[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_choosepar.R:31:15:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_loglik_choosepar.R#L31) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
  namepars <- get_mbd_param_names()
              ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:5:1:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_loglik_utils.R#L5) *style:* **Variable or function name should be snake_case.**
```r
hyperA_HannoX <- function(n_species, k, q) {
^~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:14:3:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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:93:15:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L93) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
  namepars <- get_mbd_param_names()
              ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:99:3:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L194) *style:* **Variable or function name should be snake_case.**
```r
  MLtrpars <- as.numeric(unlist(out$par))
  ^~~~~~~~
```
[R/mbd_ml.R:197:5:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L197) *style:* **Variable or function name should be snake_case.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
    ^~~~~~
```
[R/mbd_ml.R:197:12:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L197) *style:* **Use <-, not =, for assignment.**
```r
    MLpars = MLtrpars / (1 - MLtrpars)
           ^
```
[R/mbd_ml.R:199:5:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L199) *style:* **Variable or function name should be snake_case.**
```r
    MLpars <- MLtrpars
    ^~~~~~
```
[R/mbd_ml.R:201:3:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L201) *style:* **Variable or function name should be snake_case.**
```r
  MLpars1 <- rep(0, n_pars); names(MLpars1) <- namepars
  ^~~~~~~
```
[R/mbd_ml.R:203:31:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L203) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                              ^
```
[R/mbd_ml.R:203:61:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L203) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(idparsfix) != 0) {MLpars1[idparsfix] <- parsfix}
                                                            ^
```
[R/mbd_ml.R:204:3:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_ml.R#L204) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_ml.R:205:1:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_pure_multiple_birth.R#L139) *style:* **Commented code should be removed.**
```r
  # cond <- 0
    ^~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:140:15:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_pure_multiple_birth.R#L140) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
  namepars <- get_mbd_param_names()
              ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:145:1:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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:194:15:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_pure_multiple_birth.R#L194) *warning:* **no visible global function definition for ‘get_mbd_param_names’**
```r
  namepars <- get_mbd_param_names()
              ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:195:1:](https://github.com/Giappo/mbd/blob/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/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/55078f8935d9b12741a0fcce5f50718999f50028/R/mbd_pure_multiple_birth.R#L236) *style:* **Lines should not be more than 80 characters.**
```r
                                               idparsfix = idparsfix, brts = brts, soc = soc,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


@Vizvezdenec Sorry,  I did not recognize this


      <img class="team-block__image" src="<?php echo get_template_directory_uri(); ?>/public/images/team/board-member-4.jpg">

Latifa Akay

Advisor

Latifa is currently exploring culturally and socially relevant teaching pedagogies and curriculum in her role as Director of Education at the charity Maslaha. She focused on Islamic feminisms and international law in her LLM at SOAS, and previously worked as a journalist in Istanbul.


см CargoTrain


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

* https://cafe.ethtective.com


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

* https://cafe.ethtective.com


nice work


Added config.yml


아아니 근데 이분 마스터에 직접?


드디어 귀찮음이 하늘을 뚫은건가!


welcome to me in 100dayofcode


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

* https://cafe.ethtective.com


Thanks!


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

* https://cafe.ethtective.com


Thanks! I've just seen that this error is also present in the CalculatorPRO. I'll change the code immediately!


排序所需


As it is it does nothing. But if(0) can be linked e.g. to highlight_reconstruction to use the checkbox to try this out. Someone had the wish to change saturation in dependency to luminance. So this was the try to desaturate shadows and highlights... but was not too good.


'FSCロゴ'に流れ込むテキストは「ある」「なし」
'FSCロゴ画像'に流れ込むテキストは「画像素材のID」


kernel: busy timeout[0], (60s), kextd wait(0): 'X86PlatformPlugin', 'IOHDACodecFunction', 'BCM20702A0', 'ETPD', 'IOResources'

boots but touchpad doesn’t work:

2018-02-28 19:13:23.265834+0000 0x3e6 Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerNub::pci8086,a160 SSCN not implemented in ACPI tables
2018-02-28 19:13:23.268749+0000 0x3de Default 0x0 0 kernel: (VoodooGPIO) VoodooGPIOSunrisePointH::VoodooGPIO Initializing Community 0
2018-02-28 19:13:23.269130+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a161 Probing controller
2018-02-28 19:13:23.269203+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a161 Found valid Synopsys component, continuing with initialisation
2018-02-28 19:13:23.269228+0000 0x3de Default 0x0 0 kernel: (VoodooGPIO) VoodooGPIOSunrisePointH::VoodooGPIO Initializing Community 1
2018-02-28 19:13:23.269433+0000 0x3de Default 0x0 0 kernel: (VoodooGPIO) VoodooGPIOSunrisePointH::VoodooGPIO Initializing Community 2
2018-02-28 19:13:23.269767+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a161 Got bus configuration values
2018-02-28 19:13:23.277532+0000 0x117 Default 0x0 0 kernel: (VoodooGPIO) VoodooGPIOSunrisePointH::GPIO Controller is already awake! Not reinitializing.
2018-02-28 19:13:23.277706+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a161 Publishing device nubs
2018-02-28 19:13:23.280621+0000 0x3d7 Default 0x0 0 kernel: (BrcmPatchRAM2) BrcmPatchRAM2: Published new IOKit personality for BrcmFirmwareStore.
2018-02-28 19:13:23.281078+0000 0x3ce Default 0x0 0 kernel: (VoodooI2CServices) class: IOPCIDevice
2018-02-28 19:13:23.284624+0000 0x3e6 Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerNub::pci8086,a160 FMCN not implemented in ACPI tables
2018-02-28 19:13:23.284632+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a161 Found I2C device: ELAN1200
2018-02-28 19:13:23.284871+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::ETPD Could not find GPIO controller, exiting
2018-02-28 19:13:23.284875+0000 0x3ff Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a161 Could not initialise nub for ELAN1200
2018-02-28 19:13:23.285056+0000 0x3e6 Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a160 Warning: Error getting bus config, using defaults where necessary
2018-02-28 19:13:23.285110+0000 0x3ff Default 0x0 0 kernel: (VoodooI2CServices) class: VoodooI2CControllerNub
2018-02-28 19:13:23.285617+0000 0x418 Default 0x0 0 kernel: (VoodooI2CServices) class: VoodooI2CControllerDriver
2018-02-28 19:13:23.286141+0000 0x3e6 Default 0x0 0 kernel: (VoodooI2C) VoodooI2CControllerDriver::pci8086,a160 Publishing device nubs
2018-02-28 19:13:23.286270+0000 0x419 Default 0x0 0 kernel: (VoodooI2CServices) class: VoodooI2CControllerDriver
2018-02-28 19:13:23.293037+0000 0x3ce Default 0x0 0 kernel: (VoodooI2CServices) class: IOPCIDevice
2018-02-28 19:13:23.293061+0000 0x3e6 Default 0x0 0 kernel: (VoodooI2CServices) class: VoodooI2CControllerNub
2018-02-28 19:13:23.293206+0000 0x3ce Default 0x0 0 kernel: (VoodooI2CServices) class: VoodooI2CPCIController
2018-02-28 19:13:23.293402+0000 0x3ce Default 0x0 0 kernel: (VoodooI2CServices) class: VoodooI2CPCIController


![](https://github.trello.services/images/mini-trello-icon.png) [Add 'AssertIsDisplayed' method to element classes](https://trello.com/c/UWzqCbR4/30-add-assertisdisplayed-method-to-element-classes)


hhhhhheeellllllllloo


The problem here is that `nixos-manual.nix` now requires that you *only* evaluate via `config.system.build` and any other way will potentially trigger an evaluation error, for example (eg. when on 563d5b1c87d7e4ca996c00a4df5b734ccd985095):

```
nix-instantiate nixos --arg configuration '{ services.nixosManual.enable = false; services.nixosManual.showManual = true; }' -A config.system.build.etc
```

... and really anything that triggers unboxing `config.systemd.services.nixos-manual`.

> In any case, I think the change to `nixos/modules/profiles/installation-device.nix` here is superfluous

It is not, because it defaults to `false` for the tests:

https://github.com/NixOS/nixpkgs/blob/e0f46105aa30c4814899f16449859ed89578ecc0/nixos/lib/build-vms.nix#L31

While setting it to `true` in the `installation-device` profile is a no-op for eg. building an ISO image it doesn't hurt to set it to `false` here instead of adding another special case in say `test-instrumentation.nix` and giving a comment referring to `installation-device.nix`.


how are you


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

* https://cafe.ethtective.com


OK, I think I see your point, there will be only one ticket forwarded from the Roundcube (HTTP/[...]).. so actually the mail server probably needs to be configured to expect HTTP/[...] on the SMTP port... I have just started to configure this and did not get so far yet.


CrackingTheCodingInterview/Chapter - 4 Trees & Graphs/Problem_4_4_Check_Balanced.java

You are doing a lot of computation here. Just suppose a tree with 1000 Plus nodes and Intermediate level nodes' height will be calculated for many times. Try to use memoization with recursion, instead of core recursion.


The test OXP has a mistake. It sets gloss to 6. Maybe it was meant as 0.6, but in any case this is what triggers the shader error, because the function that synthesizes the specular part of the shader exits early, before havinga a chance to set OOSTD_SPECULAR to 1. Still, this should not happen. There should be guards for clamping the gloss value to [0.0 … 1.0] and that is taken care of with the subsequent commit. Thanks for bringing this to my attention.

In any case, I think that keeping this fix as it stands now is OK.


Is there no bulky storage usage with apk? (rm -rf /var/lib/apt/lists/*)


得到


Awesome!


could see output using cam


Hey @brentleyjones. I'm updating to xcodeproj 6 and I have a question. These header files in the `xpc-target` don't seem to be added to any build phase. For example this `XPC_Service.h` build file is not referenced anywhere.
From the code headers are only added if `target.type == .framework || target.type == .dynamicLibrary`.
Is this correct, or should there be a special case for xpc service targets? I'm unfamiliar with the type, so don't know


interesting Аpple approves this driver, it is necessary to ask


hello world


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

* https://cafe.ethtective.com


I've been made the changes to make it **mobile friendly**


@panwarnaveen9 I think current codebase is using PyTorch 0.3.1
I can see instances of Variable peppered around.


**不会跑路，请放心使用** ==> 🐂牛逼！


GITHUB


The issue is that `xcodeproj` loops through all the build phases and their build files to generate the UUID's. As these aren't referenced anywhere they still have a temporary UUID.
Tagging @pepibumur as well


@ZakMan228 Вот тут у тебя уже str не работает


Are you referring to the board having 28 pins where the chip is only 14 pin?


I'm curious, how did you discover this root cause?


Error


Here's the file after generation with `xcodeproj` 6 https://github.com/yonaskolb/XcodeGen/blob/84f1c656323ed3cf3830ff46a1eee66fdffa7552/Tests/Fixtures/TestProject/Project.xcodeproj/project.pbxproj#L98


@ZakMan228 Дробная часть это как раз с 0. в начале, можно было её не обрезать


@Fronun А че ты там модифицируешь такое


👍 缓存键的确应当是使用小写命名，`:`分隔命名空间，`_`连接单词的


Hi @mrbell321

This backend has no special ties to linux yet, but it is the main target for future development. You can try producing  bare metal ELFs using similar invocations to https://github.com/m4yers/llvm-dev-scripts/blob/master/scripts/sample-to-sim.sh. There i link against newlib and use sim.ld linker script to produce a bare simulator executable.


fixed,thanks


Why?


was pushst du denn da für’n quatsch?


@Giappo: please use the `develop` branch. @Neves-P will help you with that.


@ZakMan228 У тебя последняя формула работает и про числах у которых целая часть 0, так что не нужно было этих двух случаев


BE PATIENT. BE CONFIDENT.


Deposit requierd credit ok


final


*new contributor .


Что за говнокод? Почему нет модельки под все это? Это же просто звездец.


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

* https://paul.kinlan.me


lapply, thx!


This is our program


Why not "country_code in SNAILMAIL_COUNTRIES" ?


line 29, in <module>
    an = msg[-1].text
IndexError: list index out of range


Bitte Update-Script 1.2.5 nachziehen


dfgshghgfjhuhgj


Ticketing Application based on JavaFX For PHILHEALTH