[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)) )
                                                                    ^
```


используй less нормалайз
у тебя сейчас через import нормалайз не рендерится в css
хотя должен


Great!
Hoping, now this would work like a charm. Trained model is still missing, should have provided though.


am trying


Oh never mind, I now see that this was fixed in a subsequent commit in the PR.


`this->` or `Base::` (equivalents in this case) is required because inhertited things are not dependent-names in case of templates
https://stackoverflow.com/questions/1567730/inheritance-and-templates-in-c-why-are-methods-invisible


I would not count on greet and dispose to be always cheap ref-counting functions, maybe make `removeObject` and `insert` into functions implemented entirely by template functions `removeObject_impl` and `insert_impl` which take a template parameter whether to use greet/dispose functions.

And then use `removeObject_impl` and `insert_impl` within here.

Or implement `changeObjectKey` explicitly without using insert and remove.


@oxij Can you, perchance, explain how I should use this?


without it would compile on msvc, but fails on gcc or clang


this version sucks


address-sanitizer will still complain on nullptr deletes


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

* https://jwt.wezeit.co


Не могу понять, что даёт новый класс.


this is my comment


The GUI language is not affected by this workaround.


Wew.


Was this a merge error that re-added this in?


Pak, sy tolong ditambahin ke contributor trims..


Видимо это где-то надо.
Но зачем дублироваться?
Варианты: всем <a> всегда ставить такие параметры.
Сделать класс с этими параметрами и навешивать нужным <a>.


TeamCity Xbim :: Xbim Essentials :: XbimEssentials [Build 165](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1951&buildTypeId=XbimEssentials_XbimEssentials) outcome was **SUCCESS**
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第一处不合适哦
因为一旦没有评测集机用，那就必须等着一个评测机死亡，如果非阻塞的waitpid的话，那么某个用户提交时评测机被占满了，那么非阻塞waitpid立马返回，并且返回值为0，因为没有任何子进程的结束。这样就会出现莫名其妙的结果，相当于你的tmp_id就是0，后面得代码完全就走不下去，用户看到的结果是莫名其妙的。

如果非要这么加，可以这样处理，如果在那个地方非阻塞waitpid发现无死亡的子进程，那么本次work直接结束，给所有该judged提取到的solution队列添加当前判题繁忙的数据项，那么可以让web端显示当前判题机繁忙，请稍后提交。当然，这样的话solution表里需要添加一项了。
------------------------------------------------------------------------------------------------------------------
第二处改得好，之前忘说了，如果按之前的waitpid(-1,NULL,0)那样，事实上非常不好和奇怪。
while ((tmp_pid = waitpid(-1, NULL, 0)) > 0)
只有所有子进程退出了循环才会跳出来，当然得用非阻塞的：你有死亡的我就清理，有几个清理几个，没有就算了，就应该这样。
可能之前没有进行合适的压测，根本没发现这个问题会导致明显的延迟。


See meetod eeldab, et sisendiks on on HEX kujul String. Kuna selleks otsest vajadust ei ole, siis võiks seda meetodit refaktoreerida nii, et sisendiks on byte array. MINIMUM_HASH_LENGTH oleks siis 20.

Lisaks võiks see klass testidega ka kaetud olla


Сложна, можно проще.
Как вариант, декорировать сразу класс active.


Начальная и конечная станции тоже принадлежат маршруту, поэтому удобнее все в одном массиве хранить. Тогда не нужно будет каждый раз создавать массив, чтобы показать список всех станций.


А что изменилось с введения justify-content-center?
Здесь и ниже.


ah ok, generally `Base::` is better as it implies no virtual polymorphism and nobody is thinking someone is trying to use it.


У класса content были навешаны стили. Ты его выпилил, а стили?


Шрифты стали несколько огромными.


maybe we could fix this bug one day


Можно записать `[@station_start, *@stations_in_route, @station_end]`, тогда flatten! не нужен. Но лучше избавиться от этой строчки и в один массив все.


Question : why in 3.14.8 it work ? Calling subaction as subaction seems clear ?


This is not what we discussed!!!!

Just kidding: I don't recall being meeting with you. ;-) So you've probably tagged the wrong Clemens.


@aribrill during training I had several times to deal with training stopping on run maybe 07 out of 14. I lacked a way of resuming training exactly on run 07.


If the loop took less than a millisecond to run, you could end up with a duplicate ids in the batch list. Why cant we just use a counter ?


Eu vi que ele tá selecionando qualquer texto da página, mas tudo bem... você tirou nota 6/10. Passou na média. Vamos para a próxima tarefa...


Daggerfall Unity builds without error but has problems.  Game start doesn't trigger the tutorial properly which may be more an issue of scripting than building.


It wasn't an intended goal but a known side effect and was clarified in the description, which at the time mentioned the keys should appear "exactly as [they] would appear in its `id_*.pub` file".

This also helps the user avoid a module issue we'd previously encountered where a user with multiple keys is fine, but multiple keys of the same type with no name defined causes an unexpected error since the lack of a name causes a lookup problem later on as the module attempts to store multiple SSH keys with the same lookup key, composed of "${user}_{$key_type}_".


> Trained model is still missing, should have provided though.
Yes I can, but I have no duty to provide pretrained model. You should know that.


Now could not deploy this pull request due to an error while parsing the `now.json` file:

> It should NOT have additional properties (`redirects`)

Click here to see the contents of `now.json`

{
  "name": "distance-learning-lp",
  "type": "static",
  "alias": [
    "lp.stage-onlineschool.ru"
  ],
  "redirects": [
    { "source": "/", "destination": "https://www.onlineschool.ru" }
  ],
  "scale": {
    "bru1": {
      "min": 1,
      "max": "auto"
    }
  }
}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


当tmp_pid=0且没有可用ID时，i会在第一个循环中自增到max_running，从而导致后面的if(i<max_running)不成立，然后去第二次waitpid尝试，然后退出work.
应该不会对用户产生可见的影响。


Re: your question in the Slack channel, you could go nuts here and add

```
function changeOwner(address newOwner) public onlyOwner returns(bool success) {
   emit LogOwnerChanged(msg.sender, newOwner);
   owner = newOwner;
   return true;
}

```


fd


Considering he is the author of `if (spellScript && !spellScript)` code a long time ago, I don't think this is really needed.


This was an overwriting push.  Sorry that makes it a bit hard to track the actual changes.


那个父进程部分既然已经改了，好像是可以了，但是我建议：不如在work函数的waitpid处如果没有可死亡的子进程work直接return 0吧，后面的走的必要性不是很大，后面的回收僵尸进程部分一次不做对性能的影响不大，而且这样这样还避免了其他不必要的问题。


Not a good idea, see my comments to the previous comments, `getHighestMip` is very appropriate, anything else not really.


Agreed


What?


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Do not release it until Magento 2.3 is out.
Proxy generation will fail.


第一处没必要改的，阻塞的等一个挺好


what are you lower_bound'ing for ? `_mipLvl` is missing.

Also function should return a range since many `CImageData`s can have same mip level (disjoint rectangles).