[R/create_mbd_params.R:23:16:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/create_mbd_params.R#L23) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (q < 0.0) {
               ^
```
[R/create_mbd_params.R:23:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/create_mbd_params.R#L23) *style:* **Trailing whitespace is superfluous.**
```r
  if (q < 0.0) {
                ^
```
[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_choosepar.R:23:67:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_choosepar.R#L23) *style:* **Trailing whitespace is superfluous.**
```r
  #This function provides a likelihood for a subset of parameters.
                                                                  ^
```
[R/mbd_loglik_choosepar.R:24:65:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_choosepar.R#L24) *style:* **Trailing whitespace is superfluous.**
```r
  # This is built to work inside mbd_minusLL_vs_single_parameter
                                                                ^
```
[R/mbd_loglik_choosepar.R:31:43:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_choosepar.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
  namepars <- c("lambda", "mu", "nu", "q")
                                          ^
```
[R/mbd_loglik_choosepar.R:63:79:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_choosepar.R#L63) *style:* **Trailing whitespace is superfluous.**
```r
    warning("There are parameter values used which cause numerical problems:",
                                                                              ^
```
[R/mbd_loglik_utils.R:5:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:8:29:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
  #it produces the structure
                            ^
```
[R/mbd_loglik_utils.R:9:44:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
  # q ^ (m - n) * (1 - q) ^ (k + 2 * n-m) *
                                           ^
```
[R/mbd_loglik_utils.R:14:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L31) *style:* **Variable or function name should be snake_case.**
```r
create_A0 <- function(
^~~~~~~~~
```
[R/mbd_loglik_utils.R:32:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
  max_number_of_species,
                        ^
```
[R/mbd_loglik_utils.R:33:10:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L33) *style:* **Trailing whitespace is superfluous.**
```r
  lambda,
         ^
```
[R/mbd_loglik_utils.R:34:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L34) *style:* **Trailing whitespace is superfluous.**
```r
  mu,
     ^
```
[R/mbd_loglik_utils.R:35:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L35) *style:* **Trailing whitespace is superfluous.**
```r
  q,
    ^
```
[R/mbd_loglik_utils.R:36:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L36) *style:* **Trailing whitespace is superfluous.**
```r
  k,
    ^
```
[R/mbd_loglik_utils.R:41:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:44:69:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L44) *style:* **Trailing whitespace is superfluous.**
```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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L54) *style:* **Variable or function name should be snake_case.**
```r
create_B0 <- function(
^~~~~~~~~
```
[R/mbd_loglik_utils.R:55:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L55) *style:* **Trailing whitespace is superfluous.**
```r
  max_number_of_species,
                        ^
```
[R/mbd_loglik_utils.R:56:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L56) *style:* **Trailing whitespace is superfluous.**
```r
  q,
    ^
```
[R/mbd_loglik_utils.R:57:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
  k,
    ^
```
[R/mbd_loglik_utils.R:58:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L58) *style:* **Trailing whitespace is superfluous.**
```r
  b,
    ^
```
[R/mbd_loglik_utils.R:71:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L71) *style:* **Variable or function name should be snake_case.**
```r
create_A <- function(
^~~~~~~~
```
[R/mbd_loglik_utils.R:72:10:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L72) *style:* **Trailing whitespace is superfluous.**
```r
  lambda,
         ^
```
[R/mbd_loglik_utils.R:73:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L73) *style:* **Trailing whitespace is superfluous.**
```r
  mu,
     ^
```
[R/mbd_loglik_utils.R:74:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L74) *style:* **Trailing whitespace is superfluous.**
```r
  nu,
     ^
```
[R/mbd_loglik_utils.R:75:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L75) *style:* **Trailing whitespace is superfluous.**
```r
  q,
    ^
```
[R/mbd_loglik_utils.R:76:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L76) *style:* **Trailing whitespace is superfluous.**
```r
  k,
    ^
```
[R/mbd_loglik_utils.R:83:55:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
  m[row(m) == col(m) + 1] <- m[row(m) == col(m) + 1] +
                                                      ^
```
[R/mbd_loglik_utils.R:87:67:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
  m[row(m) == col(m)] <- m[row(m) == col(m)] - lambda * (nvec + k)
                                                                  ^
```
[R/mbd_loglik_utils.R:97:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L97) *style:* **Variable or function name should be snake_case.**
```r
create_B <- function(
^~~~~~~~
```
[R/mbd_loglik_utils.R:98:10:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
  lambda,
         ^
```
[R/mbd_loglik_utils.R:99:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L99) *style:* **Trailing whitespace is superfluous.**
```r
  nu,
     ^
```
[R/mbd_loglik_utils.R:100:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
  q,
    ^
```
[R/mbd_loglik_utils.R:101:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L101) *style:* **Trailing whitespace is superfluous.**
```r
  k,
    ^
```
[R/mbd_loglik_utils.R:102:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L102) *style:* **Trailing whitespace is superfluous.**
```r
  b,
    ^
```
[R/mbd_loglik_utils.R:106:51:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L106) *style:* **Trailing whitespace is superfluous.**
```r
    max_number_of_species = max_number_of_species,
                                                  ^
```
[R/mbd_loglik_utils.R:107:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L107) *style:* **Trailing whitespace is superfluous.**
```r
    q = q,
          ^
```
[R/mbd_loglik_utils.R:108:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L108) *style:* **Trailing whitespace is superfluous.**
```r
    k = k,
          ^
```
[R/mbd_loglik_utils.R:111:49:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L111) *style:* **Trailing whitespace is superfluous.**
```r
  lambda * k * diag(max_number_of_species + 1) *
                                                ^
```
[R/mbd_loglik_utils.R:120:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L120) *style:* **Use <-, not =, for assignment.**
```r
create_A.no_mbd = function(
                ^
```
[R/mbd_loglik_utils.R:132:51:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L132) *style:* **Trailing whitespace is superfluous.**
```r
    max_number_of_species = max_number_of_species,
                                                  ^
```
[R/mbd_loglik_utils.R:135:64:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L135) *style:* **Trailing whitespace is superfluous.**
```r
  m[row(m) == col(m) + 1] <- m[row(m) == col(m) + 1] + lambda *
                                                               ^
```
[R/mbd_loglik_utils.R:137:47:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L137) *style:* **Trailing whitespace is superfluous.**
```r
  m[row(m) == col(m)] <- m[row(m) == col(m)] -
                                              ^
```
[R/mbd_loglik_utils.R:148:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L148) *style:* **Use <-, not =, for assignment.**
```r
create_B.no_mbd = function(
                ^
```
[R/mbd_loglik_utils.R:149:10:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L149) *style:* **Trailing whitespace is superfluous.**
```r
  lambda,
         ^
```
[R/mbd_loglik_utils.R:150:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L150) *style:* **Trailing whitespace is superfluous.**
```r
  nu,
     ^
```
[R/mbd_loglik_utils.R:151:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L151) *style:* **Trailing whitespace is superfluous.**
```r
  q,
    ^
```
[R/mbd_loglik_utils.R:152:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L152) *style:* **Trailing whitespace is superfluous.**
```r
  k,
    ^
```
[R/mbd_loglik_utils.R:153:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L153) *style:* **Trailing whitespace is superfluous.**
```r
  b,
    ^
```
[R/mbd_loglik_utils.R:154:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L154) *style:* **Trailing whitespace is superfluous.**
```r
  max_number_of_species,
                        ^
```
[R/mbd_loglik_utils.R:158:51:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L158) *style:* **Trailing whitespace is superfluous.**
```r
    max_number_of_species = max_number_of_species,
                                                  ^
```
[R/mbd_loglik_utils.R:161:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:161:54:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L161) *style:* **Trailing whitespace is superfluous.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) *
                                                     ^
```
[R/mbd_loglik_utils.R:172:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_utils.R:173:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L173) *style:* **Trailing whitespace is superfluous.**
```r
  Q,
    ^
```
[R/mbd_loglik_utils.R:174:21:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L174) *style:* **Trailing whitespace is superfluous.**
```r
  transition_matrix,
                    ^
```
[R/mbd_loglik_utils.R:175:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L175) *style:* **Trailing whitespace is superfluous.**
```r
  time_interval,
                ^
```
[R/mbd_loglik_utils.R:177:20:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L177) *style:* **Trailing whitespace is superfluous.**
```r
  a_abstol = 1e-16,
                   ^
```
[R/mbd_loglik_utils.R:178:20:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L178) *style:* **Trailing whitespace is superfluous.**
```r
  a_reltol = 1e-10,
                   ^
```
[R/mbd_loglik_utils.R:190:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:197:54:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L197) *style:* **Trailing whitespace is superfluous.**
```r
    while ((result.nan == 1 | result.negative == 1) &
                                                     ^
```
[R/mbd_loglik_utils.R:202:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L202) *style:* **Trailing whitespace is superfluous.**
```r
          v = Q,
                ^
```
[R/mbd_loglik_utils.R:203:33:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L203) *style:* **Trailing whitespace is superfluous.**
```r
          x = transition_matrix,
                                ^
```
[R/mbd_loglik_utils.R:204:29:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L204) *style:* **Trailing whitespace is superfluous.**
```r
          t = time_interval,
                            ^
```
[R/mbd_loglik_utils.R:206:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L206) *style:* **Trailing whitespace is superfluous.**
```r
        ),
          ^
```
[R/mbd_loglik_utils.R:210:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:235:13:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L235) *style:* **Trailing whitespace is superfluous.**
```r
      y = Q,
            ^
```
[R/mbd_loglik_utils.R:236:21:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L236) *style:* **Trailing whitespace is superfluous.**
```r
      times = times,
                    ^
```
[R/mbd_loglik_utils.R:237:29:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L237) *style:* **Trailing whitespace is superfluous.**
```r
      func = mbd_loglik_rhs,
                            ^
```
[R/mbd_loglik_utils.R:238:26:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L238) *style:* **Trailing whitespace is superfluous.**
```r
      parms = ode_matrix,
                         ^
```
[R/mbd_loglik_utils.R:239:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L239) *style:* **Trailing whitespace is superfluous.**
```r
      atol = a_abstol,
                      ^
```
[R/mbd_loglik_utils.R:240:26:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:240:30:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L240) *style:* **Trailing whitespace is superfluous.**
```r
      rtol = a_reltol)[2,-1],
                             ^
```
[R/mbd_loglik_utils.R:254:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L254) *style:* **Trailing whitespace is superfluous.**
```r
  t,
    ^
```
[R/mbd_loglik_utils.R:255:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L255) *style:* **Trailing whitespace is superfluous.**
```r
  x,
    ^
```
[R/mbd_loglik_utils.R:260:21:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L265) *style:* **Use <-, not =, for assignment.**
```r
    names(out) = names(x)
               ^
```
[R/mbd_loglik_utils.R:276:8:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L276) *style:* **Trailing whitespace is superfluous.**
```r
  pars,
       ^
```
[R/mbd_loglik_utils.R:277:8:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L277) *style:* **Trailing whitespace is superfluous.**
```r
  brts,
       ^
```
[R/mbd_loglik_utils.R:278:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L278) *style:* **Trailing whitespace is superfluous.**
```r
  lx,
     ^
```
[R/mbd_loglik_utils.R:279:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L279) *style:* **Trailing whitespace is superfluous.**
```r
  soc,
      ^
```
[R/mbd_loglik_utils.R:280:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L280) *style:* **Trailing whitespace is superfluous.**
```r
  methode,
          ^
```
[R/mbd_loglik_utils.R:281:18:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L281) *style:* **Trailing whitespace is superfluous.**
```r
  abstol = 1e-16,
                 ^
```
[R/mbd_loglik_utils.R:284:20:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L284) *style:* **Trailing whitespace is superfluous.**
```r
  lambda <- pars[1]
                   ^
```
[R/mbd_loglik_utils.R:285:4:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L285) *style:* **Commented code should be removed.**
```r
  #mu <- pars[2]
   ^~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:285:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L285) *style:* **Trailing whitespace is superfluous.**
```r
  #mu <- pars[2]
                ^
```
[R/mbd_loglik_utils.R:289:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L291) *style:* **Variable or function name should be snake_case.**
```r
  T0 <- create_A(
  ^~
```
[R/mbd_loglik_utils.R:292:21:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L292) *style:* **Trailing whitespace is superfluous.**
```r
    lambda = lambda,
                    ^
```
[R/mbd_loglik_utils.R:293:12:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L293) *style:* **Trailing whitespace is superfluous.**
```r
    mu = 0,
           ^
```
[R/mbd_loglik_utils.R:294:13:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L294) *style:* **Trailing whitespace is superfluous.**
```r
    nu = nu,
            ^
```
[R/mbd_loglik_utils.R:295:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
    q = q,
          ^
```
[R/mbd_loglik_utils.R:299:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L299) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- A_operator(
  ^~
```
[R/mbd_loglik_utils.R:300:12:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L300) *style:* **Trailing whitespace is superfluous.**
```r
    Q = Qi,
           ^
```
[R/mbd_loglik_utils.R:301:28:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L301) *style:* **Trailing whitespace is superfluous.**
```r
    transition_matrix = T0,
                           ^
```
[R/mbd_loglik_utils.R:303:22:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L303) *style:* **Trailing whitespace is superfluous.**
```r
    precision = 250L,
                     ^
```
[R/mbd_loglik_utils.R:304:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L304) *style:* **Trailing whitespace is superfluous.**
```r
    methode = methode,
                      ^
```
[R/mbd_loglik_utils.R:305:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L305) *style:* **Trailing whitespace is superfluous.**
```r
    a_abstol = abstol,
                      ^
```
[R/mbd_loglik_utils.R:308:45:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:333:36:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L333) *style:* **Trailing whitespace is superfluous.**
```r
  Qi <- rep(0, lx + 1);  Qi[3] <- 1
                                   ^
```
[R/mbd_loglik_utils.R:335:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:341:12:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L341) *style:* **Trailing whitespace is superfluous.**
```r
    Q = Qi,
           ^
```
[R/mbd_loglik_utils.R:342:28:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L342) *style:* **Trailing whitespace is superfluous.**
```r
    transition_matrix = TM,
                           ^
```
[R/mbd_loglik_utils.R:344:22:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L344) *style:* **Trailing whitespace is superfluous.**
```r
    precision = 250L,
                     ^
```
[R/mbd_loglik_utils.R:345:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L345) *style:* **Trailing whitespace is superfluous.**
```r
    methode = methode,
                      ^
```
[R/mbd_loglik_utils.R:346:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L346) *style:* **Trailing whitespace is superfluous.**
```r
    a_abstol = abstol,
                      ^
```
[R/mbd_loglik_utils.R:351:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L351) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:352:46:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L352) *style:* **Trailing whitespace is superfluous.**
```r
  #these are the components I want to exclude
                                             ^
```
[R/mbd_loglik_utils.R:354:29:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L354) *style:* **Trailing whitespace is superfluous.**
```r
  tips_components <- 1 + 0:1
                            ^
```
[R/mbd_loglik_utils.R:364:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:386:12:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L386) *style:* **Trailing whitespace is superfluous.**
```r
    Q = Qi,
           ^
```
[R/mbd_loglik_utils.R:387:28:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L387) *style:* **Trailing whitespace is superfluous.**
```r
    transition_matrix = TM,
                           ^
```
[R/mbd_loglik_utils.R:389:22:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L389) *style:* **Trailing whitespace is superfluous.**
```r
    precision = 250L,
                     ^
```
[R/mbd_loglik_utils.R:390:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L390) *style:* **Trailing whitespace is superfluous.**
```r
    methode = methode,
                      ^
```
[R/mbd_loglik_utils.R:391:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L391) *style:* **Trailing whitespace is superfluous.**
```r
    a_abstol = abstol,
                      ^
```
[R/mbd_loglik_utils.R:395:54:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:398:67:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L398) *style:* **Trailing whitespace is superfluous.**
```r
  tips_components <- 1 + c(missingspecies_min, missingspecies_max)
                                                                  ^
```
[R/mbd_loglik_utils.R:408:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L414) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:420:16:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L420) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (mu != 0) {
               ^
```
[R/mbd_loglik_utils.R:420:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L420) *style:* **Trailing whitespace is superfluous.**
```r
  if (mu != 0) {
                ^
```
[R/mbd_loglik_utils.R:421:9:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L430) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_A(
  ^~
```
[R/mbd_loglik_utils.R:431:21:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L431) *style:* **Trailing whitespace is superfluous.**
```r
    lambda = lambda,
                    ^
```
[R/mbd_loglik_utils.R:432:13:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L432) *style:* **Trailing whitespace is superfluous.**
```r
    mu = mu,
            ^
```
[R/mbd_loglik_utils.R:433:13:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L433) *style:* **Trailing whitespace is superfluous.**
```r
    nu = nu,
            ^
```
[R/mbd_loglik_utils.R:434:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L434) *style:* **Trailing whitespace is superfluous.**
```r
    q = q,
          ^
```
[R/mbd_loglik_utils.R:439:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:440:12:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L440) *style:* **Trailing whitespace is superfluous.**
```r
    Q = Qi,
           ^
```
[R/mbd_loglik_utils.R:441:28:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L441) *style:* **Trailing whitespace is superfluous.**
```r
    transition_matrix = TM,
                           ^
```
[R/mbd_loglik_utils.R:443:22:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L443) *style:* **Trailing whitespace is superfluous.**
```r
    precision = 250L,
                     ^
```
[R/mbd_loglik_utils.R:444:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L444) *style:* **Trailing whitespace is superfluous.**
```r
    methode = methode,
                      ^
```
[R/mbd_loglik_utils.R:445:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L445) *style:* **Trailing whitespace is superfluous.**
```r
    a_abstol = abstol,
                      ^
```
[R/mbd_loglik_utils.R:450:54:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:453:67:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L453) *style:* **Trailing whitespace is superfluous.**
```r
  tips_components <- 1 + c(missingspecies_min, missingspecies_max)
                                                                  ^
```
[R/mbd_loglik_utils.R:454:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L476) *style:* **Put spaces around all infix operators.**
```r
  step1 <- floor(interval_width/a)
                              ~^~
```
[R/mbd_loglik_utils.R:479:8:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L479) *style:* **Trailing whitespace is superfluous.**
```r
    NA,
       ^
```
[R/mbd_loglik_utils.R:481:4:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L481) *style:* **Trailing whitespace is superfluous.**
```r
  )
   ^
```
[R/mbd_loglik_utils.R:483:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:512:8:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L512) *style:* **Trailing whitespace is superfluous.**
```r
    NA,
       ^
```
[R/mbd_loglik_utils.R:516:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:530:29:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L530) *style:* **Trailing whitespace is superfluous.**
```r
        right.lx_coord2 <- j
                            ^
```
[R/mbd_loglik_utils.R:531:38:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L531) *style:* **Trailing whitespace is superfluous.**
```r
        lx <- lxvec2[right.lx_coord2]
                                     ^
```
[R/mbd_loglik_utils.R:536:3:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:613:54:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L613) *style:* **Trailing whitespace is superfluous.**
```r
  # alpha is the proportionality factor between max_k
                                                     ^
```
[R/mbd_loglik_utils.R:619:14:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:625:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L625) *style:* **Lines should not be more than 80 characters.**
```r
    tips_components <- (1 + min_tips):(1 + min(max_tips, max_number_of_species))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:625:81:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L625) *style:* **Trailing whitespace is superfluous.**
```r
    tips_components <- (1 + min_tips):(1 + min(max_tips, max_number_of_species))
                                                                                ^
```
[R/mbd_loglik_utils.R:627:66:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L627) *style:* **Trailing whitespace is superfluous.**
```r
      # I am already considering the starting species to survive.
                                                                 ^
```
[R/mbd_loglik_utils.R:632:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:634:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L634) *style:* **Trailing whitespace is superfluous.**
```r
      lambda = lambda,
                      ^
```
[R/mbd_loglik_utils.R:635:15:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L635) *style:* **Trailing whitespace is superfluous.**
```r
      mu = mu,
              ^
```
[R/mbd_loglik_utils.R:636:15:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L636) *style:* **Trailing whitespace is superfluous.**
```r
      nu = nu,
              ^
```
[R/mbd_loglik_utils.R:637:13:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L637) *style:* **Trailing whitespace is superfluous.**
```r
      q = q,
            ^
```
[R/mbd_loglik_utils.R:641:5:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:642:14:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L642) *style:* **Trailing whitespace is superfluous.**
```r
      Q = Qi,
             ^
```
[R/mbd_loglik_utils.R:643:37:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L643) *style:* **Trailing whitespace is superfluous.**
```r
      transition_matrix = mk_n_zero,
                                    ^
```
[R/mbd_loglik_utils.R:645:23:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L645) *style:* **Trailing whitespace is superfluous.**
```r
      precision = 50L,
                      ^
```
[R/mbd_loglik_utils.R:646:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L646) *style:* **Trailing whitespace is superfluous.**
```r
      methode = methode,
                        ^
```
[R/mbd_loglik_utils.R:647:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L647) *style:* **Trailing whitespace is superfluous.**
```r
      a_abstol = abstol,
                        ^
```
[R/mbd_loglik_utils.R:651:46:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L651) *style:* **Trailing whitespace is superfluous.**
```r
      # it removes some small negative values
                                             ^
```
[R/mbd_loglik_utils.R:653:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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:654:6:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L654) *style:* **Trailing whitespace is superfluous.**
```r
    }
     ^
```
[R/mbd_loglik_utils.R:658:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:659:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L659) *style:* **Trailing whitespace is superfluous.**
```r
        lambda = lambda,
                        ^
```
[R/mbd_loglik_utils.R:660:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L660) *style:* **Trailing whitespace is superfluous.**
```r
        mu = mu,
                ^
```
[R/mbd_loglik_utils.R:661:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L661) *style:* **Trailing whitespace is superfluous.**
```r
        nu = nu,
                ^
```
[R/mbd_loglik_utils.R:662:15:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L662) *style:* **Trailing whitespace is superfluous.**
```r
        q = q,
              ^
```
[R/mbd_loglik_utils.R:663:17:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L663) *style:* **Trailing whitespace is superfluous.**
```r
        k = soc,
                ^
```
[R/mbd_loglik_utils.R:664:55:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L664) *style:* **Trailing whitespace is superfluous.**
```r
        max_number_of_species = max_number_of_species,
                                                      ^
```
[R/mbd_loglik_utils.R:667:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:668:16:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L668) *style:* **Trailing whitespace is superfluous.**
```r
        Q = Qi,
               ^
```
[R/mbd_loglik_utils.R:669:46:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L669) *style:* **Trailing whitespace is superfluous.**
```r
        transition_matrix = mk_n_zero.no_mbd,
                                             ^
```
[R/mbd_loglik_utils.R:670:36:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L670) *style:* **Trailing whitespace is superfluous.**
```r
        time_interval = total_time,
                                   ^
```
[R/mbd_loglik_utils.R:671:25:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L671) *style:* **Trailing whitespace is superfluous.**
```r
        precision = 50L,
                        ^
```
[R/mbd_loglik_utils.R:672:27:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L672) *style:* **Trailing whitespace is superfluous.**
```r
        methode = methode,
                          ^
```
[R/mbd_loglik_utils.R:673:27:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L673) *style:* **Trailing whitespace is superfluous.**
```r
        a_abstol = abstol,
                          ^
```
[R/mbd_loglik_utils.R:676:7:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L752) *style:* **Commented code should be removed.**
```r
    # print(alpha)
      ^~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:771:21:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L771) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (count >= 100) {
                    ^
```
[R/mbd_loglik_utils.R:771:22:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L771) *style:* **Trailing whitespace is superfluous.**
```r
  if (count >= 100) {
                     ^
```
[R/mbd_loglik_utils.R:780:1:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik_utils.R#L781) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/mbd_loglik.R:3:65:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L3) *style:* **Trailing whitespace is superfluous.**
```r
#' @description mbd_loglik provides the likelihood for a process
                                                                ^
```
[R/mbd_loglik.R:4:72:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#'   in which multiple births (from different parents) at the same time
                                                                       ^
```
[R/mbd_loglik.R:15:54:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
#' @return The function returns the natural logarithm
                                                     ^
```
[R/mbd_loglik.R:59:31:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L59) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (print_errors == TRUE) {
                              ^
```
[R/mbd_loglik.R:59:32:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
    if (print_errors == TRUE) {
                               ^
```
[R/mbd_loglik.R:64:31:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L64) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (print_errors == TRUE) {
                              ^
```
[R/mbd_loglik.R:64:32:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L64) *style:* **Trailing whitespace is superfluous.**
```r
    if (print_errors == TRUE) {
                               ^
```
[R/mbd_loglik.R:69:31:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L69) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (print_errors == TRUE) {
                              ^
```
[R/mbd_loglik.R:69:32:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L69) *style:* **Trailing whitespace is superfluous.**
```r
    if (print_errors == TRUE) {
                               ^
```
[R/mbd_loglik.R:79:15:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:79:62:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L79) *style:* **Trailing whitespace is superfluous.**
```r
    loglik <- pmb_loglik(pars = pars, brts = brts, soc = soc)
                                                             ^
```
[R/mbd_loglik.R:84:13:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:107:60:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L107) *style:* **Trailing whitespace is superfluous.**
```r
    # alpha is the proportionality factor between max_k and
                                                           ^
```
[R/mbd_loglik.R:110:11:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/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:110:50:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L110) *style:* **Trailing whitespace is superfluous.**
```r
    lx <- max_number_of_species <- alpha * max_k;
                                                 ^
```
[R/mbd_loglik.R:130:58:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L130) *style:* **Trailing whitespace is superfluous.**
```r
      # alpha is the proportionality factor between max_k
                                                         ^
```
[R/mbd_loglik.R:132:52:](https://github.com/Giappo/mbd/blob/37f148497cbce23bff9306eacd9bca2945875b0d/R/mbd_loglik.R#L132) *style:* **Trailing whitespace is superfluous.**
```r
      lx <- max_number_of_species <- alpha * max_k;


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

* https://cafe.ethtective.com


think you can amend the commit message to 'add white space to config' :0