[R/default_params_doc.R:17:67:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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:21:1:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
#' @param idparsopt The ids of the parameters that must be optimized. The ids are defined as follows:
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:48:18:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L48) *style:* **Trailing whitespace is superfluous.**
```r
#' @param methode
                 ^
```
[R/default_params_doc.R:51:44:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
#'     \item \code{sexpm}: use \code{sexpm}
                                           ^
```
[R/default_params_doc.R:52:46:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
#'     \item \code{expo}: use \code{expoRkit}
                                             ^
```
[R/default_params_doc.R:56:1:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L56) *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:89:28:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
#' @param results something
                           ^
```
[R/default_params_doc.R:108:62:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L108) *style:* **Trailing whitespace is superfluous.**
```r
#'   You can also define the tips_interval as you can usually
                                                             ^
```
[R/default_params_doc.R:125:1:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
#' @author Documentation by Giovanni Laudanno, use of this function by Richel J.C. Bilderbeek
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:130:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L130) *style:* **Variable or function name should be snake_case.**
```r
  A_abstol,
  ^~~~~~~~
```
[R/default_params_doc.R:131:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L131) *style:* **Variable or function name should be snake_case.**
```r
  A_reltol,
  ^~~~~~~~
```
[R/default_params_doc.R:142:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L142) *style:* **Variable or function name should be snake_case.**
```r
  checked.functions,
  ^~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:145:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L145) *style:* **Variable or function name should be snake_case.**
```r
  function.name,
  ^~~~~~~~~~~~~
```
[R/default_params_doc.R:145:17:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
  function.name,
                ^
```
[R/default_params_doc.R:149:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L149) *style:* **Variable or function name should be snake_case.**
```r
  INPUT.TREES,
  ^~~~~~~~~~~
```
[R/default_params_doc.R:150:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L150) *style:* **Variable or function name should be snake_case.**
```r
  INPUT.XML,
  ^~~~~~~~~
```
[R/default_params_doc.R:151:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L151) *style:* **Variable or function name should be snake_case.**
```r
  interval.max,
  ^~~~~~~~~~~~
```
[R/default_params_doc.R:152:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L152) *style:* **Variable or function name should be snake_case.**
```r
  interval.min,
  ^~~~~~~~~~~~
```
[R/default_params_doc.R:167:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L167) *style:* **Variable or function name should be snake_case.**
```r
  mbd.lambda,
  ^~~~~~~~~~
```
[R/default_params_doc.R:173:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:174:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L174) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_params_doc.R:175:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L175) *style:* **Variable or function name should be snake_case.**
```r
  Nsteps,
  ^~~~~~
```
[R/default_params_doc.R:176:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L176) *style:* **Variable or function name should be snake_case.**
```r
  Nsubs,
  ^~~~~
```
[R/default_params_doc.R:180:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L180) *style:* **Variable or function name should be snake_case.**
```r
  pars.transform,
  ^~~~~~~~~~~~~~
```
[R/default_params_doc.R:184:11:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L184) *style:* **Trailing whitespace is superfluous.**
```r
  printit,
          ^
```
[R/default_params_doc.R:185:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L185) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/default_params_doc.R:188:13:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L188) *style:* **Trailing whitespace is superfluous.**
```r
  recursive,
            ^
```
[R/default_params_doc.R:191:11:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L191) *style:* **Trailing whitespace is superfluous.**
```r
  results,
          ^
```
[R/default_params_doc.R:212:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L212) *style:* **Variable or function name should be snake_case.**
```r
  x.name,
  ^~~~~~
```
[R/default_params_doc.R:213:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L213) *style:* **Variable or function name should be snake_case.**
```r
  x.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:215:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L215) *style:* **Variable or function name should be snake_case.**
```r
  y.name,
  ^~~~~~
```
[R/default_params_doc.R:216:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L216) *style:* **Variable or function name should be snake_case.**
```r
  y.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:218:3:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/default_params_doc.R#L218) *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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/mbd_loglik_utils.R#L24) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="windows"){matrix_builder = hyperA:::hyperA}
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:1:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/mbd_loglik_utils.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
# if (.Platform$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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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:120:24:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/mbd_loglik_utils.R#L120) *style:* **Variable or function name should be snake_case.**
```r
                       A_abstol = 1e-16, A_reltol = 1e-10, methode = "expo"){
                       ^~~~~~~~
```
[R/mbd_loglik_utils.R:120:42:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/mbd_loglik_utils.R#L120) *style:* **Variable or function name should be snake_case.**
```r
                       A_abstol = 1e-16, A_reltol = 1e-10, methode = "expo"){
                                         ^~~~~~~~
```
[R/mbd_loglik_utils.R:121:1:](https://github.com/Giappo/mbd/blob/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/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/d04236d685553847a7b23126c0d5c0ae8e0bfb3a/R/mbd_loglik_utils.R#L183) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```


Yea, when reading the code I also assumed that it helps with the multiple key issue.
I just wanted to throw it out there, that users might run into issues there. But I also wasn't sure if that's a common thing to not have the user in the string or not - we just somehow happened to have it that way.

Whatever.. all good!
Thank you for your answer


The problem is that if we do a balance check against the original purse there could be a situation in which the balance changes between the check and the transfer to the PoS purse. This is because Rholang is totally concurrent and we don't know who else holds the given purse's name (and thus could do operations on it at the same time). The way I try to get around this is to create a new purse which I know only I have control over, but this means that I need to return the tokens to the original purse at the end if there is a problem.


Successfully aliased the URL <https://maintainable-scalable-css-ycpturrfor.now.sh> to the following alias.

* https://maintainable-scalable-css.now.sh


I checked 'prisms' which I think is a more advanced 'lens' which can allow use trace back the data type the other way around. But when I look at `TraceTable`, I feel the parts I want to get is using the forward order to get the next data type, not the reverse order. I am not very sure where should I think of putting the `prisms` in. @JacquesCarette


trocando oitavo por vinte


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

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

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

### Deployments updated

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

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


Only see this now; `steamid` is a big integer so I think `IgnoreCase` doesn't do us a favor other than slowing down the query :D


При получении списка нам чаще всего не нужен побочный эффект в виде вывода на консоль. Поэтому тут лучше просто вернуть все станции. Вывод сделать в коде, который вызывает метод.


Assignment 2 Problem 1


Hmmm, they could bomb that anyway, just spawn multiple copies of rngd over
and over again.   Prevention for that should be managed on the host side.

Regarding rdrand usage in virt guests, the trust in that instruction only
goes so far as the guests trust of the hypervisor and the host.  Its
supposed to execute on the bare metal, but theres nothing stopping the host
from trapping that instruction, and returning some other bogus data.  From
that standpoint the use of AES is beneficial there as it provides some
obfuscation, but the host can also snoop the guests memory, so its not that
big an aid.  I say we default disable it.

On Tue, Sep 25, 2018 at 9:26 AM Lonnie Abelbeck <notifications@github.com>
wrote:

>
>    1. I wonder if its worth enhancing test mode to take an integer
>    argument on
>    the command line representing number of iterations before exit
>
> Followup, how about putting in a fixed upper limit, say 100, for the
> number of iterations per test ? This would prevent someone from easily
> sucking out all the entropy, particularly for shared entropy devices in
> VM's. Thoughts ?
>
> —
> 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-30637989>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AA_C3iB5Y5SlVrlnDP1X2d7R4iEtd2Zyks5uei78gaJpZM4W3gyN>
> .
>


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

I updated the Github team because of this commit.

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

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

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

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


В all_stations должны хранится объекты класса Station. Поэтому при выводе нужно получать title у объекта: `all_stations.each { |station| puts station.title }`


Для названия нужен геттер.


Aliasing failed with the following error:

~~~
Error! Instance verification timed out (3m)
~~~


Аналогично, лучше вернуть список всех станций. Вывод в вызывающем коде


push worked as expected - used terminal i.e.

git commit -m "text"
git push

after having saved file and ticking staged.


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

* https://jwt.wezeit.co


Good. I will take a deep look at the TCEC game again.

Since there is not so many OCB endings, (and most are probable draws anyway) we will have to find more general rules that could apply to other endings as well.

For example, when we evaluate passed pawns, we can use different king distance weights in some circumstances.


var_dump()? :)


Ma arvan, et teegi kasutaja ei peaks teadma serveri pathi.
Parem äkki tee antud method ümber nii, et tal ei oleks ühtegi sisendit, tõsta AUTHENTICATION_SESSION_PATH konstant siia klassi


@diversys, I might be wrong, but if the app did not make use of `libQt5Sql` would it still link against that lib just because it was available àt build time?
Here's what I have before updating to your commit:
```bash
$ objdump -x /system/apps/Al-Anvar | grep NEEDED | grep -i sql
  NEEDED      libQt5Sql.so.5
```
Maybe this is an optional dependency.

Anyway, since I don't have enough time to investigate I'm not even going to consider a revert :)
But if anyone else is willing to dig and finds out some functionality depends on it then please do not hesitate to open a PR!


@gabehassler -- please revert most of these changes (they could break usages elsewhere) and use `boolean[]` only *inside* `RepeatedMeasuresModel`.


..ning siin siis võiks niimoodi teha:
SessionStatus sessionStatus = getSessionStatusPoller().fetchFinalSessionStatus(response.getSessionId(), AUTHENTICATION_SESSION_PATH);


Thanks for continued work. SnapKit is a game-changer for me.


rebase + change commit message to something meaningful
#bossMakesMeDoIt


Added mammogram.


#yoco


I will


Seda klassi vast ei ole vaja teegi töötamikeks


the reduction from 10000 to 2048 has broken a few use cases of mine, and I think the same limit is applied to find and replace as well -- I've ended up resorting to command line tools when I have to replace a large number of instances of text, which isnt as good as multiple cursors if I want to insert linebreaks, etc


Seda klassi vast samuti mitte


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

* https://kitay.co


Hi


Log _FAST_CHECK_DF_SERIALIZABLE


При увеличении количества типов поездов, метод будет раздуваться. Можно сделать его более универсальным. Пусть он принимает тип поезда и возвращает количество поездов данного типа.  Тогда мы сможем легко получить нужную информацию: station.train_type_list('passanger') / station.train_type_list('cargo') / station.train_type_list('...')


may worth to mention how to share a scheme: https://devcenter.bitrise.io/troubleshooting/frequent-ios-issues/#xcode-scheme-not-found


can you reuse the current request ?


Пользователи класса будут ожидать что при вызове метода вернется количество, puts вернет nil.


when code is pushed to your repository or a pull request created.

(we set up trigger map for this git events)


#6982-EngRefEquationFixPart6 (RKStrand) - i386-Windows-7-VisualStudio-14: OK (3033 of 3033 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


Kusjuures üks selline test võiks jääda, kus antakse sisse invaliidne base 64 ning expectitakse Excpetionit nii nagu eelnevalt kirjeldatud


Successfully aliased the URL <https://brainfuck-at-dusseldorf-bkpgcyernz.now.sh> to the following alias.

* https://brainfuck-at-dusseldorf.now.sh


Вернуть количество, сейчас puts возвращает nil


having trouble intestingh


> I say we default disable it (AES).

I agree.

So then should jitter not have AES by default as well to be consistent ?


if your project contains tests Bitrise creates two workflows: primary for testing and deploy for deployment. If the project does not contain test target only one workflow will be generated: primary which will build and deploy to bitrise.io (like the `deploy` workflow if you have tests)


I would not drive the users to `Automatically manage signing`. i would just mention: setup the project codesigning either using Xcode managed or manual codesigning and generate an ipa file locally to make sure your setup is correct.


Thanks for this - would love this to get released soon :)


Лучше добавить проверку @carriages > 0, чтобы случайно не уйти в минус.


"Generalized changes to layout rules can be provided, instead."?
Isn't the idea to just have things auto-formatted and that's it?


Successfully aliased the URL <https://just-another-todo-app-ethpmbgvot.now.sh> to the following alias.

* https://just-another-todo-app.now.sh


a **Distribution** type Provisioning Profile -> App Store type Provisioning Profile


Can this throw an exception as state not found on the table?
The old `get_action()` would handle such exception.


The +1 here is unnecessary I believe. In line 604 you already subtract the padding byte.


@Mike-Dax Could you do an npm release with these changes ? 🙏 Thanks!