[R/default_params_doc.R:15:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/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/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param initparsopt The initial values of the parameters that must be optimized
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:17:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
#' \item Fifth column contains the number of additional species coming from multiple births in the evaluated tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:26:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L26) *style:* **Variable or function name should be snake_case.**
```r
mbd_ML_cluster <- function(
^~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:35:3:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  mbd_ML,
  ^~~~~~
```
[R/mbd_ml_cluster.R:40:26:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L40) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/mbd_ml_cluster.R:40:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L40) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/mbd_ml_cluster.R:40:36:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L40) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```
[R/mbd_ml_cluster.R:40:42:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L40) *style:* **Variable or function name should be snake_case.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                         ^~~~~
```
[R/mbd_ml_cluster.R:43:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
  #load general sim settings in order to make the estimation coherent with sim conditions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:44:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:44:5:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L44) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:46:30:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L46) *style:* **Commas should always have a space after.**
```r
  datapath <- paste0(simpath,"/data")
                             ^
```
[R/mbd_ml_cluster.R:47:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L47) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/general_settings"))
                              ^
```
[R/mbd_ml_cluster.R:48:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L48) *style:* **Commas should always have a space after.**
```r
  load(file = paste0(datapath,"/sim_data"))
                              ^
```
[R/mbd_ml_cluster.R:50:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:50:35:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L50) *style:* **Commas should always have a space after.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                  ^
```
[R/mbd_ml_cluster.R:50:47:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L50) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                              ^
```
[R/mbd_ml_cluster.R:50:74:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L50) *style:* **Commas should always have a space after.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                                                         ^
```
[R/mbd_ml_cluster.R:50:85:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L50) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!file.exists(paste0(simpath,"/errors"))){dir.create(paste0(simpath,"/errors"))}
                                                                                ^
```
[R/mbd_ml_cluster.R:51:30:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L51) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = TRUE)
                             ^
```
[R/mbd_ml_cluster.R:51:55:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L51) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = TRUE)
                                                      ^
```
[R/mbd_ml_cluster.R:51:57:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L51) *style:* **Commas should always have a space after.**
```r
  sink(file = paste0(simpath,"/errors/mbd_MLE_errors",s,".txt"), append = TRUE)
                                                        ^
```
[R/mbd_ml_cluster.R:67:19:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L67) *style:* **Only use double-quotes.**
```r
    optimmethod = 'simplex',
                  ^~~~~~~~~
```
[R/mbd_ml_cluster.R:74:3:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L74) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_ml_cluster.R:76:25:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                        ^
```
[R/mbd_ml_cluster.R:76:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                              ^
```
[R/mbd_ml_cluster.R:77:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:77:49:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                ^
```
[R/mbd_ml_cluster.R:77:52:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                   ^
```
[R/mbd_ml_cluster.R:77:69:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                    ^
```
[R/mbd_ml_cluster.R:77:85:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Use <-, not =, for assignment.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/mbd_ml_cluster.R:77:88:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/mbd_ml_cluster.R:77:89:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L77) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    test2 <- test1; for (iii in 2:length(test1)){if(test1[iii] == T){test2[iii - 1] = T}} #considering also the first species at each multiple event
                                                                                ^
```
[R/mbd_ml_cluster.R:79:43:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L79) *style:* **Put spaces around all infix operators.**
```r
    percent_multiple  <- how_many_multiple/length(test2);
                                         ~^~
```
[R/mbd_ml_cluster.R:81:5:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L81) *style:* **Commented code should be removed.**
```r
  # additional_species = sum( duplicated(sim_data[[s]]) );
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:85:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
  out2 <- out; #names(out2)=c("lambda","mu","nu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:85:17:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L85) *style:* **Commented code should be removed.**
```r
  out2 <- out; #names(out2)=c("lambda","mu","nu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:86:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L86) *style:* **Lines should not be more than 80 characters.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:86:29:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                            ^
```
[R/mbd_ml_cluster.R:86:34:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                 ^
```
[R/mbd_ml_cluster.R:86:70:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                     ^
```
[R/mbd_ml_cluster.R:86:87:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                                ^
```
[R/mbd_ml_cluster.R:86:137:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L86) *style:* **Commas should always have a space after.**
```r
  names(out2) <- c(parnames,"LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
                                                                                ^
```
[R/mbd_ml_cluster.R:88:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L88) *style:* **Commented code should be removed.**
```r
  #out[1] = lambda
   ^~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:89:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L89) *style:* **Commented code should be removed.**
```r
  #out[2] = mu
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:90:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L90) *style:* **Commented code should be removed.**
```r
  #out[3] = nu
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:91:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L91) *style:* **Commented code should be removed.**
```r
  #out[4] = q
   ^~~~~~~~~~
```
[R/mbd_ml_cluster.R:92:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L92) *style:* **Commented code should be removed.**
```r
  #out[5] = LL
   ^~~~~~~~~~~
```
[R/mbd_ml_cluster.R:100:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:100:33:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                ^
```
[R/mbd_ml_cluster.R:100:53:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                    ^
```
[R/mbd_ml_cluster.R:100:74:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                         ^
```
[R/mbd_ml_cluster.R:100:85:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:87:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:94:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:100:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Only use double-quotes.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^~
```
[R/mbd_ml_cluster.R:100:104:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:115:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:100:129:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L100) *style:* **Commas should always have a space after.**
```r
  utils::write.table(matrix(out,ncol = length(out)),file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),append = T,row.names = F,col.names = F, sep = ",")
                                                                                ^
```
[R/mbd_ml_cluster.R:101:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml_cluster.R:101:34:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                 ^
```
[R/mbd_ml_cluster.R:101:52:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                   ^
```
[R/mbd_ml_cluster.R:101:66:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                 ^
```
[R/mbd_ml_cluster.R:101:82:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:107:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:109:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:116:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:119:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ml_cluster.R:101:121:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ml_cluster.R#L101) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (res[1:4] != rep(-1, Npars)){suppressWarnings(  file.remove( paste0(simpath,"/errors/mbd_MLE_errors",s,".txt") )  )}
                                                                                ^
```
[R/mbd_ML_cluster0.R:3:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Maximization of the loglikelihood under a multiple birth-death diversification model, wrapped for cluster usage.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:4:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @description mbd_ML_cluster0 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_dataset0.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:7:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L7) *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_cluster0.R:8:70:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
#' @param idparsopt The ids of the parameters that must be optimized.
                                                                     ^
```
[R/mbd_ML_cluster0.R:22:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L22) *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_cluster0.R:30:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L30) *style:* **Variable or function name should be snake_case.**
```r
mbd_ML_cluster0 <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:31:5:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
  s,
    ^
```
[R/mbd_ML_cluster0.R:34:5:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L34) *style:* **Commented code should be removed.**
```r
  # initparsopt=c(1.8,0.3,0.15);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:35:26:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L35) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q")
                         ^
```
[R/mbd_ML_cluster0.R:35:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L35) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q")
                              ^
```
[R/mbd_ML_cluster0.R:35:36:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L35) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q")
                                   ^
```
[R/mbd_ML_cluster0.R:39:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L39) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:40:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L40) *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_cluster0.R:40:5:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L40) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims/",sim_pars[1],"-",sim_pars[2],"-",sim_pars[3],"/",sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:41:11:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L41) *style:* **Use <-, not =, for assignment.**
```r
  simpath = getwd()
          ^
```
[R/mbd_ML_cluster0.R:42:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L42) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:43:38:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L43) *style:* **Commas should always have a space after.**
```r
  datapath <- paste(simpath, "/data",sep = '')
                                     ^
```
[R/mbd_ML_cluster0.R:43:44:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L43) *style:* **Only use double-quotes.**
```r
  datapath <- paste(simpath, "/data",sep = '')
                                           ^~
```
[R/mbd_ML_cluster0.R:44:51:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L44) *style:* **Commas should always have a space after.**
```r
  load(file = paste(datapath, "/general_settings",sep = ''))
                                                  ^
```
[R/mbd_ML_cluster0.R:44:57:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L44) *style:* **Only use double-quotes.**
```r
  load(file = paste(datapath, "/general_settings",sep = ''))
                                                        ^~
```
[R/mbd_ML_cluster0.R:45:43:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L45) *style:* **Commas should always have a space after.**
```r
  load(file = paste(datapath, "/sim_data",sep = ''))
                                          ^
```
[R/mbd_ML_cluster0.R:45:49:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L45) *style:* **Only use double-quotes.**
```r
  load(file = paste(datapath, "/sim_data",sep = ''))
                                                ^~
```
[R/mbd_ML_cluster0.R:47:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L47) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:48:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:48:7:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
      ^
```
[R/mbd_ML_cluster0.R:48:35:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Commas should always have a space after.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                  ^
```
[R/mbd_ML_cluster0.R:48:45:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Commas should always have a space after.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                            ^
```
[R/mbd_ML_cluster0.R:48:51:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Only use double-quotes.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                  ^~
```
[R/mbd_ML_cluster0.R:48:55:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                      ^
```
[R/mbd_ML_cluster0.R:48:57:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                        ^
```
[R/mbd_ML_cluster0.R:48:83:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Commas should always have a space after.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                                                ^
```
[R/mbd_ML_cluster0.R:48:93:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Commas should always have a space after.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                                                ^
```
[R/mbd_ML_cluster0.R:48:99:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Only use double-quotes.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                                                ^~
```
[R/mbd_ML_cluster0.R:48:103:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L48) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if ( !file.exists(paste(simpath,"/errors",sep = '')) ){dir.create(paste(simpath,"/errors",sep = ''))}
                                                                                ^
```
[R/mbd_ML_cluster0.R:49:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
  sink(file = paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = ''), append = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:49:29:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L49) *style:* **Commas should always have a space after.**
```r
  sink(file = paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = ''), append = T)
                            ^
```
[R/mbd_ML_cluster0.R:49:54:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L49) *style:* **Commas should always have a space after.**
```r
  sink(file = paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = ''), append = T)
                                                     ^
```
[R/mbd_ML_cluster0.R:49:56:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L49) *style:* **Commas should always have a space after.**
```r
  sink(file = paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = ''), append = T)
                                                       ^
```
[R/mbd_ML_cluster0.R:49:63:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L49) *style:* **Commas should always have a space after.**
```r
  sink(file = paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = ''), append = T)
                                                              ^
```
[R/mbd_ML_cluster0.R:49:69:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L49) *style:* **Only use double-quotes.**
```r
  sink(file = paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = ''), append = T)
                                                                    ^~
```
[R/mbd_ML_cluster0.R:50:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:54:14:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L54) *style:* **Put spaces around all infix operators.**
```r
    idparsopt=idparsopt,
            ~^~
```
[R/mbd_ML_cluster0.R:61:13:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L61) *style:* **Put spaces around all infix operators.**
```r
    res = 10*(1+length(brts)+missnumspec),
           ~^~
```
[R/mbd_ML_cluster0.R:61:14:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    res = 10*(1+length(brts)+missnumspec),
             ^
```
[R/mbd_ML_cluster0.R:61:16:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L61) *style:* **Put spaces around all infix operators.**
```r
    res = 10*(1+length(brts)+missnumspec),
              ~^~
```
[R/mbd_ML_cluster0.R:61:29:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L61) *style:* **Put spaces around all infix operators.**
```r
    res = 10*(1+length(brts)+missnumspec),
                           ~^~
```
[R/mbd_ML_cluster0.R:65:19:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L65) *style:* **Only use double-quotes.**
```r
    optimmethod = 'subplex'
                  ^~~~~~~~~
```
[R/mbd_ML_cluster0.R:67:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L67) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:69:20:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L69) *style:* **Use <-, not =, for assignment.**
```r
  how_many_multiple=percent_multiple <- -1;
                   ^
```
[R/mbd_ML_cluster0.R:69:20:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L69) *style:* **Put spaces around all infix operators.**
```r
  how_many_multiple=percent_multiple <- -1;
                  ~^~
```
[R/mbd_ML_cluster0.R:71:14:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L71) *warning:* **no visible binding for global variable ‘sim_data’**
```r
    test0 <- sim_data[[s]][-1]; #actual branching events
             ^~~~~~~~
```
[R/mbd_ML_cluster0.R:72:25:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L72) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                        ^
```
[R/mbd_ML_cluster0.R:72:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L72) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    test1 <- duplicated( test0 ); #additional species
                              ^
```
[R/mbd_ML_cluster0.R:75:9:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L75) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(test1[iii] == TRUE) {
        ^
```
[R/mbd_ML_cluster0.R:79:22:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L79) *style:* **Use <-, not =, for assignment.**
```r
    how_many_multiple=sum(test2);
                     ^
```
[R/mbd_ML_cluster0.R:79:22:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L79) *style:* **Put spaces around all infix operators.**
```r
    how_many_multiple=sum(test2);
                    ~^~
```
[R/mbd_ML_cluster0.R:80:42:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L80) *style:* **Put spaces around all infix operators.**
```r
    percent_multiple <- how_many_multiple/length(test2);
                                        ~^~
```
[R/mbd_ML_cluster0.R:82:5:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L82) *style:* **Commented code should be removed.**
```r
  # additional_species = sum( duplicated(sim_data[[s]]) );
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:83:18:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L83) *warning:* **no visible binding for global variable ‘sim_data’**
```r
  tips <- length(sim_data[[s]])+1;
                 ^~~~~~~~
```
[R/mbd_ML_cluster0.R:83:32:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L83) *style:* **Put spaces around all infix operators.**
```r
  tips <- length(sim_data[[s]])+1;
                              ~^~
```
[R/mbd_ML_cluster0.R:84:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L84) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:85:25:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L85) *style:* **Put spaces around all infix operators.**
```r
  out <- c(res[1:(n_pars+1)],how_many_multiple,tips,percent_multiple,s);
                       ~^~
```
[R/mbd_ML_cluster0.R:85:30:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L85) *style:* **Commas should always have a space after.**
```r
  out <- c(res[1:(n_pars+1)],how_many_multiple,tips,percent_multiple,s);
                             ^
```
[R/mbd_ML_cluster0.R:85:48:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L85) *style:* **Commas should always have a space after.**
```r
  out <- c(res[1:(n_pars+1)],how_many_multiple,tips,percent_multiple,s);
                                               ^
```
[R/mbd_ML_cluster0.R:85:53:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L85) *style:* **Commas should always have a space after.**
```r
  out <- c(res[1:(n_pars+1)],how_many_multiple,tips,percent_multiple,s);
                                                    ^
```
[R/mbd_ML_cluster0.R:85:70:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L85) *style:* **Commas should always have a space after.**
```r
  out <- c(res[1:(n_pars+1)],how_many_multiple,tips,percent_multiple,s);
                                                                     ^
```
[R/mbd_ML_cluster0.R:86:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L86) *style:* **Lines should not be more than 80 characters.**
```r
  out2 <- out;#names(out2)=c("lambda","mu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:86:16:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L86) *style:* **Commented code should be removed.**
```r
  out2 <- out;#names(out2)=c("lambda","mu","q","LL","species born from multiple events","number of tips","percentage of species born from multiple events","tree id")
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:87:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *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_cluster0.R:87:14:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *style:* **Use <-, not =, for assignment.**
```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_cluster0.R:87:14:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *style:* **Put spaces around all infix operators.**
```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_cluster0.R:87:26:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *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_cluster0.R:87:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *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_cluster0.R:87:67:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *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_cluster0.R:87:84:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *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_cluster0.R:87:134:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L87) *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_cluster0.R:89:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L89) *style:* **Commented code should be removed.**
```r
  #out[1] = lambda
   ^~~~~~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:90:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L90) *style:* **Commented code should be removed.**
```r
  #out[2] = mu
   ^~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:91:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L91) *style:* **Commented code should be removed.**
```r
  #out[3] = q
   ^~~~~~~~~~
```
[R/mbd_ML_cluster0.R:92:4:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L92) *style:* **Commented code should be removed.**
```r
  #out[4] = LL
   ^~~~~~~~~~~
```
[R/mbd_ML_cluster0.R:99:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L99) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/mbd_ML_cluster0.R:105:26:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L105) *style:* **Commas should always have a space after.**
```r
    file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),
                         ^
```
[R/mbd_ML_cluster0.R:105:37:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L105) *style:* **Commas should always have a space after.**
```r
    file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),
                                    ^
```
[R/mbd_ML_cluster0.R:105:39:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L105) *style:* **Commas should always have a space after.**
```r
    file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),
                                      ^
```
[R/mbd_ML_cluster0.R:105:46:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L105) *style:* **Commas should always have a space after.**
```r
    file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),
                                             ^
```
[R/mbd_ML_cluster0.R:105:52:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L105) *style:* **Only use double-quotes.**
```r
    file = paste(simpath,"/mbd_MLE",s,".txt",sep = ''),
                                                   ^~
```
[R/mbd_ML_cluster0.R:108:23:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L108) *style:* **Trailing whitespace is superfluous.**
```r
    col.names = FALSE,
                      ^
```
[R/mbd_ML_cluster0.R:111:24:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L111) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != c(-1,-1,-1,-1)) {
                       ^
```
[R/mbd_ML_cluster0.R:111:27:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L111) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != c(-1,-1,-1,-1)) {
                          ^
```
[R/mbd_ML_cluster0.R:111:30:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L111) *style:* **Commas should always have a space after.**
```r
  if (res[1:4] != c(-1,-1,-1,-1)) {
                             ^
```
[R/mbd_ML_cluster0.R:114:23:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L114) *style:* **Commas should always have a space after.**
```r
        paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '')
                      ^
```
[R/mbd_ML_cluster0.R:114:48:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L114) *style:* **Commas should always have a space after.**
```r
        paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '')
                                               ^
```
[R/mbd_ML_cluster0.R:114:50:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L114) *style:* **Commas should always have a space after.**
```r
        paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '')
                                                 ^
```
[R/mbd_ML_cluster0.R:114:57:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L114) *style:* **Commas should always have a space after.**
```r
        paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '')
                                                        ^
```
[R/mbd_ML_cluster0.R:114:63:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L114) *style:* **Only use double-quotes.**
```r
        paste(simpath,"/errors/mbd_MLE_errors",s,".txt",sep = '')
                                                              ^~
```
[R/mbd_ML_cluster0.R:115:8:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/mbd_ML_cluster0.R#L115) *style:* **Trailing whitespace is superfluous.**
```r
      )
       ^~
```
[R/pmb_ml_cluster.R:10:1:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/pmb_ml_cluster.R#L10) *style:* **Variable or function name should be snake_case.**
```r
pmb_ML_cluster <- function(
^~~~~~~~~~~~~~
```
[R/pmb_ml_cluster.R:16:3:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/pmb_ml_cluster.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  mbd_ML,
  ^~~~~~
```
[R/pmb_ml_cluster.R:24:26:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                         ^
```
[R/pmb_ml_cluster.R:24:31:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                              ^
```
[R/pmb_ml_cluster.R:24:36:](https://github.com/richelbilderbeek/razzo/blob/a92a34ad76e4d15ec21f61c3a3b76d0d13289c1a/R/pmb_ml_cluster.R#L24) *style:* **Commas should always have a space after.**
```r
  parnames <- c("lambda","mu","nu","q"); Npars <- length(parnames)
                                   ^
```


For the reviewer

Describe the audience for the text.
Beginners learning to use Spredfast.

Is it clear who it is written for?
Yes, the intended audience is clearly someone in a marketing field or public relations field that is learning to use a knew tool in order to manage media.

Could it be clearer?
The audience is clearly stated in the introduction paragraph so I don't think it could be clearer.

If it is clear, does the text serve that audience at all points?
The text does serve the audience at all points. The language is very easy to understand and the instructions are easy to follow. I think images could improve the instructional document if they were to help show the step by step process of creating an account and using the tool in action.

Is the process chosen sufficiently complex to sustain the project, or is it too simple?
The process is sufficient in complexity to the project because it's explaining how to use a brand new tool. Many people reading this will be fairly new to the subject and it will be alot to absorb. So the instructional process will definitely be useful to the user.

Could you follow the instructions at all points?
The instructions were very clear throughout the document. Her ideas were concise and easy to follow.

Is there anything you don't understand, or could not follow?
No, the document was easy to read.

Does the document include all required elements, or a plan to add them?
Yes.


This should be the same as the original file you pulled from Matthew Kim but it was changed once and returned back to the original to make the pull request possible.


Also this bit `"lower(cuisine) = lower(?)"` isn't in the course, but basically means you can put in "chicken" or "Chicken" and it'll still match


@lomlonde - Be aware that calling this will increment the counter immediately, so you never see it at 0. Calling `showCounter()` here instead just displays value, and then you can call `incrementCounter()` from the console (or eventually attach it to a browser event like a click or key press).


Umm yeah, it's quite odd. So thank you for the info but I'm not sure whether having `make update-unicode` and `make update-gems` help the situation or not, since we don't know the root cause of it.


For the writer

Before passing your draft to your peer for review, take a moment to add a comment - either at the top of the document itself, or in a comment. Describe the state of the draft (incomplete, rough, or polished) and what you're most hoping to get feedback on.

For the reviewer

In reviewing your peer's draft, be sure to follow all guidelines from the reading for today. Then copy the questions below and answer them in a comment on the draft.

•Describe the audience for the text.
The audience seems like they are completely new to riding a horse, and have no prior knowledge to riding a horse.

Is it clear who it is written for?
It does not specifically say who the instructions are meant for. I would draw attention in a line in the intro with either bold or italics and specifically say who it is meant for.

Could it be clearer?
The intro could be clearer who it is written for and why they should want/need to know how to ride a horse.

If it is clear, does the text serve that audience at all points?
The text is simple enough that novice horse riders would understand the language fairly easy.

•Is the process chosen sufficiently complex to sustain the project, or is it too simple?
The process is complex enough to sustain enough instructions, but also simple enough to easily explain. Riding a horse takes several steps and they are drawn out well throughout the paper.

•Could you follow the instructions at all points?
Yes

Is there anything you don't understand, or could not follow?
Maybe just better organization and formatting, but the steps are easy to follow as they are written.

•Does the document include all required elements, or a plan to add them?
It is missing FAQ and pitfalls section, and intro paragraphs may need expansion for listing safety, background, and jargon. They are planned to be added in though.

Braden Farris


Copy of this build can be found at https://www.mewbuilds.com/build/4d6ff9c6d9c54d166ecea2c9a074dd7311ca111a/index.html