[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L194) *style:* **Variable or function name should be snake_case.**
```r
  MLtrpars <- as.numeric(unlist(out$par))
  ^~~~~~~~
```
[R/mbd_ml.R:197:5:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L197) *style:* **Variable or function name should be snake_case.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
    ^~~~~~
```
[R/mbd_ml.R:197:12:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L197) *style:* **Use <-, not =, for assignment.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
           ^
```
[R/mbd_ml.R:199:5:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L199) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars
    ^~~~~~
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  MLpars1 <- rep(0, n_pars); names(MLpars1) <- namepars
  ^~~~~~~
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L203) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:203:61:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L203) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                                                            ^
```
[R/mbd_ml.R:204:3:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/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/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_pure_multiple_birth.R#L257) *style:* **Put spaces around all infix operators.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
                             ~^~
```
[R/mbd_pure_multiple_birth.R:257:32:](https://github.com/Giappo/mbd/blob/3fa07a817eb80666318c99abebaaab34f4bb43c8/R/mbd_pure_multiple_birth.R#L257) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            MLpars <- MLtrpars/(1 - MLtrpars)
                               ^
```


Sir, Any progress ? Did you find him or the at least project link?


deneme


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{}
//test

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


Can you please update your F-Droid Repository.... I've found no new release here @postapczuk


<slaps forehead> Aw, man. Why couldn't I see that! Argh.
Well, at least we got some slightly more robust code out of this. Thanks, a_c.


Este metodo se agrego para limpiar el codigo, anteriormente el codigo era asi :

```
render(){
 let classes = "badge m-2 badge-";
 classes += this.state.count === 0 ? "danger" : "primary";
}
```


Testing 123


ㅋㅋ 재밌는거 만들었네


我叫做傅詠平


Updating a few more Maven plugins will probably fix the Java 11 build @fbacchella.

I made a fork and did some tests, see:
* [wborn/rrd4j commit](https://github.com/wborn/rrd4j/commit/678eac9253dada3e72a8dc8edfce6903fbc495ad)
* [wborn/rrd4j Travis CI](https://travis-ci.org/wborn/rrd4j/builds/433442585?utm_source=github_status&utm_medium=notification)

The sonar and deploy goals needed to be disabled in `.travis.yml` because of permissions.


好的。
有件事想和您说一下，因为我在开发过程中学习了hustoj很多东西，最后会在我的源码里面注明学习了hustoj，但是最后部署的时候就仍然用自己的名字了，项目不打算商用，这样您不介意吧？


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

* https://paul.kinlan.me


test


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

* https://paul.kinlan.me


> ability of iteration is needed for debug dump

doesnt debug dump use another public method anyway?


I will update them, or you can do a pull request for versions in `pom.xml`, I will merge it. You don't have permissions for sonar and deploy. That's why they fail.


Please use plain `if`/`else` construct instead of ternary operator in cases like this when different functions are called conditionally.


Hi,

When you write "@dk" in the commit message, one little innocent spam alert is firing in my mail server and I get a mail sent. That's not your problem, that's a github bug/feature, -- but anyway I'd like to ask not to do that, if possible. Thank you :)


Problem N1: Table cache

Generally the idea is such that table gets opened for every statement and then it gets closed when statement ends. Except for `LOCK TABLES`, where table stays open over multiple statements until `UNLOCK TABLES` is issued.

This is of course horribly expensive and thus we have table cache, which complicates things.

From SQL layer point of view, we don't call `storage_engine::open()/storage_engine::close()` for every statement, but instead:
- when statement starts SQL layer asks table cache for open `TABLE` instance
- when statement ends SQL layer  release `TABLE` instance back to table cache

From storage engine point of view this means: `open()` and `close()` don't mark beginning and end of statement. To some extent this is marked with `external_lock()`.

Some statements (like DDL) need to invalidate old `TABLE` objects, so that subsequent queries to this table see updated definition. Effectively it means evicting unused `TABLE` objects from table cache and waiting for used ones to get released and eventually evicted as well.

Original code bypassed table cache, thus there's no way to track such instances as well as there's no way  to invalidate them.

If you plan to keep backing `TABLE` instance open between `open()` and `close()`, this is a bit too much. E.g. consider the following scenario:
- `SELECT * FROM oqgraph_table` would open oqgraph table and then backing table
- statement ends, oqgraph table gets released to table cache but backing table is not
- now `ALTER TABLE backing_table` (be it concurrent or not) attempts to evict backing `TABLE` instance, but it is marked as used and `ALTER` has to wait... may be forever (strictly speaking until somebody comes and closes oqgraph table).

But in fact, what most probably happens with your patch is that `open_table()` adds backing `TABLE` instance to `thd->open_tables`. And then, when statement ends, it gets closed by `close_thread_tables()`. This effectively invalidates `edges` for subsequent statement.

Also there's no need to call `closefrm()` and `free_table_share()` anymore. It is table cache job.

What we could do is to try moving `open_table()` to `external_lock()`. And we don't need to do anything on unlock, because it will be done automatically when statement ends (or `UNLOCK TABLES` is issued).

Some statements may work, but then there's "Problem N2", which I will describe in next comment.


Nothing very different


@pepibumur as explained above, it's because the build file isn't included in any build phases, which probably shouldn't be the case


I think our intro needs to start from a slightly more elementary vantage point (e.g. perhaps describe the class text embeddings case and then point out that the same could be done for any categorical variable)


<img src="" style="border-radius: 100%; text-align: center;">


BTW, this is done in the devo branch of Alyx.


So maybe these next two paragraph need to be at the top? I think starting with *distributed representation* as a concept will lose people. Better to frame it as a richer way to encode categorical variables I think.


some more comments added


### Before
![ownerif](https://user-images.githubusercontent.com/5862206/46077365-399f1f80-c1ae-11e8-920f-82a05d9e2c02.png)

### After
![iown](https://user-images.githubusercontent.com/5862206/46077384-53d8fd80-c1ae-11e8-84b2-9ff432dddd49.png)


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{}
//test

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


I feel like we also might want to re-order this: first show the application of embeddings then show how they work under the hood.


мм.... Хочу сделать тёмной, уж люблю все тёмное, только не добавляй в обычный клиент, не отбирай мне работу)))


Este es mi primer commit


well, we are working with eight-days products, se end will be either 2018-01-04 or 2017-12-28, right?


for dumping asset caches `outputAll` is used, and for writers/loaders containers range-based-for is used. So.. actually iterator getters can be removed completely if i remember everything correctly but IMO it can be of use in non-concurrent as long as they're just const getters


因为Sempr最开始开源选择的是GPLv2协议，所以如果你借鉴了一些源码的话，在未来如果开源或者出售，记得仍然采用GPL协议会比较稳妥。


Created multidev environment [hollandtopcampings#ci-3](https://dashboard.pantheon.io/sites/d27eaed7-8a7c-447a-865e-1040f1a0183d#ci-3).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-3-hollandtopcampings.pantheonsite.io/)


Yes, we definitely should use canned `layer_embedding` first then make it clear to readers that the custom layer is an advanced/optional sub-topic (most readers will have never even seen a Keras custom layer so showing that right up front is too much)


Для этого файла надо тоже проверить, что всё ок


No, memory is not coming with the g, and must be kept....I'll push release-1.2.1 changes that should fix this.


We need to call `trade_with` here, just replicate https://github.com/rubykube/peatio/blob/feature/ranger/app/trading/matching/engine.rb#L76 without actual `fill` and `publish` calls


3 пробела


hello,

sorry for asking again, but what is this commit for? :+1:


![](https://github.trello.services/images/mini-trello-icon.png) [Change double jump to 4 + 2 meters.](https://trello.com/c/Xj9K4VGa/10-change-double-jump-to-4-2-meters)


"user-movie interaction"


Здесь нужна проверка с учётом погрешности, о которой я говорил на занятии


"some users are intrinsically more critical"


Oops, typo in the commit message: "not update" -> "now update"


ММММ ЦВЕТОВЫЕ СХЕМЫ А ЕТО ИДЕЯ


> So you guys are basically saying that a "healthy" working environment implies bad code? do you know what code reviews are for? I can tell you that your code is bad and maybe guide you in the correct way of writing code without making you feel like you are a piece of crap.

Problem is, people tend to become invested in their works, and any criticism levelled at those works _feels like_ an attack, even when it's not intended to be. This is just a part of the human condition, I guess, and it's an integral part of putting anything you make out into the public, whether it be a piece of code, a statue, or a poem. Someone is bound to say bad things about it (not necessarily _you_, though!) and you _will_ feel bad about it, even though it wasn't directed at you.


如果是科研用途，只需要论文里提及就可以。仅仅学校内部使用的话，应该没有特别的要求。


+ Attribute LastOrderLinesKey test and code


См строку 116. Лучше выдерживать один стиль, and или &&. Принято писать &&


We should also very briefly introduce the concept of keras custom models


We should use `os.scandir` for efficiency reasons.

https://docs.python.org/3/library/os.html#os.scandir


При делении нужно проверить, что знаменатель не равен нулю, тоже с учётом погрешности


Лучше сделать набор констант — кодов ошибок, и возвращать и проверять их


For 88W8997.


![f05b59cb-7a87-43a6-8076-5607f2bfaf8e](https://user-images.githubusercontent.com/22727137/46077854-912f9200-c192-11e8-86cd-48be6d208cab.jpeg)

Is this my pin list?


Ошибка. При подмене стороны контрагента по знаку операции не учел что это необходимо делать только для данных PL


This was incorrectly doced, but the old code never worked AFAIK, so I'm not considering this change to be backwards incompatible.


I'd argue the other way around: Since tracking is now off by default and it takes a conscious decision to _add_ a header, merely providing said header can be interpreted as user consent.


`Modal wrapper` is background color of the overlay window when users open the new toot modal.


one change


yes, I can see that


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

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

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

### Deployments updated

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

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


Fixes #8


i got the 3200acm, but is it an enhancement or i will not sense anything with this commit. :)


okay - I don't see the comment reg. saving/restoring model weights, so I add that here - I feel like it's not totally "on-topic" for this post ...


This line is wrong. It has to be `if (strpos($value, 'v') !== 0) {`


Created multidev environment [hollandtopcampings#ci-7](https://dashboard.pantheon.io/sites/d27eaed7-8a7c-447a-865e-1040f1a0183d#ci-7).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-7-hollandtopcampings.pantheonsite.io/)


随便打点字


tabs


Do you use `rufo` for formatting?


Don't put `em_` into filename, since we're not interested in implementation details in file name.


Error with PHP 7.2.10

> [ErrorException]
  Use of undefined constant LF - assumed 'LF' (this will throw an Error in a future version of PHP)


1 second


I don't know... it's the way Hinton introduces it in his Coursera class ... also reg. comment 1, I'm not totally sure I understand ... I'll switch to slack


三段反


We have same signal binding block above, please move them together and use same approach, e.g. `%w(...).each` for binding.


lol


好的。
张老师，请教一个关于mysql的问题
while (res!=NULL && (row = mysql_fetch_row(res)) != NULL) {
		jobs[i++] = atoi(row[0]);
	}
mysql_fetch_row每次取出结果集当前行后滑动到下一行，下次去就会取下一行了，那么滑动会影响结果集本身吗？
就是说如果结果中内容取完了后res会走到空吗？我想res本身应该是没有滑动才合适的吧