[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/R/mbd_loglik.R#L132) *style:* **Trailing whitespace is superfluous.**
```r
      lx <- max_number_of_species <- alpha * max_k;
                                                   ^
```
[R/mbd_loglik.R:133:9:](https://github.com/Giappo/mbd/blob/e1fde40d254495c620b882cefab5d091fe101ea9/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/e1fde40d254495c620b882cefab5d091fe101ea9/R/mbd_loglik.R#L134) *style:* **Commented code should be removed.**
```r
      # nvec <- 0:lx


update


@maziminke
the issue 1 can not be from this commit. Have a look at the code. The commit just adds input a filter to `trim()` the value.

I initiated the fix due to a similar issue I faced. To be really sure what you have there I suggest you check the Database. Or try to replace the url by something else and then overwrite it by the original.


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

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

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

### Deployments updated

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

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


Btw - I've provided a potential solution for this FIXME, which should settle it for now (and not affecting the case where only one is assigned).


Make sure to run:
```
php artisan clear-compiled
php artisan cache:clear
```


in EditSlides.js :

* functiun select slide is ok, but you can do it in 1 line :
function selectSlide() {
    goToSlide(parseInt(selectorsSlide.value, 10));
}

* same thing to selectOptionSelector functiun and without argument:
function selectOptionInSelector() {
    selectorSlide.selectedIndex = numCurrentSlide;
}

* function goToSlide is perfect

* function updateSlideselector 💯 :
I tried to improved the code, because for each new slide you remove and add all the html, but
that looks hard, so we can just maybe upgrade that later

Parameter (num) isn't use in your function

* functiun addImage :

this two lines
  let src = inTxt.value;
  image.src = src;
can be only one :
 image.src = inTxt.value;

I tkink this line : image.onclick = scaleImage;
do nothing actually (maybe usefull later but we don't have yet scaleImage function)

Very nice job Suzanna 🥇


Awesome @JayBazuzi. About the commit messages, do you think they're understandable enough?


@ZakMan228 Хороший метод:) А как это решить используя числа? И т.к. ты уже знаешь циклы подумай как это решить с любым целым числом


Then : maybe don't test upload max file size in zipbomb ? See https://www.limesurvey.org/forum/installation-a-update-issues/116503-abort-pclzip-lib-php-error-during-comfort-update

zip bomb must test only if it's a zip bomb, no ?


![screen shot 2018-09-26 at 2 56 43 pm](https://user-images.githubusercontent.com/32328857/46071000-bb864d00-c19c-11e8-96c6-61f0279d571d.png)


@ZakMan228 Не надо называть переменные как встроенные функции, т.к. теперь у тебя в программе больше нет функции str, теперь у тебя есть только переменная str. Вот попробуй дальше в коде что-то преобразовать в строку и посмотри, что у тебя получится


Hey! Indeterminations such as 0 / 0 should be controlled by the calculator


Yeah, bug exists as predicted. The cause for it is in fact the RED FLAG comment down in checkForAllDiagonals.js file


What about `txt` as the alias for `plaintext`


I know your meaning here, but still it looks a bit weird.
+1 to keep the placeholder service child resource of route.


Remove that statement..


My first Commit


Mixed up numbers and bits. Should be: "`f16` numbers" ... "`u16` bits" instead.


Well it's fixed now so lol


Is this how the current signature behaves?


I'd write this as:
```cpp
 if (auto host = get_if<std::string>(&cfg, "database.host")) {
   std::cout << "connect to database host " << *host << std::endl;
   // ...
 } else {
   std::cerr << "database host missing" << std::endl;
   // ...
 }
```


Do we still need this, post the introduction of ``buildPages`` method?


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @datapythonista was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


I think that the 'g' is for gigabytes in the Java command line....I'm not sure if this is now coming in the %memory variable.


For completeness, you could mention `get`, even though it's not as nice as `get_or` and `get_if`.


@pb00068 it will not since it's tested against this PR :)


d


a


This is actually not so different from `process.nextTick()` in Node.js, and is not uncommon to do if you need the frame to render first. If you'd like you can read up on what's going behind the scenes here: https://nodejs.org/en/docs/guides/event-loop-timers-and-nexttick/#setimmediate-vs-settimeout


This is not new, why is this here ?


This doesn't contain any test related with index, where are they ? Documentation needs also to be prepare for this.


> Dear @artulloss:
> I regret to inform you that the release you submitted, named "**VPNBlock**" (v1.3.1), for the project [VPNBlock](https://poggit.pmmp.io/ci/artulloss/VPNBlocker/VPNBlock) on 2018-09-26T09:35:49.000Z, has been rejected.

Multi line messages
https://github.com/artulloss/VPNBlocker/blob/130ef0d018c9d4f87df5bcb7b90edab4bfc76bb2/VPNBlock/src/VPNBlock/VPNBlock.php#L40-L42
please condense it into one line

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


![](https://github.trello.services/images/mini-trello-icon.png) [Открытие ссылок в другом окне](https://trello.com/c/bjLo6Z8E/125-%D0%BE%D1%82%D0%BA%D1%80%D1%8B%D1%82%D0%B8%D0%B5-%D1%81%D1%81%D1%8B%D0%BB%D0%BE%D0%BA-%D0%B2-%D0%B4%D1%80%D1%83%D0%B3%D0%BE%D0%BC-%D0%BE%D0%BA%D0%BD%D0%B5)


Commit end


function startGame() {
    myGamePiece = new component(30, 30, "red", 10, 120);
    myGamePiece.gravity = 0.05;
    myScore = new component("30px", "Consolas", "black", 280, 40, "text");
    myGameArea.start();
}

var myGameArea = {
    canvas : document.createElement("canvas"),
    start : function() {
        this.canvas.width = 480;
        this.canvas.height = 270;
        this.context = this.canvas.getContext("2d");
        document.body.insertBefore(this.canvas, document.body.childNodes[0]);
        this.frameNo = 0;
    },
    clear : function() {
        this.context.clearRect(0, 0, this.canvas.width, this.canvas.height);
    }
}


ok


There's nothing wrong in doing this but it would be more natural if this was a function call. Events usually run before or after an action to allow other components to respond to it. It's not so common to have it trigger the actual action/work and it may therefore behave a bit differently than others would expect it to.


remove the incomplete user_name field from the userSchema


apply changes


It's necessary and conveniently already using `org.example.greeting`. 😉

Thanks for making it more consistent! 👍


@chrisbra Yeah, I just tried the latest master branch, I think the issue is still there.

Here is how I tried to reproduced the issue.

1. Enable airline
2. Start vim and open a few files in windows, tabs, view the current content of `:echo g:airline#themes#{g:airline_theme}#palette`
3. Close them one by one, and check `:echo g:airline#themes#{g:airline_theme}#palette`.

The content just kept growing monotonically.  Not sure whether this is the expected behavior but I am afraid it will degrade the performance gradually over a time span of editing.


ok I take it

Solange

On 26/09/2018 10:11, Ivars Karpics wrote:
>
> Hi @delageniere <https://github.com/delageniere> and @rhfogh
> <https://github.com/rhfogh>
>
> Here is a tiny typo which breaks the script. NULLL should be NULL
> I am fighting with my local fork and I am not able to prepare a PR.
> Could one of you fix this?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/ispyb/ISPyB/commit/c419c16cdf5d361e5ae8523e90ee97e06886bc63#commitcomment-30651881>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ALsNf-hHSs9VEM1P66X1yQq5wZQaTN-yks5uezbDgaJpZM4W6Hdj>.
>


This line should be: `*(*slot).msg.get() = Some(msg)`


the .pdg file


This line should be: `(*slot.msg.get()).take()`


This line should be: `drop((*slot.msg.get()).take())`


Fixed with `php artisan package:discover`