Nope, there still seems to be some bugs


Note, you did use quite an old version of airline. There have been many enhancements made since then, also performance improvements.


On ne laisse pas trainer de commentaires


fix


[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/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/0fb363240e380150eef5c44489492949a6e5adb2/R/mbd_loglik.R#L134) *style:* **Commented code should be removed.**
```r
      # nvec <- 0:lx


not sure what you're talking about. Isn't it at least related to this PR, is it? Please comment to the appropriate person at appropriate revision.


@adr-odoo that one is green on runbot


dang i was too slow


Thanks, fixed in https://github.com/nih-at/libzip/commit/0adef8f5a2e6934aa33bcc8517fd273d5f953e7f.


Successfully aliased the URL <https://micro-readweb-vxrforcdzv.now.sh> to the following alias.

* https://readweb.wezeit.co


Fantastic project. I'm looking at 20180314_175112.jpg and the wiring doesn't seem to match the connection information. Has the wiring been updated?


production.ERROR: Class 'Eventy' not found (View: /home/freescout/public_html/resources/views/layouts/app.blade.php)

Seems Eventy is not declared as facade in config.


You guys need to sleep and get off Github.