[R/default_params_doc.R:15:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/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:15:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L15) *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:24:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L24) *style:* **Variable or function name should be snake_case.**
```r
mbd_ML_cluster <- function(s, initparsopt = c(0.6, 0.1, 1.3, 0.16)){
^~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:26:26:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L26) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/mbd_ml_cluster.R:26:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L26) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/mbd_ml_cluster.R:26:36:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L26) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```
[R/mbd_ml_cluster.R:26:42:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L26) *style:* **Variable or function name should be snake_case.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                         ^~~~~
```
[R/mbd_ml_cluster.R:29:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L29) *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:30:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L30) *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:30:5:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L30) *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:32:30:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L32) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```
[R/mbd_ml_cluster.R:33:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L33) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/general_settings"))
                              ^
```
[R/mbd_ml_cluster.R:34:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L34) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/sim_data"))
                              ^
```
[R/mbd_ml_cluster.R:36:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L36) *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:36:35:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L36) *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:36:47:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L36) *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:36:74:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L36) *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:36:85:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L36) *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:37:30:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L37) *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:37:55:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L37) *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:37:57:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L37) *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:53:19:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L53) *style:* **Only use double-quotes.**
```r
    optimmethod = 'simplex',
                  ^~~~~~~~~
```
[R/mbd_ml_cluster.R:60:3:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L60) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml_cluster.R:61:14:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L61) *warning:* **no visible binding for global variable ‘sim_data’**
```r
    test0 <- sim_data[[s]][-1]; #actual branching events
             ^~~~~~~~
```
[R/mbd_ml_cluster.R:62:25:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L62) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                        ^
```
[R/mbd_ml_cluster.R:62:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L62) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                              ^
```
[R/mbd_ml_cluster.R:63:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:63:49:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:63:52:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:63:69:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:63:85:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:63:88:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:63:89:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L63) *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:65:43:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L65) *style:* **Put spaces around all infix operators.**
```r
    percent_multiple  <- how_many_multiple/length(test2);
                                         ~^~
```
[R/mbd_ml_cluster.R:67:5:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L67) *style:* **Commented code should be removed.**
```r
  # additional_species = sum( duplicated(sim_data[[s]]) );
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:68:18:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L68) *warning:* **no visible binding for global variable ‘sim_data’**
```r
  tips <- length(sim_data[[s]]) + 1;
                 ^~~~~~~~
```
[R/mbd_ml_cluster.R:71:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L71) *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:71:17:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L71) *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:72:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L72) *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:72:29:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L72) *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:72:34:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L72) *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:72:70:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L72) *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:72:87:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L72) *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:72:137:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L72) *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:74:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L74) *style:* **Commented code should be removed.**
```r
  #out[1] = lambda
   ^~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:75:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L75) *style:* **Commented code should be removed.**
```r
  #out[2] = mu
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:76:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L76) *style:* **Commented code should be removed.**
```r
  #out[3] = nu
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:77:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L77) *style:* **Commented code should be removed.**
```r
  #out[4] = q
   ^~~~~~~~~~
```
[R/mbd_ml_cluster.R:78:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L78) *style:* **Commented code should be removed.**
```r
  #out[5] = LL
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:86:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:33:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:53:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:74:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:85:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:87:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:94:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:100:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:104:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:115:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:86:129:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L86) *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:87:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:34:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:52:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:66:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:82:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:107:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:109:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:116:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:119:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:87:121:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/mbd_ml_cluster.R#L87) *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:6:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L6) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML_cluster <- function(
^~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:11:26:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L11) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/pmb_ml_cluster.R:11:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L11) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/pmb_ml_cluster.R:11:36:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L11) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```
[R/pmb_ml_cluster.R:11:42:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                         ^~~~~
```
[R/pmb_ml_cluster.R:14:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L14) *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:15:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L15) *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:15:5:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L15) *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:17:30:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L17) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```
[R/pmb_ml_cluster.R:18:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L18) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/general_settings"))
                              ^
```
[R/pmb_ml_cluster.R:19:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L19) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/sim_data"))
                              ^
```
[R/pmb_ml_cluster.R:24:40:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
    parsfix2 <- initparsopt2 <- rep(NA,4);
                                       ^
```
[R/pmb_ml_cluster.R:29:38:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L29) *style:* **Commas should always have a space after.**
```r
    initparsopt2 <- initparsopt2[c(1,3,4)]
                                     ^
```
[R/pmb_ml_cluster.R:29:40:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L29) *style:* **Commas should always have a space after.**
```r
    initparsopt2 <- initparsopt2[c(1,3,4)]
                                       ^
```
[R/pmb_ml_cluster.R:37:7:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L37) *warning:* **no visible binding for global variable ‘sim_pars’**
```r
  if (sim_pars[2] != 0) {stop("You should not use this function if mu > 0")}
      ^~~~~~~~
```
[R/pmb_ml_cluster.R:37:25:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L37) *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:37:76:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L37) *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:39:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L39) *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:39:35:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L39) *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:39:47:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L39) *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:39:74:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L39) *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:39:85:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L39) *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:40:30:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L40) *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:40:55:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L40) *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:40:57:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L40) *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:56:19:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L56) *style:* **Only use double-quotes.**
```r
    optimmethod = 'simplex',
                  ^~~~~~~~~
```
[R/pmb_ml_cluster.R:63:3:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L63) *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:64:14:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L64) *warning:* **no visible binding for global variable ‘sim_data’**
```r
    test0 <- sim_data[[s]][-1]; #actual branching events
             ^~~~~~~~
```
[R/pmb_ml_cluster.R:65:25:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                        ^
```
[R/pmb_ml_cluster.R:65:31:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                              ^
```
[R/pmb_ml_cluster.R:66:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:66:49:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:66:52:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:66:69:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:66:85:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:66:88:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:66:89:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L66) *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:68:43:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L68) *style:* **Put spaces around all infix operators.**
```r
    percent_multiple  <- how_many_multiple/length(test2);
                                         ~^~
```
[R/pmb_ml_cluster.R:70:5:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L70) *style:* **Commented code should be removed.**
```r
  # additional_species = sum( duplicated(sim_data[[s]]) );
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:71:18:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L71) *warning:* **no visible binding for global variable ‘sim_data’**
```r
  tips <- length(sim_data[[s]]) + 1;
                 ^~~~~~~~
```
[R/pmb_ml_cluster.R:74:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L74) *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:74:17:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L74) *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:75:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L75) *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:75:29:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L75) *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:75:34:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L75) *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:75:70:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L75) *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:75:87:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L75) *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:75:137:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L75) *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:77:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L77) *style:* **Commented code should be removed.**
```r
  #out[1] = lambda
   ^~~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:78:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L78) *style:* **Commented code should be removed.**
```r
  #out[2] = mu
   ^~~~~~~~~~~
```
[R/pmb_ml_cluster.R:79:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L79) *style:* **Commented code should be removed.**
```r
  #out[3] = nu
   ^~~~~~~~~~~
```
[R/pmb_ml_cluster.R:80:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L80) *style:* **Commented code should be removed.**
```r
  #out[4] = q
   ^~~~~~~~~~
```
[R/pmb_ml_cluster.R:81:4:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L81) *style:* **Commented code should be removed.**
```r
  #out[5] = LL
   ^~~~~~~~~~~
```
[R/pmb_ml_cluster.R:89:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:33:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:53:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:74:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:85:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:87:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:94:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:100:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:104:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:115:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:89:129:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L89) *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:90:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:34:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:52:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:66:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:81:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:106:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:108:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:115:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:121:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:124:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:127:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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:90:129:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/pmb_ml_cluster.R#L90) *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/simulate_alignments.R:5:1:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L5) *style:* **Variable or function name should be snake_case.**
```r
P_t1_t2 <- function(lambda, mu, t1, t2) {
^~~~~~~
```
[R/simulate_alignments.R:6:3:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
  ^~~~~~~
```
[R/simulate_alignments.R:6:21:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                   ~^~
```
[R/simulate_alignments.R:6:29:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                           ~^~
```
[R/simulate_alignments.R:6:30:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                             ^
```
[R/simulate_alignments.R:6:38:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                    ~^~
```
[R/simulate_alignments.R:6:54:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                     ^
```
[R/simulate_alignments.R:6:68:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                                   ^~
```
[R/simulate_alignments.R:6:69:](https://github.com/richelbilderbeek/razzo/blob/a86cfeadfa3e7d6671a2675ad5ea351c64f875c1/R/simulate_alignments.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                                    ^
```


Действительно, ххп в полный рост.


About the new criteria, it is a "human criteria". If the opponent king is far from passed pawn, you king will support the pawn and opponent will have to sacrifice its bishop to stop the passed pawn. Of course you must have at least one other pawn to have a new queen ...


I fixed it via
https://github.com/rear/rear/commit/88f6d22a3b3812d1ca33cbf06000aafd352fabe1


@matzew Yes, 0.9.0.Alpha2 is planned for next week.


@JayTurnr that's what this patch does


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

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

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

### Deployments updated

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

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


直接return 0在单机判题时可能会有一定比例的情况出现明明还有任务没做完，判题休息了一秒。
不去阻塞的考虑是在多机判题时，等阻塞结束，这个手头上的任务可能已经被其他判题机抢走了，总体上可能会有一定比例的机器处于饥饿状态。


Thank you @achugo


W03: TKU60


I got `makeRef` and `mkRefFrmLbl` reversed before. I have changed them.


I need help to install mimic data automatically in my Mac (locally)128 GB?


>           hi, do you know how to add new songs in client?
> i think modifying 'music_data.bin' file in '.TRO' will make answer but i don't know how to do it.

music_data.bin is encrypted by a 4096 bytes xor noise.
After decryption, you can get the readable information according to the "Arrowgene.Ez2Off/Arrowgene.Ez2Off.Data/BinFiles/" code below.