[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")
                             ^
```


#6982-EngRefEquationFixPart6 (RKStrand) - Win64-Windows-7-VisualStudio-14: OK (3032 of 3033 tests passed, 2 test warnings)

Messages:

 * 3 tests had: EIO diffs.
 * 1 test had: ESO big diffs.
 * 1 test had: MTR big diffs.
 * 1 test had: Table big diffs.
 * 2 tests had: ESO small diffs.
 * 2 tests had: MTR small diffs.
 * 1 test had: Table small diffs.

Failures:

regression Test Summary
 * Passed: 630
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.97%25-yellow.png)


Настройки специфичные для твоего окружения лучше в глобальный gitignore вынести: [gist.github.com](https://gist.github.com/subfuzion/db7f57fff2fb6998a16c)


udah semua kan ag?


@elizac95 - You don't need to specify this array in the function definition, as long as you call it with an array argument (which you've done correctly in line 72 of index.html), the function will know to treat `threeOriginalPrices` as an array!


It should be `community`


nice :)


yeah, i also changed it to `250`


It doesn't seem autorejoin_delay is being added to the settings correctly. The command /set autorejoin_delay returns "unknown setting".


Okay.
Here's another idea: are the coordinates in the event rounded to character size?


Create README.md

:package: demo


Heads-up @layik it's not yet easy to create ical objects or events without `read_ical()`. But it should be. I think we can add `CREATED` attributes easily. Couple of questions: which other attributes should go into a minimum viable product for an event? And should we create an `ical_event` object akin to the `sfg` objects in **sf** (demonstrated below)?

``` r
class(sf::st_point(1:2))
#> [1] "XY"    "POINT" "sfg"
```

Created on 2018-09-25 by the [reprex package](http://reprex.tidyverse.org) (v0.2.0).

In `sf` dataframes there is one `sfg` per row. Perhaps there could be one event object per row in `ical` objects. "List columns" could resolve the 'NA` issue but add unwanted complexity...


Aliasing failed with the following error:

~~~
Error! The alias chronoscio is a deployment URL or it's in use by a different team.
~~~


@elizac95 - Since the function definition of `getClasses` doesn't take any arguments (see functions.js: `function getClasses()` has no parameters between the parentheses), anything you pass it here will be ignored. The body of the function you wrote in functions.js looks good!


DEVELOPED WITH intellij Idea


@elizac95 - (as mentioned in class) you can actually use the `name` function parameter as a variable without needing to redefine it inside the function. When you call the function in index.html, you assign whatever value you put between the parentheses to `name`.


Spent about 20~30 minutes considering this, if a real issue or not nowadays.
After investigating a bit, spice_playback_channel_set_delay() is only called by audio backed, either spice-pulse or spice-gstaudio; Spice-gstaudio is the one that can trigger this when we initialize it without proper audio channel (it happens for audio-volume sync on startup)

Still, this should have been fixed by:
https://gitlab.freedesktop.org/spice/spice-gtk/commit/4cdd6e07d3f7ec07dc

In case that's the case, you could remove this patch from your branch ;)
Cheers


ur gay


I just merged this one
https://gitlab.freedesktop.org/spice/spice-gtk/commit/8f38461e31bec98e4d3e1bc503da07f33931d0b7

Cheers,


This should not be changed. Copyright should only be asserted in NOTICE not in the license


One thing I noticed is that 3.1 errored out with the emit statements in the jingle player code. This may be a bug with 3.1, or (and more likely) that the way signals are dealt with has changed a bit.


Heads-up @layik I fixed the readme example! I think this will be stable now. I don't like the strange column names that need to be enclosed in backticks but I prefer them to what we had before: more faithful to the input data.


@elizac95 - Careful here with datatypes! `"true"` with quotation marks is a String, so it won't be treated the same as if you return `true` without quotation marks (Boolean).


Automatic (well, "cyborg" if you count manual edits) processing isn't without its benefits :)


Hi, has some queries about this commit:-

1.  I just make a change in ArchStairs.py that railing make is named 'Railxxxx', before check this commit ...
-  lrRail = ArchPipe.makePipe(baseobj=None,diameter=0,length=0,placement=None,name="Rail")
-  Noted this commit is not applied to ArchPipe, so this works

2.  Thinking also if the 'multi-edges landing' should be better named as 'Landing', and a flight of Stairs be named as 'Flight' ... etc ...

3.  So a 'master' may house each portion like below:-

   'Master' Stairs , w/ Addition:-
- Flight
- Landing
- Flight001
- Rail
- Rail001

Maybe similar to other Arch Objects... WindowFrame, WindowPane...?

See what you think about this approach.


Successfully aliased the URL <https://mtikkanen-ytfyjmhvfv.now.sh> to the following aliases.

* https://mtikkanen.fi
* https://www.mtikkanen.fi


O método chamado aqui deveria ser [**`prepare()`**](http://php.net/manual/pt_BR/pdo.prepare.php), já que você ainda vai terminar de compor a consulta SQL com as chamadas a `bindParam()` abaixo.


Are these files or directories?


> > You are still, even now, trying to make this political. It's not political, how is this difficult?
>
> The creator of the CoC himself says otherwise:
>
> "Some people are saying that the Contributor Covenant is a political document, and they’re right."
>
> https://mobile.twitter.com/coralineada/status/1041465346656530432?lang=de

Again, some of you seem to be confusing Greg with Coraline, on purpose.  If that person has an agenda, it feels a little irrelevant, I dunno.  I mean, to be fair, I can see why a version 2 of these rules might be needed, lol.  But Greg's intent in this matter has always felt pretty clear to me -- professionalism == productivity,  Protecting the brand == wider adoption.  Being good human beings to each other is nice, too.  It's not that I know, it's a supposition.  From what I have read from Greg, he seems pretty level headed to me.  His standards for kernel development for example is always awesome to read, something I apply to my own crap -- and I have barely even left user space.  So given the choice between trusting his intentions behind this commit, or throwing him under a bus because he used excerpts from the contributor covenant?  Well I am going to go with the former.  Intentions is king in everything, everything else is for tweaking.


updated - thanks!


updated - sorry yes this can be provided


updated


removed