[R/default_params_doc.R:15:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L15) *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:95:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
#' @param cond Set 1 if you want to condition on stem or crown age and non-extinction of the phylogeny. Set 0 otherwise.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:98:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L98) *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:103:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L103) *style:* **Variable or function name should be snake_case.**
```r
  A_abstol,
  ^~~~~~~~
```
[R/default_params_doc.R:104:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L104) *style:* **Variable or function name should be snake_case.**
```r
  A_reltol,
  ^~~~~~~~
```
[R/default_params_doc.R:117:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L117) *style:* **Variable or function name should be snake_case.**
```r
  interval.max,
  ^~~~~~~~~~~~
```
[R/default_params_doc.R:118:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L118) *style:* **Variable or function name should be snake_case.**
```r
  interval.min,
  ^~~~~~~~~~~~
```
[R/default_params_doc.R:133:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L133) *style:* **Variable or function name should be snake_case.**
```r
  mbd.lambda,
  ^~~~~~~~~~
```
[R/default_params_doc.R:139:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L139) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:140:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L140) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_params_doc.R:141:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L141) *style:* **Variable or function name should be snake_case.**
```r
  Nsteps,
  ^~~~~~
```
[R/default_params_doc.R:142:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L142) *style:* **Variable or function name should be snake_case.**
```r
  Nsubs,
  ^~~~~
```
[R/default_params_doc.R:145:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L145) *style:* **Variable or function name should be snake_case.**
```r
  pars.transform,
  ^~~~~~~~~~~~~~
```
[R/default_params_doc.R:149:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L149) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/default_params_doc.R:169:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L169) *style:* **Variable or function name should be snake_case.**
```r
  x.name,
  ^~~~~~
```
[R/default_params_doc.R:170:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L170) *style:* **Variable or function name should be snake_case.**
```r
  x.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:172:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L172) *style:* **Variable or function name should be snake_case.**
```r
  y.name,
  ^~~~~~
```
[R/default_params_doc.R:173:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  y.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:175:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/default_params_doc.R#L175) *style:* **Variable or function name should be snake_case.**
```r
  z.name,
  ^~~~~~
```
[R/mbd_ml_cluster.R:5:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @description mbd_ML_cluster computes the maximum likelihood estimates of the parameters of a multiple birth-death diversification model. Differently from mbd_ML it needs only the number "s" of the simulations, making it suitable to run on a cluster. You will need two files to make it work: "general_settings","sim_data"; they are both generated by mbd_sim_dataset. This second version supports both sympatric and allopatric speciations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:8:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param initparsopt The initial values of the parameters that must be optimized
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:17:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
#' \item Fifth column contains the number of additional species coming from multiple births in the evaluated tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:26:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L26) *style:* **Variable or function name should be snake_case.**
```r
mbd_ML_cluster <- function(
^~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:35:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  mbd_ML,
  ^~~~~~
```
[R/mbd_ml_cluster.R:40:26:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L40) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/mbd_ml_cluster.R:40:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L40) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/mbd_ml_cluster.R:40:36:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L40) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```
[R/mbd_ml_cluster.R:40:42:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L40) *style:* **Variable or function name should be snake_case.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                         ^~~~~
```
[R/mbd_ml_cluster.R:43:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
  #load general sim settings in order to make the estimation coherent with sim conditions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:44:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:44:5:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L44) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:46:30:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L46) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```
[R/mbd_ml_cluster.R:47:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L47) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/general_settings"))
                              ^
```
[R/mbd_ml_cluster.R:48:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L48) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/sim_data"))
                              ^
```
[R/mbd_ml_cluster.R:50:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:50:35:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L50) *style:* **Commas should always have a space after.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                  ^
```
[R/mbd_ml_cluster.R:50:47:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L50) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                              ^
```
[R/mbd_ml_cluster.R:50:74:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L50) *style:* **Commas should always have a space after.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                                                         ^
```
[R/mbd_ml_cluster.R:50:85:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L50) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                                                                ^
```
[R/mbd_ml_cluster.R:51:30:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L51) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = TRUE)
                             ^
```
[R/mbd_ml_cluster.R:51:55:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L51) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = TRUE)
                                                      ^
```
[R/mbd_ml_cluster.R:51:57:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L51) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = TRUE)
                                                        ^
```
[R/mbd_ml_cluster.R:67:19:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L67) *style:* **Only use double-quotes.**
```r
    optimmethod = 'simplex',
                  ^~~~~~~~~
```
[R/mbd_ml_cluster.R:74:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L74) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml_cluster.R:76:25:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                        ^
```
[R/mbd_ml_cluster.R:76:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                              ^
```
[R/mbd_ml_cluster.R:77:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:77:49:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                ^
```
[R/mbd_ml_cluster.R:77:52:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                   ^
```
[R/mbd_ml_cluster.R:77:69:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                    ^
```
[R/mbd_ml_cluster.R:77:85:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Use <-, not =, for assignment.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/mbd_ml_cluster.R:77:88:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/mbd_ml_cluster.R:77:89:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L77) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/mbd_ml_cluster.R:79:43:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L79) *style:* **Put spaces around all infix operators.**
```r
    percent_multiple  <- how_many_multiple/length(test2);
                                         ~^~
```
[R/mbd_ml_cluster.R:81:5:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L81) *style:* **Commented code should be removed.**
```r
  # additional_species = sum( duplicated(sim_data[[s]]) );
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:85:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
  out2 <- out; #names(out2)=c("lambda","mu","nu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:85:17:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L85) *style:* **Commented code should be removed.**
```r
  out2 <- out; #names(out2)=c("lambda","mu","nu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:86:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L86) *style:* **Lines should not be more than 80 characters.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:86:29:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                            ^
```
[R/mbd_ml_cluster.R:86:34:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                 ^
```
[R/mbd_ml_cluster.R:86:70:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                     ^
```
[R/mbd_ml_cluster.R:86:87:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                                ^
```
[R/mbd_ml_cluster.R:86:137:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                                ^
```
[R/mbd_ml_cluster.R:88:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L88) *style:* **Commented code should be removed.**
```r
  #out[1] = lambda
   ^~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:89:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L89) *style:* **Commented code should be removed.**
```r
  #out[2] = mu
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:90:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L90) *style:* **Commented code should be removed.**
```r
  #out[3] = nu
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:91:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L91) *style:* **Commented code should be removed.**
```r
  #out[4] = q
   ^~~~~~~~~~
```
[R/mbd_ml_cluster.R:92:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L92) *style:* **Commented code should be removed.**
```r
  #out[5] = LL
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:100:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:100:33:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                ^
```
[R/mbd_ml_cluster.R:100:53:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                    ^
```
[R/mbd_ml_cluster.R:100:74:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                         ^
```
[R/mbd_ml_cluster.R:100:85:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:87:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:94:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:100:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Only use double-quotes.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^~
```
[R/mbd_ml_cluster.R:100:104:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:115:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:129:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:101:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:101:34:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                 ^
```
[R/mbd_ml_cluster.R:101:52:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                   ^
```
[R/mbd_ml_cluster.R:101:66:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                 ^
```
[R/mbd_ml_cluster.R:101:82:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:107:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:109:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:116:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:119:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:121:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/mbd_ml_cluster.R#L101) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:10:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L10) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML_cluster <- function(
^~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:16:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  mbd_ML,
  ^~~~~~
```
[R/pmb_ml_cluster.R:24:26:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/pmb_ml_cluster.R:24:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/pmb_ml_cluster.R:24:36:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```
[R/pmb_ml_cluster.R:24:42:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                         ^~~~~
```
[R/pmb_ml_cluster.R:27:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
  #load general sim settings in order to make the estimation coherent with sim conditions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:28:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:28:5:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L28) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:30:30:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L30) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```
[R/pmb_ml_cluster.R:31:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L31) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/general_settings"))
                              ^
```
[R/pmb_ml_cluster.R:32:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L32) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/sim_data"))
                              ^
```
[R/pmb_ml_cluster.R:37:40:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L37) *style:* **Commas should always have a space after.**
```r
    parsfix2 <- initparsopt2 <- rep(NA,4);
                                       ^
```
[R/pmb_ml_cluster.R:42:38:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L42) *style:* **Commas should always have a space after.**
```r
    initparsopt2 <- initparsopt2[c(1,3,4)]
                                     ^
```
[R/pmb_ml_cluster.R:42:40:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L42) *style:* **Commas should always have a space after.**
```r
    initparsopt2 <- initparsopt2[c(1,3,4)]
                                       ^
```
[R/pmb_ml_cluster.R:50:25:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L50) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (sim_pars[2] != 0) {stop("You should not use this function if mu > 0")}
                        ^
```
[R/pmb_ml_cluster.R:50:76:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L50) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (sim_pars[2] != 0) {stop("You should not use this function if mu > 0")}
                                                                           ^
```
[R/pmb_ml_cluster.R:52:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:52:35:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L52) *style:* **Commas should always have a space after.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                  ^
```
[R/pmb_ml_cluster.R:52:47:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L52) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                              ^
```
[R/pmb_ml_cluster.R:52:74:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L52) *style:* **Commas should always have a space after.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                                                         ^
```
[R/pmb_ml_cluster.R:52:85:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L52) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                                                                ^
```
[R/pmb_ml_cluster.R:53:30:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L53) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = T)
                             ^
```
[R/pmb_ml_cluster.R:53:55:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L53) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = T)
                                                      ^
```
[R/pmb_ml_cluster.R:53:57:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L53) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = T)
                                                        ^
```
[R/pmb_ml_cluster.R:69:19:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L69) *style:* **Only use double-quotes.**
```r
    optimmethod = 'simplex',
                  ^~~~~~~~~
```
[R/pmb_ml_cluster.R:76:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L76) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/pmb_ml_cluster.R:78:25:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L78) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                        ^
```
[R/pmb_ml_cluster.R:78:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L78) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                              ^
```
[R/pmb_ml_cluster.R:79:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:79:49:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                ^
```
[R/pmb_ml_cluster.R:79:52:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                   ^
```
[R/pmb_ml_cluster.R:79:69:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                    ^
```
[R/pmb_ml_cluster.R:79:85:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Use <-, not =, for assignment.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/pmb_ml_cluster.R:79:88:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/pmb_ml_cluster.R:79:89:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L79) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/pmb_ml_cluster.R:81:43:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L81) *style:* **Put spaces around all infix operators.**
```r
    percent_multiple  <- how_many_multiple/length(test2);
                                         ~^~
```
[R/pmb_ml_cluster.R:83:5:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L83) *style:* **Commented code should be removed.**
```r
  # additional_species = sum( duplicated(sim_data[[s]]) );
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:87:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
  out2 <- out; #names(out2)=c("lambda","mu","nu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:87:17:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L87) *style:* **Commented code should be removed.**
```r
  out2 <- out; #names(out2)=c("lambda","mu","nu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:88:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:88:29:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L88) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                            ^
```
[R/pmb_ml_cluster.R:88:34:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L88) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                 ^
```
[R/pmb_ml_cluster.R:88:70:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L88) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                     ^
```
[R/pmb_ml_cluster.R:88:87:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L88) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                                ^
```
[R/pmb_ml_cluster.R:88:137:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L88) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                                ^
```
[R/pmb_ml_cluster.R:90:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L90) *style:* **Commented code should be removed.**
```r
  #out[1] = lambda
   ^~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:91:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L91) *style:* **Commented code should be removed.**
```r
  #out[2] = mu
   ^~~~~~~~~~~
```
[R/pmb_ml_cluster.R:92:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L92) *style:* **Commented code should be removed.**
```r
  #out[3] = nu
   ^~~~~~~~~~~
```
[R/pmb_ml_cluster.R:93:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L93) *style:* **Commented code should be removed.**
```r
  #out[4] = q
   ^~~~~~~~~~
```
[R/pmb_ml_cluster.R:94:4:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L94) *style:* **Commented code should be removed.**
```r
  #out[5] = LL
   ^~~~~~~~~~~
```
[R/pmb_ml_cluster.R:102:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:102:33:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                ^
```
[R/pmb_ml_cluster.R:102:53:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                    ^
```
[R/pmb_ml_cluster.R:102:74:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                         ^
```
[R/pmb_ml_cluster.R:102:85:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/pmb_ml_cluster.R:102:87:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/pmb_ml_cluster.R:102:94:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/pmb_ml_cluster.R:102:100:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Only use double-quotes.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^~
```
[R/pmb_ml_cluster.R:102:104:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/pmb_ml_cluster.R:102:115:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/pmb_ml_cluster.R:102:129:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L102) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/pmb_ml_cluster.R:103:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:103:34:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                 ^
```
[R/pmb_ml_cluster.R:103:52:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                   ^
```
[R/pmb_ml_cluster.R:103:66:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                 ^
```
[R/pmb_ml_cluster.R:103:81:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:103:106:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:103:108:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:103:115:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:103:121:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Only use double-quotes.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^~
```
[R/pmb_ml_cluster.R:103:124:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:103:127:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:103:129:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L103) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '') )  )}
                                                                                ^
```
[R/pmb_ml_cluster.R:117:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L117) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML_cluster2 <- function(
^~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:119:23:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L119) *style:* **Commas should always have a space after.**
```r
  initparsopt = c(0.5,0.15,0.1),
                      ^
```
[R/pmb_ml_cluster.R:119:28:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L119) *style:* **Commas should always have a space after.**
```r
  initparsopt = c(0.5,0.15,0.1),
                           ^
```
[R/pmb_ml_cluster.R:120:3:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L120) *style:* **Variable or function name should be snake_case.**
```r
  pmb_ML,
  ^~~~~~
```
[R/pmb_ml_cluster.R:124:5:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L124) *style:* **Commented code should be removed.**
```r
  # initparsopt=c(1.8,0.3,0.15);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:125:26:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L125) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/pmb_ml_cluster.R:125:31:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L125) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/pmb_ml_cluster.R:125:36:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L125) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```
[R/pmb_ml_cluster.R:125:42:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L125) *style:* **Variable or function name should be snake_case.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                         ^~~~~
```
[R/pmb_ml_cluster.R:126:25:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L126) *warning:* **local variable ‘parsfix’ assigned but may not be used**
```r
  idparsopt <- 1:Npars; parsfix <- NULL;
                        ^~~~~~~
```
[R/pmb_ml_cluster.R:128:1:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:128:5:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L128) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:131:30:](https://github.com/richelbilderbeek/razzo/blob/c0bc68f82e08fa2d8e45a598fc2b93191ace26b9/R/pmb_ml_cluster.R#L131) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```


@eharkins Let's take the `maxWidth` out of here; I think we want to let this expand, especially as the number of metrics etc grows, no? At the very least, for now, I'd also settled for a relatively higher max width to make it feel a bit more expansive.


Where is this Maven package available?


New Pattern Added


Sorry I found the issue and looking into doing a PR now. A bit of too much copy-paste (SetHelp was used instead of SetLabel)


ok 👍