_conditional_probability(alpha = alpha, ...)$pc
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:745:35:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L745) *style:* **Put spaces around all infix operators.**
```r
      delta_pc <- abs(pc_2 - pc_1)/pc_1;
                                 ~^~
```
[R/mbd_loglik_utils.R:751:11:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L751) *style:* **Use <-, not =, for assignment.**
```r
    count = count + 1
          ^
```
[R/mbd_loglik_utils.R:752:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L752) *style:* **Commented code should be removed.**
```r
    # print(alpha)
      ^~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:780:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L780) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik_utils.R:781:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik_utils.R#L781) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik.R:79:15:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:139:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L139) *style:* **Variable or function name should be snake_case.**
```r
      Qt <- matrix(0, ncol = (lx + 1), nrow = length(time_intervals))
      ^~
```
[R/mbd_loglik.R:140:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L140) *style:* **Commas should always have a space after.**
```r
      Qt[1,] <- Qi
           ^
```
[R/mbd_loglik.R:160:14:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L160) *style:* **Commas should always have a space after.**
```r
        Qt[t,] <- A_operator(
             ^
```
[R/mbd_loglik.R:161:26:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L161) *style:* **Commas should always have a space after.**
```r
          Q = Qt[(t - 1),],
                         ^
```
[R/mbd_loglik.R:172:16:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L172) *style:* **Commas should always have a space after.**
```r
          Qt[t,] <- negatives_correction(Qt[t,], pars)
               ^
```
[R/mbd_loglik.R:172:21:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L172) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
          Qt[t,] <- negatives_correction(Qt[t,], pars)
                    ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:172:47:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L172) *style:* **Commas should always have a space after.**
```r
          Qt[t,] <- negatives_correction(Qt[t,], pars)
                                              ^
```
[R/mbd_loglik.R:174:29:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L174) *style:* **Commas should always have a space after.**
```r
        if (any(is.nan(Qt[t,])))
                            ^
```
[R/mbd_loglik.R:175:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:178:37:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L178) *style:* **Commas should always have a space after.**
```r
            print(pars); print(Qt[t,])
                                    ^
```
[R/mbd_loglik.R:182:22:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L182) *style:* **Commas should always have a space after.**
```r
        if (any(Qt[t,] < 0)) {
                     ^
```
[R/mbd_loglik.R:188:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L188) *style:* **Commas should always have a space after.**
```r
        C[t] <- 1 / (sum(Qt[t,])); Qt[t,] <- Qt[t,] * C[t]
                              ^
```
[R/mbd_loglik.R:188:41:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L188) *style:* **Commas should always have a space after.**
```r
        C[t] <- 1 / (sum(Qt[t,])); Qt[t,] <- Qt[t,] * C[t]
                                        ^
```
[R/mbd_loglik.R:188:51:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L188) *style:* **Commas should always have a space after.**
```r
        C[t] <- 1 / (sum(Qt[t,])); Qt[t,] <- Qt[t,] * C[t]
                                                  ^
```
[R/mbd_loglik.R:191:9:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:195:16:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L195) *style:* **Commas should always have a space after.**
```r
          Qt[t,] <- (B %*% Qt[t,])
               ^
```
[R/mbd_loglik.R:195:33:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L195) *style:* **Commas should always have a space after.**
```r
          Qt[t,] <- (B %*% Qt[t,])
                                ^
```
[R/mbd_loglik.R:197:18:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L197) *style:* **Commas should always have a space after.**
```r
            Qt[t,] <- negatives_correction(Qt[t,], pars)
                 ^
```
[R/mbd_loglik.R:197:23:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L197) *warning:* **no visible global function definition for ‘negatives_correction’**
```r
            Qt[t,] <- negatives_correction(Qt[t,], pars)
                      ^~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik.R:197:49:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L197) *style:* **Commas should always have a space after.**
```r
            Qt[t,] <- negatives_correction(Qt[t,], pars)
                                                ^
```
[R/mbd_loglik.R:199:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L199) *style:* **Commas should always have a space after.**
```r
          if (any(is.nan(Qt[t,])))
                              ^
```
[R/mbd_loglik.R:200:11:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:203:39:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L203) *style:* **Commas should always have a space after.**
```r
              print(pars); print(Qt[t,])
                                      ^
```
[R/mbd_loglik.R:207:24:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L207) *style:* **Commas should always have a space after.**
```r
          if (any(Qt[t,] < 0)) {
                       ^
```
[R/mbd_loglik.R:213:33:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L213) *style:* **Commas should always have a space after.**
```r
          D[t] <- 1 / (sum(Qt[t,])); Qt[t,] <- Qt[t,] * D[t]
                                ^
```
[R/mbd_loglik.R:213:43:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L213) *style:* **Commas should always have a space after.**
```r
          D[t] <- 1 / (sum(Qt[t,])); Qt[t,] <- Qt[t,] * D[t]
                                          ^
```
[R/mbd_loglik.R:213:53:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L213) *style:* **Commas should always have a space after.**
```r
          D[t] <- 1 / (sum(Qt[t,])); Qt[t,] <- Qt[t,] * D[t]
                                                    ^
```
[R/mbd_loglik.R:237:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_loglik.R#L237) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * Qt[t, (missnumspec + 1)] #I have to include +1 because of Q0
    ^
```
[R/mbd_ml.R:66:17:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:115:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L115) *style:* **Use <-, not =, for assignment.**
```r
    optstr = "nothing"
           ^
```
[R/mbd_ml.R:117:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L117) *style:* **Use <-, not =, for assignment.**
```r
    optstr = namepars[idparsopt]
           ^
```
[R/mbd_ml.R:123:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L123) *style:* **Use <-, not =, for assignment.**
```r
    fixstr = "nothing"
           ^
```
[R/mbd_ml.R:125:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L125) *style:* **Use <-, not =, for assignment.**
```r
    fixstr = namepars[idparsfix]
           ^
```
[R/mbd_ml.R:134:15:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L194) *style:* **Variable or function name should be snake_case.**
```r
  MLtrpars <- as.numeric(unlist(out$par))
  ^~~~~~~~
```
[R/mbd_ml.R:197:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L197) *style:* **Variable or function name should be snake_case.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
    ^~~~~~
```
[R/mbd_ml.R:197:12:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L197) *style:* **Use <-, not =, for assignment.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
           ^
```
[R/mbd_ml.R:199:5:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L199) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars
    ^~~~~~
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  MLpars1 <- rep(0, n_pars); names(MLpars1) <- namepars
  ^~~~~~~
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L203) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:203:61:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L203) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                                                            ^
```
[R/mbd_ml.R:204:3:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml.R#L219) *style:* **Commas should always have a space after.**
```r
    s2 <- sprintf('Maximum loglikelihood: %f',ML)
                                              ^
```
[R/mbd_ml2.R:78:4:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml2.R#L78) *style:* **Commented code should be removed.**
```r
  #idparsopt <- which(estimated_params %in% get_mbd_param_names())
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml2.R:79:4:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml2.R#L79) *style:* **Commented code should be removed.**
```r
  #idparsfix <- which(fixed_params %in% get_mbd_param_names())
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml2.R:83:19:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_ml2.R#L83) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
    param_name <- get_mbd_param_names()[i]
                  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:13:24:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:28:15:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L28) *style:* **Use <-, not =, for assignment.**
```r
    th_loglik = -Inf
              ^
```
[R/mbd_pure_multiple_birth.R:30:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:85:15:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L85) *style:* **Use <-, not =, for assignment.**
```r
    th_loglik = -Inf
              ^
```
[R/mbd_pure_multiple_birth.R:87:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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/e7ec5310f64708589dd930dc2f61061a0c3a80a3/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:226:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L226) *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:227:19:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L227) *style:* **Use <-, not =, for assignment.**
```r
        trparsopt = initparsopt/(1 + initparsopt)
                  ^
```
[R/mbd_pure_multiple_birth.R:227:32:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L227) *style:* **Put spaces around all infix operators.**
```r
        trparsopt = initparsopt/(1 + initparsopt)
                              ~^~
```
[R/mbd_pure_multiple_birth.R:227:33:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L227) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt = initparsopt/(1 + initparsopt)
                                ^
```
[R/mbd_pure_multiple_birth.R:228:46:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L228) *style:* **Use <-, not =, for assignment.**
```r
        trparsopt[which(initparsopt == Inf)] = 1
                                             ^
```
[R/mbd_pure_multiple_birth.R:229:19:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L229) *style:* **Use <-, not =, for assignment.**
```r
        trparsfix = parsfix/(1 + parsfix)
                  ^
```
[R/mbd_pure_multiple_birth.R:229:28:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L229) *style:* **Put spaces around all infix operators.**
```r
        trparsfix = parsfix/(1 + parsfix)
                          ~^~
```
[R/mbd_pure_multiple_birth.R:229:29:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L229) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix = parsfix/(1 + parsfix)
                            ^
```
[R/mbd_pure_multiple_birth.R:230:42:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L230) *style:* **Use <-, not =, for assignment.**
```r
        trparsfix[which(parsfix == Inf)] = 1
                                         ^
```
[R/mbd_pure_multiple_birth.R:232:7:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L232) *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:236:17:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L236) *style:* **Use <-, not =, for assignment.**
```r
      optimpars = c(tol, maxiter)
                ^
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L237) *style:* **Lines should not be more than 80 characters.**
```r
      initloglik <- pmb_loglik_choosepar(trparsopt = trparsopt, trparsfix = trparsfix, idparsopt = idparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:238:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L238) *style:* **Lines should not be more than 80 characters.**
```r
                                               idparsfix = idparsfix, brts = brts, soc = soc,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:239:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
                                               pars_transform = pars_transform) #there's no pars2 here and instead 3 more args at the end
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:240:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L240) *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:243:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L243) *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:247:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:252:1:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L252) *style:* **Lines should not be more than 80 characters.**
```r
          cat("Optimization has not converged. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:255:11:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L255) *style:* **Variable or function name should be snake_case.**
```r
          MLtrpars <- as.numeric(unlist(out$par))
          ^~~~~~~~
```
[R/mbd_pure_multiple_birth.R:257:13:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L257) *style:* **Variable or function name should be snake_case.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
            ^~~~~~
```
[R/mbd_pure_multiple_birth.R:257:31:](https://github.com/Giappo/mbd/blob/e7ec5310f64708589dd930dc2f61061a0c3a80a3/R/mbd_pure_multiple_birth.R#L257) *style:* **Put spaces around all infix operators.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)


rm empty line


@StephanOsthold $aLocalTo oder $localTo fände ich treffender, würde sonst eher erwarten, dass in $eachLocalTo eine ArrayRef enthalten ist. Block noch überschaubar, daher aber auch vernachlässigbar.


確認しました。ありがとうございます。


merged


This commit has nothing to do with WRT3200ACM.


delimiters defined (orch.h)


This is because otherwise we will be breaking the CSS (there has been some updates)


ohh, thanks very much!


I just realized I used to write `.then()` and `.catch()` in new lines. Eh, whatever, I'll fix them in next commit, whenever that is.


@maziminke check bottom of my comment for ideas.

But it seems that we hit a similar issue. What I discovered was that I had the HTML entities in the url while the url was initially saved with a leading space. It was also a first time for me to face such an issue. Maybe there was some other commit prior to this fix somehow initiating this type of errors.

Anyway it seems that while the url field is trimmed of the leading/trailing spaces, the it will not store HTML entities. Anyhow, its very reasonable to trim the urls anyway so even if there is some other issue related, this commit should be ok anyway.


柴田
用意しているクラスが定数を持っているので、その定数を使用しませんか？


useless, rubbish, shit, haha.