[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/is_mbd_params.R:1:44:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/is_mbd_params.R#L1) *style:* **Trailing whitespace is superfluous.**
```r
#' Is object \code{x} an MBD parameter set,
                                           ^
```
[R/is_mbd_params.R:5:35:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/is_mbd_params.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#' @return TRUE if yes, else FALSE
                                  ^
```
[R/mbd_loglik_utils.R:14:3:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/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:21:52:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_loglik_utils.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    A[s, src] <- A[s, src] * q ^ (m - n) * (1 - q)^(2 * n - m)
                                                   ^
```
[R/mbd_loglik_utils.R:23:27:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/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:31:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_loglik_utils.R#L31) *style:* **Variable or function name should be snake_case.**
```r
create_A0 <- function(
^~~~~~~~~
```
[R/mbd_loglik_utils.R:41:3:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/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:44:39:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_loglik_utils.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  diag(M) <= (-lambda) * (1 - (1 - q)^(k + nvec) ) - mu * (nvec + k)
                                      ^
```
[R/mbd_loglik_utils.R:44:49:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L194) *style:* **Variable or function name should be snake_case.**
```r
  MLtrpars <- as.numeric(unlist(out$par))
  ^~~~~~~~
```
[R/mbd_ml.R:197:5:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L197) *style:* **Variable or function name should be snake_case.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
    ^~~~~~
```
[R/mbd_ml.R:197:12:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L197) *style:* **Use <-, not =, for assignment.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
           ^
```
[R/mbd_ml.R:199:5:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L199) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars
    ^~~~~~
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  MLpars1 <- rep(0, n_pars); names(MLpars1) <- namepars
  ^~~~~~~
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L203) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:203:61:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L203) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                                                            ^
```
[R/mbd_ml.R:204:3:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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:47:33:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      a_term[t] <- sum( (1 - q)^(ii * k[t]) * poisson_term ) * # (1)
                                ^
```
[R/mbd_pure_multiple_birth.R:47:59:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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/cf3072d61562dbf23133eac2174ab34bd614deeb/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:110:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L110) *style:* **Lines should not be more than 80 characters.**
```r
      nu * choose(k[-length(k)], births) * q^births * (1 - q)^(k[-length(k)] - births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:110:63:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L110) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      nu * choose(k[-length(k)], births) * q^births * (1 - q)^(k[-length(k)] - births)
                                                              ^
```
[R/mbd_pure_multiple_birth.R:111:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L111) *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:139:5:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L139) *style:* **Commented code should be removed.**
```r
  # cond <- 0
    ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:145:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L145) *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:145:5:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L145) *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:151:33:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (min(trpars1[1:n_pars]) < 0 ) {
                                ^
```
[R/mbd_pure_multiple_birth.R:160:15:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L160) *warning:* **no visible global function definition for ‘pmb_loglik’**
```r
    loglik <- pmb_loglik(pars = pars1, brts = brts)
              ^~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:163:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:173:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L173) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML <- function(
^~~~~~
```
[R/mbd_pure_multiple_birth.R:182:17:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L182) *style:* **Only use double-quotes.**
```r
  optimmethod = 'simplex',
                ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:187:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L187) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:189:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L189) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:190:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L190) *style:* **Lines should not be more than 80 characters.**
```r
  # - optimmethod = 'simplex' (current default) or 'subplex' (default of previous versions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:195:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L195) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(namepars); #if you add more parameters to your model just change this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:196:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars; #those are the parameters that you get if something goes sideways
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:224:7:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L224) *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:225:19:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L225) *style:* **Use <-, not =, for assignment.**
```r
        trparsopt = initparsopt/(1 + initparsopt)
                  ^
```
[R/mbd_pure_multiple_birth.R:225:32:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L225) *style:* **Put spaces around all infix operators.**
```r
        trparsopt = initparsopt/(1 + initparsopt)
                              ~^~
```
[R/mbd_pure_multiple_birth.R:225:33:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L225) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsopt = initparsopt/(1 + initparsopt)
                                ^
```
[R/mbd_pure_multiple_birth.R:226:46:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L226) *style:* **Use <-, not =, for assignment.**
```r
        trparsopt[which(initparsopt == Inf)] = 1
                                             ^
```
[R/mbd_pure_multiple_birth.R:227:19:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L227) *style:* **Use <-, not =, for assignment.**
```r
        trparsfix = parsfix/(1 + parsfix)
                  ^
```
[R/mbd_pure_multiple_birth.R:227:28:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L227) *style:* **Put spaces around all infix operators.**
```r
        trparsfix = parsfix/(1 + parsfix)
                          ~^~
```
[R/mbd_pure_multiple_birth.R:227:29:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L227) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        trparsfix = parsfix/(1 + parsfix)
                            ^
```
[R/mbd_pure_multiple_birth.R:228:42:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L228) *style:* **Use <-, not =, for assignment.**
```r
        trparsfix[which(parsfix == Inf)] = 1
                                         ^
```
[R/mbd_pure_multiple_birth.R:230:7:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L230) *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:234:17:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L234) *style:* **Use <-, not =, for assignment.**
```r
      optimpars = c(tol, maxiter)
                ^
```
[R/mbd_pure_multiple_birth.R:235:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L235) *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:236:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L236) *style:* **Lines should not be more than 80 characters.**
```r
                                               idparsfix = idparsfix, brts = brts, soc = soc,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L237) *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:238:1:](https://github.com/Giappo/mbd/blob/cf3072d61562dbf23133eac2174ab34bd614deeb/R/mbd_pure_multiple_birth.R#L238) *style:* **Lines should not be more than 80 characters.**
```r
      cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Why would there be a build file without a reference?


This was not the problem I reported. What is wrong is the output of t.info in unit 21, where end_date is 2018-01-04 (jan 4, 2018) when it should be 2018-01-01. The problem comes from i.modis.import and the way it creates the file that you then use with t.register.


Is it useable for mi air i7-8550u?


Merge


save checkpoints for DNN implementation


Ошибся в знаке. Так как это финишная таблица, обороты по контрагенту в Дт записываются с знаком (-), поэтому обратные операции (отражение возврата как сторно реализации) здесь будут отображены с (+)


Hey, a bit off-topic (didn't want to create an issue) but will you be updating Nightly builds? Windows 15th build crashes on Rom load and the AppVeyor x64 builds grew from 9MB to 27MB from [build 407](https://ci.appveyor.com/project/zeromus/desmume/build/0.0.0.407)  (not an issue just don't understand why).


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