[R/default_params_doc.R:17:67:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
#' @param cond Set 1 if you want to condition on stem or crown age
                                                                  ^
```
[R/default_params_doc.R:21:70:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
#' @param idparsopt The ids of the parameters that must be optimized.
                                                                     ^
```
[R/default_params_doc.R:49:18:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L49) *style:* **Trailing whitespace is superfluous.**
```r
#' @param methode
                 ^
```
[R/default_params_doc.R:52:44:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
#'     \item \code{sexpm}: use \code{sexpm}
                                           ^
```
[R/default_params_doc.R:53:46:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L53) *style:* **Trailing whitespace is superfluous.**
```r
#'     \item \code{expo}: use \code{expoRkit}
                                             ^
```
[R/default_params_doc.R:57:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
#' @param missnumspec The number of species that are in the clade but missing in the phylogeny.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:90:28:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L90) *style:* **Trailing whitespace is superfluous.**
```r
#' @param results something
                           ^
```
[R/default_params_doc.R:109:62:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L109) *style:* **Trailing whitespace is superfluous.**
```r
#'   You can also define the tips_interval as you can usually
                                                             ^
```
[R/default_params_doc.R:126:47:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L126) *style:* **Trailing whitespace is superfluous.**
```r
#' @author Documentation by Giovanni Laudanno,
                                              ^
```
[R/default_params_doc.R:147:17:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L147) *style:* **Trailing whitespace is superfluous.**
```r
  function_name,
                ^
```
[R/default_params_doc.R:175:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L175) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:176:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L176) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_params_doc.R:182:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L182) *style:* **Variable or function name should be snake_case.**
```r
  pars.transform,
  ^~~~~~~~~~~~~~
```
[R/default_params_doc.R:186:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L186) *style:* **Trailing whitespace is superfluous.**
```r
  printit,
          ^
```
[R/default_params_doc.R:187:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L187) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/default_params_doc.R:190:13:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L190) *style:* **Trailing whitespace is superfluous.**
```r
  recursive,
            ^
```
[R/default_params_doc.R:193:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L193) *style:* **Trailing whitespace is superfluous.**
```r
  results,
          ^
```
[R/default_params_doc.R:214:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L214) *style:* **Variable or function name should be snake_case.**
```r
  x.name,
  ^~~~~~
```
[R/default_params_doc.R:215:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L215) *style:* **Variable or function name should be snake_case.**
```r
  x.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:217:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L217) *style:* **Variable or function name should be snake_case.**
```r
  y.name,
  ^~~~~~
```
[R/default_params_doc.R:218:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L218) *style:* **Variable or function name should be snake_case.**
```r
  y.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:220:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/default_params_doc.R#L220) *style:* **Variable or function name should be snake_case.**
```r
  z.name
  ^~~~~~
```
[R/mbd_loglik_choosepar.R:8:13:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
  trparsopt,
            ^
```
[R/mbd_loglik_choosepar.R:9:13:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
  trparsfix,
            ^
```
[R/mbd_loglik_choosepar.R:11:33:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L11) *style:* **Trailing whitespace is superfluous.**
```r
  idparsfix = (1:4)[-idparsopt],
                                ^
```
[R/mbd_loglik_choosepar.R:12:8:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
  brts,
       ^
```
[R/mbd_loglik_choosepar.R:13:12:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
  cond = 1,
           ^
```
[R/mbd_loglik_choosepar.R:15:29:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
  tips_interval = c(0, Inf),
                            ^
```
[R/mbd_loglik_choosepar.R:16:19:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L16) *style:* **Trailing whitespace is superfluous.**
```r
  missnumspec = 0,
                  ^
```
[R/mbd_loglik_choosepar.R:18:31:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
  minimum_multiple_births = 0,
                              ^
```
[R/mbd_loglik_choosepar.R:19:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  pars.transform = 0,
  ^~~~~~~~~~~~~~
```
[R/mbd_loglik_choosepar.R:19:22:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L19) *style:* **Trailing whitespace is superfluous.**
```r
  pars.transform = 0,
                     ^
```
[R/mbd_loglik_choosepar.R:20:20:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
  print_errors = 0,
                   ^
```
[R/mbd_loglik_choosepar.R:23:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
  #This function provides a likelihood for a subset of parameters. This is built to work inside mbd_minusLL_vs_single_parameter or any optimizer like simplex, optim or subplex
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_choosepar.R:28:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L28) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_choosepar.R:29:26:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L29) *style:* **Commas should always have a space after.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                         ^
```
[R/mbd_loglik_choosepar.R:29:31:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L29) *style:* **Commas should always have a space after.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                              ^
```
[R/mbd_loglik_choosepar.R:29:36:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L29) *style:* **Commas should always have a space after.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                                   ^
```
[R/mbd_loglik_choosepar.R:29:42:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                                         ^~~~~
```
[R/mbd_loglik_choosepar.R:30:52:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L30) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(trparsopt) == 4 && missing(trparsfix)){trparsfix <- NULL}
                                                   ^
```
[R/mbd_loglik_choosepar.R:30:70:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L30) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(trparsopt) == 4 && missing(trparsfix)){trparsfix <- NULL}
                                                                     ^
```
[R/mbd_loglik_choosepar.R:31:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L31) *style:* **Use <-, not =, for assignment.**
```r
  trpars1 = rep(0, Npars)
          ^
```
[R/mbd_loglik_choosepar.R:34:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L34) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_choosepar.R:37:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( min(trpars1[1:Npars]) < 0 ){loglik <- -Inf}else
      ^
```
[R/mbd_loglik_choosepar.R:37:33:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( min(trpars1[1:Npars]) < 0 ){loglik <- -Inf}else
                                ^
```
[R/mbd_loglik_choosepar.R:37:35:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if ( min(trpars1[1:Npars]) < 0 ){loglik <- -Inf}else
                                  ^
```
[R/mbd_loglik_choosepar.R:37:50:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if ( min(trpars1[1:Npars]) < 0 ){loglik <- -Inf}else
                                                 ^
```
[R/mbd_loglik_choosepar.R:38:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L38) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_choosepar.R:40:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L40) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_loglik_choosepar.R:42:13:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L42) *style:* **Use <-, not =, for assignment.**
```r
      pars1 = trpars1/(1 - trpars1)
            ^
```
[R/mbd_loglik_choosepar.R:42:22:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L42) *style:* **Put spaces around all infix operators.**
```r
      pars1 = trpars1/(1 - trpars1)
                    ~^~
```
[R/mbd_loglik_choosepar.R:42:23:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L42) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      pars1 = trpars1/(1 - trpars1)
                      ^
```
[R/mbd_loglik_choosepar.R:44:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L44) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_loglik_choosepar.R:48:20:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L48) *style:* **Trailing whitespace is superfluous.**
```r
      pars = pars1,
                   ^
```
[R/mbd_loglik_choosepar.R:49:19:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L49) *style:* **Trailing whitespace is superfluous.**
```r
      brts = brts,
                  ^
```
[R/mbd_loglik_choosepar.R:50:19:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
      cond = cond,
                  ^
```
[R/mbd_loglik_choosepar.R:52:37:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
      tips_interval = tips_interval,
                                    ^
```
[R/mbd_loglik_choosepar.R:54:57:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L54) *style:* **Trailing whitespace is superfluous.**
```r
      minimum_multiple_births = minimum_multiple_births,
                                                        ^
```
[R/mbd_loglik_choosepar.R:55:35:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L55) *style:* **Trailing whitespace is superfluous.**
```r
      print_errors = print_errors,
                                  ^
```
[R/mbd_loglik_choosepar.R:60:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L60) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_choosepar.R:61:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:",trpars1,"\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_choosepar.R:61:75:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L61) *style:* **Commas should always have a space after.**
```r
    cat("There are parameter values used which cause numerical problems:",trpars1,"\n")
                                                                          ^
```
[R/mbd_loglik_choosepar.R:61:83:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_choosepar.R#L61) *style:* **Commas should always have a space after.**
```r
    cat("There are parameter values used which cause numerical problems:",trpars1,"\n")
                                                                                ^
```
[R/mbd_loglik_utils.R:5:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:5:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L5) *style:* **Variable or function name should be snake_case.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
^~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:5:27:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L5) *style:* **Variable or function name should be snake_case.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
                          ^
```
[R/mbd_loglik_utils.R:5:36:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L5) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
                                   ^
```
[R/mbd_loglik_utils.R:7:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
  #it produces the structure q^(m-n)*(1-q)^(k+2*n-m)*sum_j 2^j choose(k,j)*choose(n,m-n-j)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:9:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  A1 <- (1-q)^(k) * choose(k, j) * (2)^j
  ^~
```
[R/mbd_loglik_utils.R:9:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L9) *style:* **Put spaces around all infix operators.**
```r
  A1 <- (1-q)^(k) * choose(k, j) * (2)^j
         ~^~
```
[R/mbd_loglik_utils.R:9:15:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  A1 <- (1-q)^(k) * choose(k, j) * (2)^j
              ^
```
[R/mbd_loglik_utils.R:10:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  N <- N + 1
  ^
```
[R/mbd_loglik_utils.R:11:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
  ^
```
[R/mbd_loglik_utils.R:11:24:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                      ~^~
```
[R/mbd_loglik_utils.R:11:26:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                        ~^~
```
[R/mbd_loglik_utils.R:11:34:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                                ~^~
```
[R/mbd_loglik_utils.R:11:36:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                                  ~^~
```
[R/mbd_loglik_utils.R:12:9:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L12) *style:* **Put spaces around all infix operators.**
```r
  A[1:(k+1),1] <- A1
       ~^~
```
[R/mbd_loglik_utils.R:12:13:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L12) *style:* **Commas should always have a space after.**
```r
  A[1:(k+1),1] <- A1
            ^
```
[R/mbd_loglik_utils.R:15:20:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L15) *style:* **Commas should always have a space after.**
```r
    s <- src:min(N,2*src+k-1)
                   ^
```
[R/mbd_loglik_utils.R:15:21:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L15) *style:* **Put spaces around all infix operators.**
```r
    s <- src:min(N,2*src+k-1)
                   ~^~
```
[R/mbd_loglik_utils.R:15:25:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L15) *style:* **Put spaces around all infix operators.**
```r
    s <- src:min(N,2*src+k-1)
                       ~^~
```
[R/mbd_loglik_utils.R:15:27:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L15) *style:* **Put spaces around all infix operators.**
```r
    s <- src:min(N,2*src+k-1)
                         ~^~
```
[R/mbd_loglik_utils.R:16:8:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L16) *style:* **Put spaces around all infix operators.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
      ~^~
```
[R/mbd_loglik_utils.R:16:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L16) *style:* **Commas should always have a space after.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
          ^
```
[R/mbd_loglik_utils.R:16:23:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L16) *style:* **Commas should always have a space after.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
                      ^
```
[R/mbd_loglik_utils.R:16:33:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L16) *style:* **Put spaces around all infix operators.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
                               ~^~
```
[R/mbd_loglik_utils.R:16:36:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L16) *style:* **Commas should always have a space after.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
                                   ^
```
[R/mbd_loglik_utils.R:17:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L17) *style:* **Put spaces around all infix operators.**
```r
    m <- s-1; n <- src-1;
         ~^~
```
[R/mbd_loglik_utils.R:17:23:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L17) *style:* **Put spaces around all infix operators.**
```r
    m <- s-1; n <- src-1;
                     ~^~
```
[R/mbd_loglik_utils.R:18:9:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Commas should always have a space after.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
        ^
```
[R/mbd_loglik_utils.R:18:21:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Commas should always have a space after.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                    ^
```
[R/mbd_loglik_utils.R:18:30:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *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:18:32:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                              ~^~
```
[R/mbd_loglik_utils.R:18:35:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                                 ~^~
```
[R/mbd_loglik_utils.R:18:36:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *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:18:38:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                                    ~^~
```
[R/mbd_loglik_utils.R:18:42:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *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:18:44:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                                          ~^~
```
[R/mbd_loglik_utils.R:18:46:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                                            ~^~
```
[R/mbd_loglik_utils.R:20:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L20) *style:* **Commas should always have a space after.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
      ^
```
[R/mbd_loglik_utils.R:20:10:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L20) *style:* **Use <-, not =, for assignment.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
         ^
```
[R/mbd_loglik_utils.R:20:16:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L20) *style:* **Commas should always have a space after.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
               ^
```
[R/mbd_loglik_utils.R:20:23:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L20) *style:* **Put spaces around all infix operators.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
                     ~^~
```
[R/mbd_loglik_utils.R:20:27:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
                          ^
```
[R/mbd_loglik_utils.R:20:29:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L20) *style:* **Put spaces around all infix operators.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
                           ~^~
```
[R/mbd_loglik_utils.R:21:9:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L21) *style:* **Commas should always have a space after.**
```r
  A[1:N,1:N]
        ^
```
[R/mbd_loglik_utils.R:24:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L24) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="windows"){matrix_builder = hyperA:::hyperA}
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
# if (.Platform$OS.type=="unix")   {matrix_builder = hyperA_HannoX} #this is set to work with home directory of the cluster
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L25) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="unix")   {matrix_builder = hyperA_HannoX} #this is set to work with home directory of the cluster
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:31:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L31) *style:* **Lines should not be more than 80 characters.**
```r
create_A0 <- function(max_number_of_species, lambda, mu, q, k, matrix_builder = hyperA_HannoX){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:31:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L31) *style:* **Variable or function name should be snake_case.**
```r
create_A0 <- function(max_number_of_species, lambda, mu, q, k, matrix_builder = hyperA_HannoX){
^~~~~~~~~
```
[R/mbd_loglik_utils.R:32:8:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L32) *style:* **Use <-, not =, for assignment.**
```r
  nvec = 0:max_number_of_species
       ^
```
[R/mbd_loglik_utils.R:33:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  M = lambda * matrix_builder(N = max_number_of_species, k = k, q = q)
  ^
```
[R/mbd_loglik_utils.R:33:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L33) *style:* **Use <-, not =, for assignment.**
```r
  M = lambda * matrix_builder(N = max_number_of_species, k = k, q = q)
    ^
```
[R/mbd_loglik_utils.R:35:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
  # diag(M) = (-lambda)*c( (1-(1-q)^(k+( nvec[1:max_number_of_species] ) )),0 ) - mu*(nvec+k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:35:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L35) *style:* **Commented code should be removed.**
```r
  # diag(M) = (-lambda)*c( (1-(1-q)^(k+( nvec[1:max_number_of_species] ) )),0 ) - mu*(nvec+k)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:36:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:36:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L36) *style:* **Use <-, not =, for assignment.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
          ^
```
[R/mbd_loglik_utils.R:36:26:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
                         ^
```
[R/mbd_loglik_utils.R:36:39:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
                                      ^
```
[R/mbd_loglik_utils.R:36:49:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
                                                ^
```
[R/mbd_loglik_utils.R:38:27:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L38) *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:46:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
create_B0 <- function(max_number_of_species, q, k, b, matrix_builder = hyperA_HannoX){#lambda * choose(k,b) * q^b  is going to be added in logB in the main script
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:46:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L46) *style:* **Variable or function name should be snake_case.**
```r
create_B0 <- function(max_number_of_species, q, k, b, matrix_builder = hyperA_HannoX){#lambda * choose(k,b) * q^b  is going to be added in logB in the main script
^~~~~~~~~
```
[R/mbd_loglik_utils.R:46:86:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L46) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
create_B0 <- function(max_number_of_species, q, k, b, matrix_builder = hyperA_HannoX){#lambda * choose(k,b) * q^b  is going to be added in logB in the main script
                                                                                ^
```
[R/mbd_loglik_utils.R:48:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L48) *style:* **Variable or function name should be snake_case.**
```r
  B <- matrix_builder(N = max_number_of_species, k = k2, q = q)
  ^
```
[R/mbd_loglik_utils.R:57:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L57) *style:* **Variable or function name should be snake_case.**
```r
create_A <- function(lambda, mu, nu, q, k, max_number_of_species){
^~~~~~~~
```
[R/mbd_loglik_utils.R:59:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L59) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,
  ^
```
[R/mbd_loglik_utils.R:61:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:61:97:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L61) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:61:99:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L61) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:63:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
  # M[row(M) == col(M)] = M[row(M) == col(M)] - c(lambda*(nvec[-length(nvec)]+k),0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:63:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L63) *style:* **Commented code should be removed.**
```r
  # M[row(M) == col(M)] = M[row(M) == col(M)] - c(lambda*(nvec[-length(nvec)]+k),0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:64:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M)] <- M[row(M) == col(M)] - lambda * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:74:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L74) *style:* **Variable or function name should be snake_case.**
```r
create_B <- function(lambda, nu, q, k, b, max_number_of_species){
^~~~~~~~
```
[R/mbd_loglik_utils.R:75:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:75:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L75) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
  ^
```
[R/mbd_loglik_utils.R:75:8:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L75) *warning:* **no visible global function definition for ‘create_B0’**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
       ^~~~~~~~~
```
[R/mbd_loglik_utils.R:76:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L76) *style:* **Lines should not be more than 80 characters.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k, b) * (q^b) * M
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:76:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L76) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k, b) * (q^b) * M
  ^
```
[R/mbd_loglik_utils.R:85:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L85) *style:* **Variable or function name should be snake_case.**
```r
create_A.no_mbd = function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:85:17:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L85) *style:* **Use <-, not =, for assignment.**
```r
create_A.no_mbd = function(
                ^
```
[R/mbd_loglik_utils.R:95:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:95:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
  ^
```
[R/mbd_loglik_utils.R:95:8:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *warning:* **no visible global function definition for ‘create_A0’**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
       ^~~~~~~~~
```
[R/mbd_loglik_utils.R:95:64:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
                                                               ^
```
[R/mbd_loglik_utils.R:95:76:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
                                                                           ^
```
[R/mbd_loglik_utils.R:95:84:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
                                                                                ^
```
[R/mbd_loglik_utils.R:95:90:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,lambda = nu,mu = mu,q = q,k = k)
                                                                                ^
```
[R/mbd_loglik_utils.R:96:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:96:97:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L96) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:96:99:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L96) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:97:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L97) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M)]     <- M[row(M) == col(M)] - c(lambda * (nvec[-length(nvec)] + k), 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:107:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:107:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Variable or function name should be snake_case.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:107:17:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Use <-, not =, for assignment.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                ^
```
[R/mbd_loglik_utils.R:107:35:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                  ^
```
[R/mbd_loglik_utils.R:107:38:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                     ^
```
[R/mbd_loglik_utils.R:107:40:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                       ^
```
[R/mbd_loglik_utils.R:107:42:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                         ^
```
[R/mbd_loglik_utils.R:107:44:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                           ^
```
[R/mbd_loglik_utils.R:107:66:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                                                 ^
```
[R/mbd_loglik_utils.R:108:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L108) *style:* **Lines should not be more than 80 characters.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:108:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L108) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
  ^
```
[R/mbd_loglik_utils.R:108:8:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L108) *warning:* **no visible global function definition for ‘create_B0’**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
       ^~~~~~~~~
```
[R/mbd_loglik_utils.R:109:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L109) *style:* **Lines should not be more than 80 characters.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k,b) * (q^b) * M
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:109:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L109) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k,b) * (q^b) * M
  ^
```
[R/mbd_loglik_utils.R:109:80:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L109) *style:* **Commas should always have a space after.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k,b) * (q^b) * M
                                                                               ^
```
[R/mbd_loglik_utils.R:110:48:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L110) *style:* **Use <-, not =, for assignment.**
```r
  B[row(B) > col(B) + minimum_multiple_births] = 0
                                               ^
```
[R/mbd_loglik_utils.R:119:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L119) *style:* **Variable or function name should be snake_case.**
```r
A_operator <- function(Q, transition_matrix, time_interval, precision = 50L,
^~~~~~~~~~
```
[R/mbd_loglik_utils.R:119:24:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L119) *style:* **Variable or function name should be snake_case.**
```r
A_operator <- function(Q, transition_matrix, time_interval, precision = 50L,
                       ^
```
[R/mbd_loglik_utils.R:121:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L121) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:128:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L128) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:130:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L130) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_utils.R:132:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L132) *style:* **Commented code should be removed.**
```r
    # exp_matrix <- rsexpm:::sexpm(transition_matrix * time_interval)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:133:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L133) *style:* **Commented code should be removed.**
```r
    # result     <- exp_matrix %*% Q
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:135:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L135) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:137:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L137) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_utils.R:138:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L138) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:138:19:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L138) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:140:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L140) *style:* **Lines should not be more than 80 characters.**
```r
    while ((result.nan == 1| result.negative == 1) & repetition < max_repetitions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:140:28:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L140) *style:* **Put spaces around all infix operators.**
```r
    while ((result.nan == 1| result.negative == 1) & repetition < max_repetitions)
                          ~^
```
[R/mbd_loglik_utils.R:141:5:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L141) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_loglik_utils.R:142:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
      result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:143:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L143) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/mbd_loglik_utils.R:144:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L144) *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:145:22:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
      if (result.nan)
                     ^
```
[R/mbd_loglik_utils.R:146:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L146) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/mbd_loglik_utils.R:149:7:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L149) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/mbd_loglik_utils.R:150:9:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L150) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:151:29:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L151) *style:* **Trailing whitespace is superfluous.**
```r
        if (result.negative)
                            ^
```
[R/mbd_loglik_utils.R:152:9:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L152) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        {
        ^
```
[R/mbd_loglik_utils.R:154:43:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L154) *style:* **Trailing whitespace is superfluous.**
```r
          if (precision > precision_limit)
                                          ^
```
[R/mbd_loglik_utils.R:155:11:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L155) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_loglik_utils.R:163:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:165:20:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L165) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!bad_result) {bad_result <- (any(result < 0))}
                   ^
```
[R/mbd_loglik_utils.R:165:52:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L165) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!bad_result) {bad_result <- (any(result < 0))}
                                                   ^
```
[R/mbd_loglik_utils.R:166:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L166) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:168:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L168) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_utils.R:171:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L171) *style:* **Lines should not be more than 80 characters.**
```r
    R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol = a_abstol, rtol = a_reltol)[2,-1], timeout = 1001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:171:78:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L171) *warning:* **no visible binding for global variable ‘mbd_loglik_rhs’**
```r
    R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol = a_abstol, rtol = a_reltol)[2,-1], timeout = 1001)
                                                                             ^~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:171:150:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L171) *style:* **Commas should always have a space after.**
```r
    R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol = a_abstol, rtol = a_reltol)[2,-1], timeout = 1001)
                                                                                ^
```
[R/mbd_loglik_utils.R:173:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L173) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_loglik_utils.R:181:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
#' A_operator_old <- function(Q, transition_matrix, time_interval, precision = 50L,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:183:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L183) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/mbd_loglik_utils.R:185:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L185) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/mbd_loglik_utils.R:192:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L192) *style:* **Lines should not be more than 80 characters.**
```r
#'     result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:193:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L193) *style:* **Lines should not be more than 80 characters.**
```r
#'     while ( ( any(!is.numeric(result)) || any(is.nan(result)) ) && precision < precision_limit )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:196:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
#'       result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = T)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:202:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L202) *style:* **Lines should not be more than 80 characters.**
```r
#'         result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:209:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
#'     # result<-deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix,atol=a_abstol,rtol=a_reltol)[2,-1]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:210:1:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
#'     R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix,atol=a_abstol,rtol=a_reltol)[2,-1], timeout = 1000)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:212:3:](https://github.com/Giappo/mbd/blob/bcd4352b5a0ba513a6d4f0cdc7bdfc444dbec9a5/R/mbd_loglik_utils.R#L212) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```


Thanks for the enhancement.
I tried it out and it seems that it only works if the file name is 'Jenkinsfile'.

If that is true, is there a chance that it could support other filenames like:  'Jenkinsfile-something' and 'Jenkinsfile-somethingelse' ?


Without having in-depth knowledge of that `validator`: Why revert? The code looked smart to me


Please add variables as in `BenchmarkHashAndStreamingAggregationOperators`
```
        public static final int TOTAL_PAGES = 140;
        public static final int ROWS_PER_PAGE = 10_000;
```


Для отслеживания положения поезда достаточно @stn_idx. Тогда объект текущей станции можно получить через @route:
` @route.station_list[@current_station_index]`
Чтобы везде не писать данную конструкцию, можно эту строчку вынести в отдельный метод.


Well, thats a good question.  Theres an argument to be made for turning it
off everywhere, sure, for consistency. but theres also an argument to be
made for maximizing entropy.    I'm of the opinion that we should leave it
on just to allow fast access to entropy on what might otherwise be low
entropy systems, but I'm open to arguments to the contrary

On Tue, Sep 25, 2018 at 10:16 AM Lonnie Abelbeck <notifications@github.com>
wrote:

> I say we default disable it (AES).
>
> I agree.
>
> So then should jitter not have AES by default as well to be consistent ?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/nhorman/rng-tools/commit/989730d2a5e6f27d2e63afbe086022c06af5dea9#commitcomment-30638802>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AA_C3lLsgbnIICP8WqcikkzhelhHNG28ks5uejq1gaJpZM4W3gyN>
> .
>


Sorry just a copy/paste typo.
That line is back.