[R/default_params_doc.R:15:1:](https://github.com/richelbilderbeek/razzo/blob/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/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/0f6d15010f92cfb32ec9b74a55a52ec0b54428ee/R/pmb_ml_cluster.R#L131) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```


Hi @AlexTugarev,

> not sure, what your use case is, but if you want to have the python LS (pyls) look into a dedicated virtual env, it's already prepared for this. since [palantir/python-language-server#127](https://github.com/palantir/python-language-server/pull/127), pyls can use the virtualenv of a project. it's actually the jedi inspector which reads the env var to find the python executable of a project's virtualenv, cf. https://github.com/davidhalter/jedi/blob/master/jedi/api/environment.py#L200
>
> be aware it's running two processes. first for pyls itself, and second for the [jedi](https://github.com/davidhalter/jedi) inspector. it actually doesn't matter which python you use to start pyls, the important thing is, which python is used for the jedi.

Does it really matter which python interpreter is used to _run_ jedi?  From what I understood, the VIRTUAL_ENV variable will influence how jedi will analyze the source code you are editing, but jedi itself could run any python version (it could even be written in another language than python).

> if your usecase is to configure the project's python via virtual env, that would be a really cool thing!

Yes, I want to make the user able in the context of which virtual env the source code is analyzed.  I also want the user to be able to easily switch between different virtual env.  Let's say you need to make your Python source code work with multiple Python versions, you could have one virtualenv per Python version, and switch from one to the other in Theia.  The diagnostics reported could change from a Python version to another.

Eventually, we should be able to run/launch Python scripts from Theia, so ideally they would run in the selected virtual env.

> I'd propose to check out how to inject env vars with the value of the virtualenv when restarting the child process.

This is what I do below (line 48).

Currently, we don't have a way for the frontend to influence how the language server is started by the backend.  The only way I found was for the frontend to pass query string parameters when opening an RPC channel.  So instead of opening `/services/languages/python`, the frontend will open `/services/languages/python?virtualEnv=/path/to/venv`, which the backend will then use to set the environment variable correctly.


Successfully aliased the URL <https://team-awesome-lars-prbawxmlfp.now.sh> to the following alias.

* https://team-awesome-lars.now.sh


We also need `partitionsPerGroup`, e.g:
```
@Param({"10"})
public int partitionsPerGroup = 10;
```


If you add such modules and you do not add them to the installer files the application will not be launched, when installed via the installer provided as artifact on appveyor. Therefore, always make sure that modules are really required and that they provide additional functionality. Otherwise remove them.


  bool fUseAliEvtCuts;            //
  bool fCentVsMultPlots;    //
  bool fDoSpherCuts;       //
  float fSpherCutsLow;      //
  float fSpherCutsUp;      //
ClassDef(AliFemtoDreamEventCuts,5)
 But I do have 5 ,lso thefDoSpherCuts??


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  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

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No german comments please. I hope that this tool is somehow used by international researchers.


Текущая станция не знает, что приехал поезд. Предыдущая не знает что уехал.


Successfully aliased the URL <https://distance-learning-lp-erixhgoffq.now.sh> to the following aliases.

* https://lp.stage-onlineschool.ru
* https://lp.onlineschool.ru


DeepCode analyzed this commit and found no issues.


for fourth column you could use:
```
BlockAssertions#createStringSequenceBlock
```


Done


Аналогично [https://github.com/allrom/Rubystudy/commit/55e6904ae5f3330229fad8650e596103777f20c0#r30639426](url)


Right.


@christophfriedrich:

Check is still in place in Line 38 of that file https://github.com/fs-geofs/ErstiWeTool/blob/5edb9c473ac9f364c1a0a969b200764a1ed4ec80/lib/inputvalidation.js#L37

This was duplicate (and incorrect because we actually need to check if the button checkbox is "on")


That's true, but it should never happen anyway.

If LALR reaches an illegal, unexpected state, then there's a bigger problem that exceptions won't help with.


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