[R/add_alignments.R:7:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L7) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/add_alignments.R:10:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.na(file$species_trees_with_outgroup[1])) {
    ^
```
[R/add_alignments.R:11:25:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L11) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," needs a species_trees_with_outgroup",sep=""))
                        ^
```
[R/add_alignments.R:11:34:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L11) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," needs a species_trees_with_outgroup",sep=""))
                                 ^
```
[R/add_alignments.R:11:73:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L11) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," needs a species_trees_with_outgroup",sep=""))
                                                                        ^
```
[R/add_alignments.R:11:76:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L11) *style:* **Put spaces around all infix operators.**
```r
    print(paste("file ",filename," needs a species_trees_with_outgroup",sep=""))
                                                                          ~^~
```
[R/add_alignments.R:15:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L15) *style:* **lines should not be more than 80 characters.**
```r
  rng_seed <- as.numeric(parameters$rng_seed[2]) # the extinction rate of incipient species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_alignments.R:21:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L21) *style:* **lines should not be more than 80 characters.**
```r
  testit::assert(length(file$alignments) == n_alignments * n_species_trees_samples)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_alignments.R:22:19:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L22) *style:* **Commas should always have a space after.**
```r
  for (i in seq(1,n_species_trees_samples)) {
                  ^
```
[R/add_alignments.R:25:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L25) *style:* **lines should not be more than 80 characters.**
```r
      print(paste("species_trees_with_outgroup[[", i, "]] is NA. Terminating 'add_alignments'", sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_alignments.R:28:21:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L28) *style:* **Commas should always have a space after.**
```r
    for (j in seq(1,n_alignments)) {
                    ^
```
[R/add_alignments.R:29:31:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L29) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      index <- 1 + (j - 1) + ((i - 1) * n_species_trees_samples)
                              ^
```
[R/add_alignments.R:31:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L31) *style:* **lines should not be more than 80 characters.**
```r
        print(paste("   * Already stored alignment #", j, " for species tree #",i," at index #", index, sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_alignments.R:31:81:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L31) *style:* **Commas should always have a space after.**
```r
        print(paste("   * Already stored alignment #", j, " for species tree #",i," at index #", index, sep = ""))
                                                                                ^
```
[R/add_alignments.R:31:83:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L31) *style:* **Commas should always have a space after.**
```r
        print(paste("   * Already stored alignment #", j, " for species tree #",i," at index #", index, sep = ""))
                                                                                ^
```
[R/add_alignments.R:34:39:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L34) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      new_seed <- rng_seed - 1 + j + ((i - 1) * n_species_trees_samples)
                                      ^
```
[R/add_alignments.R:43:56:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L43) *style:* **Commas should always have a space after.**
```r
      print(paste("   * Created and saved alignments[",index,"]", sep = ""))
                                                       ^
```
[R/add_alignments.R:43:62:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L43) *style:* **Commas should always have a space after.**
```r
      print(paste("   * Created and saved alignments[",index,"]", sep = ""))
                                                             ^
```
[R/add_alignments.R:46:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L46) *style:* **lines should not be more than 80 characters.**
```r
  print(paste("file ",filename," has gotten its ", n_alignments, " alignments (per species tree)",sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_alignments.R:46:23:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L46) *style:* **Commas should always have a space after.**
```r
  print(paste("file ",filename," has gotten its ", n_alignments, " alignments (per species tree)",sep = ""))
                      ^
```
[R/add_alignments.R:46:32:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L46) *style:* **Commas should always have a space after.**
```r
  print(paste("file ",filename," has gotten its ", n_alignments, " alignments (per species tree)",sep = ""))
                               ^
```
[R/add_alignments.R:46:99:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_alignments.R#L46) *style:* **Commas should always have a space after.**
```r
  print(paste("file ",filename," has gotten its ", n_alignments, " alignments (per species tree)",sep = ""))
                                                                                ^
```
[R/add_outgroup_to_phylogeny.R:22:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_outgroup_to_phylogeny.R#L22) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/add_outgroup_to_phylogeny.R:30:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_outgroup_to_phylogeny.R#L30) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/add_outgroup_to_phylogeny.R:46:23:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_outgroup_to_phylogeny.R#L46) *style:* **Commas should always have a space after.**
```r
    edge = matrix(c(2,1),1,2),
                      ^
```
[R/add_outgroup_to_phylogeny.R:46:26:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_outgroup_to_phylogeny.R#L46) *style:* **Commas should always have a space after.**
```r
    edge = matrix(c(2,1),1,2),
                         ^
```
[R/add_outgroup_to_phylogeny.R:46:28:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_outgroup_to_phylogeny.R#L46) *style:* **Commas should always have a space after.**
```r
    edge = matrix(c(2,1),1,2),
                           ^
```
[R/add_pbd_output.R:12:25:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L12) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," already has a pbd_output",sep = ""))
                        ^
```
[R/add_pbd_output.R:12:34:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L12) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," already has a pbd_output",sep = ""))
                                 ^
```
[R/add_pbd_output.R:12:62:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L12) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," already has a pbd_output",sep = ""))
                                                             ^
```
[R/add_pbd_output.R:17:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L17) *style:* **lines should not be more than 80 characters.**
```r
  species_initiation_rate_good_species  <- as.numeric(parameters$species_initiation_rate_good_species[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:17:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L17) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  species_initiation_rate_good_species  <- as.numeric(parameters$species_initiation_rate_good_species[2])
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:17:66:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L17) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  species_initiation_rate_good_species  <- as.numeric(parameters$species_initiation_rate_good_species[2])
                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:18:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L18) *style:* **lines should not be more than 80 characters.**
```r
  species_initiation_rate_incipient_species  <- as.numeric(parameters$species_initiation_rate_incipient_species[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:18:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L18) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  species_initiation_rate_incipient_species  <- as.numeric(parameters$species_initiation_rate_incipient_species[2])
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:18:71:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L18) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  species_initiation_rate_incipient_species  <- as.numeric(parameters$species_initiation_rate_incipient_species[2])
                                                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:19:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L19) *style:* **lines should not be more than 80 characters.**
```r
  speciation_completion_rate <- as.numeric(parameters$speciation_completion_rate[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:20:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L20) *style:* **lines should not be more than 80 characters.**
```r
  extinction_rate_good_species <- as.numeric(parameters$extinction_rate_good_species[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:21:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L21) *style:* **lines should not be more than 80 characters.**
```r
  extinction_rate_incipient_species <- as.numeric(parameters$extinction_rate_incipient_species[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:21:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  extinction_rate_incipient_species <- as.numeric(parameters$extinction_rate_incipient_species[2])
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:21:62:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  extinction_rate_incipient_species <- as.numeric(parameters$extinction_rate_incipient_species[2])
                                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:25:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L25) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    species_initiation_rate_good_species,
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:27:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    species_initiation_rate_incipient_species,
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:29:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    extinction_rate_incipient_species
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:38:4:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L38) *style:* **Commented code should be removed.**
```r
  #phylogeny <- pbd_output$tree
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:39:4:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L39) *style:* **Commented code should be removed.**
```r
  #file$pbd_output <- pbd_output
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_pbd_output.R:40:16:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L40) *style:* **Commas should always have a space after.**
```r
  saveRDS(file,file = filename)
               ^
```
[R/add_pbd_output.R:41:43:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L41) *style:* **Commas should always have a space after.**
```r
  print(paste("Added pbd_output to file ",filename,sep = ""))
                                          ^
```
[R/add_pbd_output.R:41:52:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_pbd_output.R#L41) *style:* **Commas should always have a space after.**
```r
  print(paste("Added pbd_output to file ",filename,sep = ""))
                                                   ^
```
[R/add_posteriors.R:7:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L7) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/add_posteriors.R:17:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L17) *style:* **lines should not be more than 80 characters.**
```r
  n_species_trees_samples <- as.numeric(file$parameters$n_species_trees_samples[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:18:19:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L18) *style:* **Commas should always have a space after.**
```r
  for (i in seq(1,n_species_trees_samples)) {
                  ^
```
[R/add_posteriors.R:19:21:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L19) *style:* **Commas should always have a space after.**
```r
    for (j in seq(1,n_alignments)) {
                    ^
```
[R/add_posteriors.R:20:41:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      alignment_index <- 1 + (j - 1) + ((i - 1) * n_species_trees_samples)
                                        ^
```
[R/add_posteriors.R:21:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L21) *style:* **lines should not be more than 80 characters.**
```r
      testit::assert(alignment_index >= 1 && alignment_index <= length(file$alignments))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:24:23:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L24) *style:* **Commas should always have a space after.**
```r
      for (k in seq(1,n_beast_runs)) {
                      ^
```
[R/add_posteriors.R:25:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L25) *style:* **lines should not be more than 80 characters.**
```r
        posterior_index <- 1 + (k - 1) + ((j - 1) * n_alignments) + ((i - 1) * n_alignments * n_species_trees_samples)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:25:43:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        posterior_index <- 1 + (k - 1) + ((j - 1) * n_alignments) + ((i - 1) * n_alignments * n_species_trees_samples)
                                          ^
```
[R/add_posteriors.R:25:70:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        posterior_index <- 1 + (k - 1) + ((j - 1) * n_alignments) + ((i - 1) * n_alignments * n_species_trees_samples)
                                                                     ^
```
[R/add_posteriors.R:26:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L26) *style:* **lines should not be more than 80 characters.**
```r
        testit::assert(posterior_index >= 1 && posterior_index <= length(file$posteriors))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:28:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L28) *style:* **lines should not be more than 80 characters.**
```r
          print(paste("   * Posterior #", k, " for alignment #", j," for species tree #", i," at posterior_index #", posterior_index, " already has a posterior", sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:28:68:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L28) *style:* **Commas should always have a space after.**
```r
          print(paste("   * Posterior #", k, " for alignment #", j," for species tree #", i," at posterior_index #", posterior_index, " already has a posterior", sep = ""))
                                                                   ^
```
[R/add_posteriors.R:28:93:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L28) *style:* **Commas should always have a space after.**
```r
          print(paste("   * Posterior #", k, " for alignment #", j," for species tree #", i," at posterior_index #", posterior_index, " already has a posterior", sep = ""))
                                                                                ^
```
[R/add_posteriors.R:34:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L34) *style:* **lines should not be more than 80 characters.**
```r
        basefilename <- paste(basename(tools::file_path_sans_ext(filename)), "_", i,"_", j, "_", k,sep = "")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:34:85:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L34) *style:* **Commas should always have a space after.**
```r
        basefilename <- paste(basename(tools::file_path_sans_ext(filename)), "_", i,"_", j, "_", k,sep = "")
                                                                                ^
```
[R/add_posteriors.R:34:100:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L34) *style:* **Commas should always have a space after.**
```r
        basefilename <- paste(basename(tools::file_path_sans_ext(filename)), "_", i,"_", j, "_", k,sep = "")
                                                                                ^
```
[R/add_posteriors.R:41:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L41) *style:* **lines should not be more than 80 characters.**
```r
        print(paste("   * Storing posterior #", k, " for alignment #", j," for species tree #",i," at posterior_index #", posterior_index, sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_posteriors.R:41:74:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L41) *style:* **Commas should always have a space after.**
```r
        print(paste("   * Storing posterior #", k, " for alignment #", j," for species tree #",i," at posterior_index #", posterior_index, sep = ""))
                                                                         ^
```
[R/add_posteriors.R:41:96:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L41) *style:* **Commas should always have a space after.**
```r
        print(paste("   * Storing posterior #", k, " for alignment #", j," for species tree #",i," at posterior_index #", posterior_index, sep = ""))
                                                                                ^
```
[R/add_posteriors.R:41:98:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_posteriors.R#L41) *style:* **Commas should always have a space after.**
```r
        print(paste("   * Storing posterior #", k, " for alignment #", j," for species tree #",i," at posterior_index #", posterior_index, sep = ""))
                                                                                ^
```
[R/add_species_trees_with_outgroup.R:12:25:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L12) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," needs a pbd_output",sep = ""))
                        ^
```
[R/add_species_trees_with_outgroup.R:12:34:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L12) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," needs a pbd_output",sep = ""))
                                 ^
```
[R/add_species_trees_with_outgroup.R:12:56:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L12) *style:* **Commas should always have a space after.**
```r
    print(paste("file ",filename," needs a pbd_output",sep = ""))
                                                       ^
```
[R/add_species_trees_with_outgroup.R:18:61:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L18) *style:* **Commas should always have a space after.**
```r
  print(paste("Adding species_trees_with_outgroup to file ",filename,sep = ""))
                                                            ^
```
[R/add_species_trees_with_outgroup.R:18:70:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L18) *style:* **Commas should always have a space after.**
```r
  print(paste("Adding species_trees_with_outgroup to file ",filename,sep = ""))
                                                                     ^
```
[R/add_species_trees_with_outgroup.R:22:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L22) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/add_species_trees_with_outgroup.R:23:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L23) *style:* **lines should not be more than 80 characters.**
```r
      print(paste(" * species_trees_with_outgroup[",i,"] already exists",sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:23:53:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L23) *style:* **Commas should always have a space after.**
```r
      print(paste(" * species_trees_with_outgroup[",i,"] already exists",sep = ""))
                                                    ^
```
[R/add_species_trees_with_outgroup.R:23:55:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L23) *style:* **Commas should always have a space after.**
```r
      print(paste(" * species_trees_with_outgroup[",i,"] already exists",sep = ""))
                                                      ^
```
[R/add_species_trees_with_outgroup.R:23:74:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L23) *style:* **Commas should always have a space after.**
```r
      print(paste(" * species_trees_with_outgroup[",i,"] already exists",sep = ""))
                                                                         ^
```
[R/add_species_trees_with_outgroup.R:27:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L27) *style:* **lines should not be more than 80 characters.**
```r
    set.seed(rng_seed + i) # Each species tree is generated from its own RNG seed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:28:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L28) *style:* **lines should not be more than 80 characters.**
```r
    species_tree <- sample_species_trees_from_pbd_sim_output(n = 1,file$pbd_output)[[1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:28:68:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L28) *style:* **Commas should always have a space after.**
```r
    species_tree <- sample_species_trees_from_pbd_sim_output(n = 1,file$pbd_output)[[1]]
                                                                   ^
```
[R/add_species_trees_with_outgroup.R:29:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L29) *style:* **lines should not be more than 80 characters.**
```r
    species_tree_with_outgroup <- add_outgroup_to_phylogeny(species_tree,stem_length = 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:29:74:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L29) *style:* **Commas should always have a space after.**
```r
    species_tree_with_outgroup <- add_outgroup_to_phylogeny(species_tree,stem_length = 0)
                                                                         ^
```
[R/add_species_trees_with_outgroup.R:32:18:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L32) *style:* **Commas should always have a space after.**
```r
    saveRDS(file,file = filename)
                 ^
```
[R/add_species_trees_with_outgroup.R:34:60:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L34) *style:* **Commas should always have a space after.**
```r
  print(paste("Added species_trees_with_outgroup to file ",filename,sep = ""))
                                                           ^
```
[R/add_species_trees_with_outgroup.R:34:69:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/add_species_trees_with_outgroup.R#L34) *style:* **Commas should always have a space after.**
```r
  print(paste("Added species_trees_with_outgroup to file ",filename,sep = ""))
                                                                    ^
```
[R/check_progress.R:7:38:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/check_progress.R#L7) *warning:* **Do not use absolute paths.**
```r
check_progress <- function(folder = "~/Slurm/") {
                                     ^~~~~~~~
```
[R/convert_alignment_to_beast_input_file.R:29:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_input_file.R#L29) *style:* **lines should not be more than 80 characters.**
```r
  options(scipen = 20) # So that mcmc_chainlength is written as 1000000 instead of 1e+7
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_posterior.R:55:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L55) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/convert_alignment_to_beast_posterior.R:62:49:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L62) *style:* **Commas should always have a space after.**
```r
  beast_filename <- paste(base_filename, ".xml",sep = "");
                                                ^
```
[R/convert_alignment_to_beast_posterior.R:64:53:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L64) *style:* **Commas should always have a space after.**
```r
  beast_log_filename <- paste(base_filename, ".log",sep = "");
                                                    ^
```
[R/convert_alignment_to_beast_posterior.R:65:57:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L65) *style:* **Commas should always have a space after.**
```r
  beast_trees_filename <- paste(base_filename, ".trees",sep = "");
                                                        ^
```
[R/convert_alignment_to_beast_posterior.R:66:61:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L66) *style:* **Commas should always have a space after.**
```r
  beast_state_filename <- paste(base_filename, ".xml.state",sep = "");
                                                            ^
```
[R/convert_alignment_to_beast_posterior.R:67:56:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L67) *style:* **Commas should always have a space after.**
```r
  temp_fasta_filename <- paste(base_filename, ".fasta",sep = "");
                                                       ^
```
[R/convert_alignment_to_beast_posterior.R:84:35:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L84) *style:* **Commas should always have a space after.**
```r
    print(paste("NOTE: removed '",beast_trees_filename, "'"), sep = "")
                                  ^
```
[R/convert_alignment_to_beast_posterior.R:88:35:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L88) *style:* **Commas should always have a space after.**
```r
    print(paste("NOTE: removed '",beast_log_filename, "'"), sep = "")
                                  ^
```
[R/convert_alignment_to_beast_posterior.R:92:35:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L92) *style:* **Commas should always have a space after.**
```r
    print(paste("NOTE: removed '",beast_state_filename, "'"), sep = "")
                                  ^
```
[R/convert_alignment_to_beast_posterior.R:99:3:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_alignment_to_beast_posterior.R#L99) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/convert_phylogeny_to_alignment.R:24:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/convert_phylogeny_to_alignment.R#L24) *style:* **lines should not be more than 80 characters.**
```r
      "parameter 'sequence_length' must be a non-zero and positive integer value"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_paths.R:62:6:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/find_paths.R#L62) *warning:* **Do not use absolute paths.**
```r
    "~/GitHubs/Cer2016/inst/extdata/is_beast_posterior.trees",
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_paths.R:67:32:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/find_paths.R#L67) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (file.exists(filename)) { return (filename) }
                               ^
```
[R/find_paths.R:67:52:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/find_paths.R#L67) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if (file.exists(filename)) { return (filename) }
                                                   ^
```
[R/is_beast_posterior.R:14:40:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_beast_posterior.R#L14) *style:* **Commas should always have a space after.**
```r
  valid_names <- grep(valid_name_regex,names(x), perl = TRUE, value = TRUE)
                                       ^
```
[R/is_beast_posterior.R:19:40:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_beast_posterior.R#L19) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (is.unsorted(as.numeric(values))) { return (FALSE) }
                                       ^
```
[R/is_beast_posterior.R:19:57:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_beast_posterior.R#L19) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (is.unsorted(as.numeric(values))) { return (FALSE) }
                                                        ^
```
[R/is_valid_file.R:11:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L11) *style:* **lines should not be more than 80 characters.**
```r
  if (as.numeric(parameters$species_initiation_rate_good_species[2]) < 0.0) return (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_valid_file.R:11:29:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  if (as.numeric(parameters$species_initiation_rate_good_species[2]) < 0.0) return (FALSE)
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_valid_file.R:12:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L12) *style:* **lines should not be more than 80 characters.**
```r
  if (as.numeric(parameters$species_initiation_rate_incipient_species[2]) < 0.0) return (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_valid_file.R:12:29:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  if (as.numeric(parameters$species_initiation_rate_incipient_species[2]) < 0.0) return (FALSE)
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_valid_file.R:14:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L14) *style:* **lines should not be more than 80 characters.**
```r
  if (as.numeric(parameters$extinction_rate_good_species[2]) < 0.0) return (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_valid_file.R:15:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L15) *style:* **lines should not be more than 80 characters.**
```r
  if (as.numeric(parameters$extinction_rate_incipient_species[2]) < 0.0) return (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_valid_file.R:15:29:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/is_valid_file.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  if (as.numeric(parameters$extinction_rate_incipient_species[2]) < 0.0) return (FALSE)
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_alignments.R:12:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L12) *style:* **lines should not be more than 80 characters.**
```r
  n_species_trees_samples <- as.numeric(file$parameters$n_species_trees_samples[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_alignments.R:14:19:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L14) *style:* **Commas should always have a space after.**
```r
  for (i in seq(1,n_species_trees_samples)) {
                  ^
```
[R/plot_alignments.R:15:21:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L15) *style:* **Commas should always have a space after.**
```r
    for (j in seq(1,n_alignments)) {
                    ^
```
[R/plot_alignments.R:16:39:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      alignment_index <- 1 + j - 1 + ((i - 1) * n_species_trees_samples)
                                      ^
```
[R/plot_alignments.R:19:31:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L19) *style:* **Commas should always have a space after.**
```r
      png(paste(base_filename,"_alignment_", i, "_", j, ".png", sep = ""))
                              ^
```
[R/plot_alignments.R:21:36:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L21) *style:* **Commas should always have a space after.**
```r
        main = paste(base_filename,"alignment",i,j)
                                   ^
```
[R/plot_alignments.R:21:48:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L21) *style:* **Commas should always have a space after.**
```r
        main = paste(base_filename,"alignment",i,j)
                                               ^
```
[R/plot_alignments.R:21:50:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_alignments.R#L21) *style:* **Commas should always have a space after.**
```r
        main = paste(base_filename,"alignment",i,j)
                                                 ^
```
[R/plot_beast_repeatabilities.R:16:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L16) *style:* **lines should not be more than 80 characters.**
```r
  for (trees_filename in list.files(path = ".", pattern = "^(toy_example|example|article)_.*_1\\.trees")) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:17:45:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L17) *style:* **Commas should always have a space after.**
```r
    other_trees_filename <- gsub("_1.trees","_2.trees", trees_filename)
                                            ^
```
[R/plot_beast_repeatabilities.R:20:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L20) *style:* **lines should not be more than 80 characters.**
```r
    parameter_filename <- substr(parameter_filename,1,nchar(parameter_filename) - 6)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:20:53:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L20) *style:* **Commas should always have a space after.**
```r
    parameter_filename <- substr(parameter_filename,1,nchar(parameter_filename) - 6)
                                                    ^
```
[R/plot_beast_repeatabilities.R:20:55:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L20) *style:* **Commas should always have a space after.**
```r
    parameter_filename <- substr(parameter_filename,1,nchar(parameter_filename) - 6)
                                                      ^
```
[R/plot_beast_repeatabilities.R:21:52:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L21) *style:* **Commas should always have a space after.**
```r
    parameter_filename <- paste(parameter_filename,".RDa", sep = "")
                                                   ^
```
[R/plot_beast_repeatabilities.R:24:41:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L24) *style:* **Commas should always have a space after.**
```r
    png_filename <- substr(png_filename,1,nchar(png_filename) - 2)
                                        ^
```
[R/plot_beast_repeatabilities.R:24:43:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L24) *style:* **Commas should always have a space after.**
```r
    png_filename <- substr(png_filename,1,nchar(png_filename) - 2)
                                          ^
```
[R/plot_beast_repeatabilities.R:25:40:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L25) *style:* **Commas should always have a space after.**
```r
    png_filename <- paste(png_filename,"_beast_repeatability.png", sep = "")
                                       ^
```
[R/plot_beast_repeatabilities.R:27:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L27) *style:* **lines should not be more than 80 characters.**
```r
    print(paste(trees_filename,other_trees_filename,parameter_filename, png_filename))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:27:32:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L27) *style:* **Commas should always have a space after.**
```r
    print(paste(trees_filename,other_trees_filename,parameter_filename, png_filename))
                               ^
```
[R/plot_beast_repeatabilities.R:27:53:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L27) *style:* **Commas should always have a space after.**
```r
    print(paste(trees_filename,other_trees_filename,parameter_filename, png_filename))
                                                    ^
```
[R/plot_beast_repeatabilities.R:29:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L29) *style:* **Commented code should be removed.**
```r
    # parameter_file <- read_file(parameter_filename)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:32:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L32) *style:* **Commented code should be removed.**
```r
    # png(png_filename)
      ^~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:33:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L33) *style:* **lines should not be more than 80 characters.**
```r
    # nLTT.plot(phy = parameter_file$species_trees_with_outgroup[[1]][[1]],replot = TRUE,lty=1,lwd = 1, main="Repeatability BEAST runs")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:33:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L33) *style:* **Commented code should be removed.**
```r
    # nLTT.plot(phy = parameter_file$species_trees_with_outgroup[[1]][[1]],replot = TRUE,lty=1,lwd = 1, main="Repeatability BEAST runs")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:34:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L34) *style:* **lines should not be more than 80 characters.**
```r
    # get_average_nltt(beast2out.read.trees(trees_filename),       replot = TRUE, lty = 3, lwd = 1, col = "red")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:34:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L34) *style:* **Commented code should be removed.**
```r
    # get_average_nltt(beast2out.read.trees(trees_filename),       replot = TRUE, lty = 3, lwd = 1, col = "red")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:35:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L35) *style:* **lines should not be more than 80 characters.**
```r
    # get_average_nltt(beast2out.read.trees(other_trees_filename), replot = TRUE, lty = 3, lwd = 1, col = "blue")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:35:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L35) *style:* **Commented code should be removed.**
```r
    # get_average_nltt(beast2out.read.trees(other_trees_filename), replot = TRUE, lty = 3, lwd = 1, col = "blue")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:39:9:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L39) *style:* **Commented code should be removed.**
```r
    #   lwd=c(1,1)
        ^~~~~~~~~~
```
[R/plot_beast_repeatabilities.R:41:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L41) *style:* **Commented code should be removed.**
```r
    # dev.off()
      ^~~~~~~~~
```
[R/plot_beast_repeatabilities.R:46:2:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_beast_repeatabilities.R#L46) *style:* **Commented code should be removed.**
```r
#setwd("~/GitHubs/R/Peregrine")
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_gene_tree.R:5:27:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree.R#L5) *style:* **Commas should always have a space after.**
```r
  png(paste(base_filename,"_gene_tree.png", sep = ""))
                          ^
```
[R/plot_gene_tree.R:6:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree.R#L6) *style:* **lines should not be more than 80 characters.**
```r
  plot(file$pbd_output[[1]], main = paste(base_filename, " gene tree", sep = ""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_gene_tree_versus_species_trees.R:9:6:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L9) *style:* **Commented code should be removed.**
```r
    #parameter_filename <- "article_0_1_2_1_0.RDa"
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_gene_tree_versus_species_trees.R:12:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L12) *style:* **Commented code should be removed.**
```r
    # base_filename <- basename(parameter_filename)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_gene_tree_versus_species_trees.R:14:41:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L14) *style:* **Commas should always have a space after.**
```r
    png_filename <- substr(png_filename,1,nchar(png_filename) - 0)
                                        ^
```
[R/plot_gene_tree_versus_species_trees.R:14:43:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L14) *style:* **Commas should always have a space after.**
```r
    png_filename <- substr(png_filename,1,nchar(png_filename) - 0)
                                          ^
```
[R/plot_gene_tree_versus_species_trees.R:25:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L25) *warning:* **local variable 'trees' assigned but may not be used**
```r
    trees <- sample_species_trees_from_pbd_sim_output(n = 100, file$pbd_output)
    ^~~~~
```
[R/plot_gene_tree_versus_species_trees.R:30:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L30) *style:* **lines should not be more than 80 characters.**
```r
    # get_average_nltt(phylogenies = trees, plot_nltts = TRUE, replot = TRUE, col = "red", lty = 3)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_gene_tree_versus_species_trees.R:30:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_gene_tree_versus_species_trees.R#L30) *style:* **Commented code should be removed.**
```r
    # get_average_nltt(phylogenies = trees, plot_nltts = TRUE, replot = TRUE, col = "red", lty = 3)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:4:17:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L4) *style:* **Commas should always have a space after.**
```r
  for (h in c(1,length(filenames))) {
                ^
```
[R/plot_multi_average_nltts.R:9:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L9) *style:* **lines should not be more than 80 characters.**
```r
    n_species_trees_samples <- as.numeric(file$parameters$n_species_trees_samples[2])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:12:21:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L12) *style:* **Commas should always have a space after.**
```r
    for (i in seq(1,n_species_trees_samples)) {
                    ^
```
[R/plot_multi_average_nltts.R:13:23:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L13) *style:* **Commas should always have a space after.**
```r
      for (j in seq(1,n_alignments)) {
                      ^
```
[R/plot_multi_average_nltts.R:14:25:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L14) *style:* **Commas should always have a space after.**
```r
        for (k in seq(1,n_beast_runs)) {
                        ^
```
[R/plot_multi_average_nltts.R:17:43:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L17) *style:* **Commas should always have a space after.**
```r
            base_filename, "_", i, "_", j,"_", k, ".trees", sep = ""
                                          ^
```
[R/plot_multi_average_nltts.R:20:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L20) *style:* **Commented code should be removed.**
```r
          # all_trees <- beast2out.read.trees(trees_filename)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:21:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L21) *style:* **Commented code should be removed.**
```r
          # linetype <- ifelse(h == 1, 1, 3)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:23:1:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L23) *style:* **lines should not be more than 80 characters.**
```r
          #   get_average_nltt(all_trees,replot = FALSE,lty=1,lwd = 2, main="Average nLTTs")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:23:15:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L23) *style:* **Commented code should be removed.**
```r
          #   get_average_nltt(all_trees,replot = FALSE,lty=1,lwd = 2, main="Average nLTTs")
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:25:15:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L25) *style:* **Commented code should be removed.**
```r
          #   get_average_nltt(all_trees,replot = TRUE, lty = linetype,lwd = 2)
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_average_nltts.R:31:14:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L31) *style:* **Commas should always have a space after.**
```r
  legend(0.7,0.3, # Top left
             ^
```
[R/plot_multi_average_nltts.R:32:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L32) *style:* **Only use double-quotes.**
```r
    c('BD', 'PBD'), # puts text in the legend
      ^~~~
```
[R/plot_multi_average_nltts.R:32:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_average_nltts.R#L32) *style:* **Only use double-quotes.**
```r
    c('BD', 'PBD'), # puts text in the legend
            ^~~~~
```
[R/plot_multi_nltt_stats_histogram.R:3:5:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L3) *style:* **Commented code should be removed.**
```r
#   data <- data.frame()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:6:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L6) *style:* **Commented code should be removed.**
```r
#     testit::assert(is_valid_file(filename))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:7:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L7) *style:* **Commented code should be removed.**
```r
#     file <- load_parameters_from_file(filename)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:9:9:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L9) *style:* **Commented code should be removed.**
```r
#       file$parameters$n_species_trees_samples[2]
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:11:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L11) *style:* **Commented code should be removed.**
```r
#     n_alignments <- as.numeric(file$parameters$n_alignments[2])
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:12:7:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L12) *style:* **Commented code should be removed.**
```r
#     n_beast_runs <- as.numeric(file$parameters$n_beast_runs[2])
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:16:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L16) *style:* **Commented code should be removed.**
```r
#           base_filename <- basename(filename)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:19:15:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L19) *style:* **Commented code should be removed.**
```r
#             sep = ""
              ^~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:21:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L21) *style:* **Commented code should be removed.**
```r
#           all_trees <- rBEAST::beast2out.read.trees(trees_filename)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:22:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L22) *style:* **Commented code should be removed.**
```r
#           all_nltt_stats <- NULL
            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:26:17:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L26) *style:* **Commented code should be removed.**
```r
#               nLTT::nLTTstat(file$species_trees_with_outgroup[[1]][[1]],tree)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:29:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L29) *style:* **Commented code should be removed.**
```r
#           this_data <- data.frame(length = all_nltt_stats)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:30:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L30) *style:* **Commented code should be removed.**
```r
#           this_data$description <- basename(filename)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_multi_nltt_stats_histogram.R:31:13:](https://github.com/richelbilderbeek/Cer2016/blob/e4f2c415beb758bbbfd8ac53a4308d1875010a12/R/plot_multi_nltt_stats_histogram.R#L31) *style:* **Commented code should be removed.**
```r
#           data <- rbind(data,this_data)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Yasss

On Tue, Apr 19, 2016, 10:55 AM Preston Fox <notifications@github.com> wrote:

> lolololololololol so excite
>
> —
> You are receiving this because you commented.
> Reply to this email directly or view it on GitHub
> <https://github.com/taylordaniellecook/PTSD/commit/4b22997dc70879cfb58691888ce9fdee6a4adc4d#commitcomment-17162871>
>


Probably I can't parse that particular response and there is a `null` or `undefined` in the `response` array.


Here's an example of fail:

```
# play1.yml
- hosts: localhost
  connection: local
  become: False
  gather_facts: no
  tasks:
    - include: play2.yml outer_loop="{{ outer_item }}"
      with_dict:
        foo:
          bar:
            - a
            - b
            - c
      loop_control:
        loop_var: outer_item
```

```
# play2.yml
- debug: var=outer_item

- name: Test the key
  debug: msg="key is {{ outer_item.key }}"

- name: Test the values
  debug: var=item
  with_dict: "{{ outer_item.value.bar }}"
```

and now the run...

```
TASK [debug] *******************************************************************
ok: [localhost] => {
    "outer_item": {
        "key": "foo",
        "value": {
            "bar": [
                "a",
                "b",
                "c"
            ]
        }
    }
}

TASK [Test the key] ************************************************************
ok: [localhost] => {
    "msg": "key is foo"
}

TASK [Test the values] *********************************************************
fatal: [localhost]: FAILED! => {"failed": true, "msg": "with_dict expects a dict"}
        to retry, use: --limit @play1.retry

PLAY RECAP *********************************************************************
localhost                  : ok=3    changed=0    unreachable=0    failed=1
```


It's very good idea to implement it. I think many people asked about this feature.

About optimizations:
- every layer (slice) of fractal should should be saved into PNG file immediately after rendering. This will save a lot of memory (try to imagine how much memory will be needed for 2000x2000x2000 array)
- do not use CalculateDistance but Compute<fractal::calcModeNormal>(fractals, fractIn, &fractOut). This will be faster. When you use Compute() then the result will be sFractalOut.maxiter which is already boolean.
- when you render slices then reduce "Maximum number of fractal iterations", e.g. something between 10 and 50 should be sufficient


Is this something that could be contributed to https://translate.cachethq.io?


Maybe this is because of a missing screenshots.js?


#13 Joined and working.


@jensens Jenkins CI reporting about code analysis
See the full report here: http://jenkins.plone.org/job/package-plone.subrequest/12/violations
```
plone/subrequest/__init__.py:0:1: I001 isort found changes, run it on the file
plone/subrequest/__init__.py:31:5: E301 expected 1 blank line, found 0
plone/subrequest/__init__.py:66:20: Q000 Remove bad quotes.
plone/subrequest/__init__.py:69:1: C901 'subrequest' is too complex (21)
plone/subrequest/__init__.py:70:29: Q000 Remove bad quotes.
plone/subrequest/__init__.py:76:9: Q000 Remove bad quotes.
plone/subrequest/__init__.py:92:25: S001 found %s formatter
plone/subrequest/__init__.py:94:22: S001 found %s formatter
plone/subrequest/__init__.py:150:9: B901 blind except: statement
plone/subrequest/__init__.py:151:30: Q000 Remove bad quotes.
plone/subrequest/__init__.py:151:60: S001 found %s formatter
plone/subrequest/interfaces.py:0:1: C101 Coding magic comment not found
plone/subrequest/interfaces.py:0:1: I001 isort found changes, run it on the file
plone/subrequest/interfaces.py:3:1: E302 expected 2 blank lines, found 1
plone/subrequest/subresponse.py:0:1: I001 isort found changes, run it on the file
plone/subrequest/subresponse.py:20:12: P002 found "hasattr", consider replacing it
plone/subrequest/subresponse.py:21:16: P002 found "hasattr", consider replacing it
plone/subrequest/subresponse.py:22:12: P002 found "hasattr", consider replacing it
plone/subrequest/subresponse.py:48:16: P002 found "hasattr", consider replacing it
plone/subrequest/testing.py:0:1: I001 isort found changes, run it on the file
plone/subrequest/testing.py:51:23: S001 found %s formatter
plone/subrequest/testing.py:87:25: Q000 Remove bad quotes.
plone/subrequest/testing.py:88:17: Q000 Remove bad quotes.
plone/subrequest/testing.py:163:10: Q000 Remove bad quotes.
plone/subrequest/testing.py:167:10: Q000 Remove bad quotes.
plone/subrequest/testing.py:169:1: W391 blank line at end of file
plone/subrequest/tests.py:0:1: I001 isort found changes, run it on the file
plone/subrequest/tests.py:22:5: Q000 Remove bad quotes.
plone/subrequest/tests.py:23:5: Q000 Remove bad quotes.
plone/subrequest/tests.py:42:61: S001 found %s formatter
plone/subrequest/tests.py:50:61: S001 found %s formatter
plone/subrequest/tests.py:58:61: S001 found %s formatter
plone/subrequest/tests.py:147:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:147:51: S001 found %s formatter
plone/subrequest/tests.py:160:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:161:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:172:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:173:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:184:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:185:13: Q000 Remove bad quotes.
plone/subrequest/tests.py:231:46: Q000 Remove bad quotes.
plone/subrequest/tests.py:241:46: Q000 Remove bad quotes.
plone/subrequest/tests.py:251:46: Q000 Remove bad quotes.
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


不美了


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 21805](https://teamcity.mesosphere.io/viewLog.html?buildId=217646&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **FAILURE**
Summary: Tests failed: 1 (1 new), passed: 0, ignored: 276 Build time: 00:14:56
### Failed tests
```
null: Kubernetes e2e suite.[k8s.io] Kubectl client [k8s.io] Guestbook application should create and stop a working application [Conformance]: <no details avaliable>

```


Spec indeed says message boundary but what is the definition of it?


By the way I have used slices when I started with 3D fractals.
Here is an example: http://www.fractalforums.com/3d-fractal-generation/true-3d-mandlebrot-type-fractal/105/


Nice 🤗


OK, that's surprisingly easy!  At the top of the base template, near where the `LANGUAGE_BIDI` variable is set up, put a line saying:

```
{% now "Y" as copyright_year %}
```

then change the copyright notice to say:

```
{% blocktrans %}Copyright {{ copyright_year }} Cadasta. All Rights Reserved.{% endblocktrans %}
```

That way, the translators will get the whole string to translate in one go, which helps with languages where the year goes in a different place relative to the other parts of the string.


Is it safe to assume this will return non-nil in all cases? (Same with `managerForAddress:` below.)


I don't know why the change is necessary. Would you mind explain it? @pm-nsimic


It may be good to meet up and discuss this more thoroughly.   I’m happy to make stuff work however but there’s several way things work today.
-	In .NET Helix runs, we put CoreRun.exe (the host), CoreCLR, api-ms shims, and other runtime-specific stuff in a folder named core_root and run from there, with the current directory set as the folder containing the test DLLs.
o	If we want to put the test’s dependencies on the TPA list, we copy them into core_root
o	If we want to not do so, we copy them into the execution folder and run from there.  This does seem to get honored by CoreRun at least.
-	In local CoreFX runs, everything is effectively put in the same folder, which has two net effects:
o	Framework assemblies are always on the Trusted Platform Assembly List  (in my exploratory run, not doing this did cause a test about TPA to fail)
o	Additional executables brought with tests somehow (not sure on the mechanism here) see that CoreRun.exe is in the same directory as they are and run in .NET Core versus Desktop (this is needed for many tests to be able to pass).
As for how the shared framework works, I had always assumed handling this would simply go in to the .targets that generate the list of dependencies to copy in the first place, simply adding the list of whatever’s in Shared to the Exclude for this, thus making copy commands only be elements that are not in the shared collection, and leaving the shared framework in the Payload directory during execution.
My main goal is to get local and .NET Helix execution in synch, so I’m happy to take specific direction about how you’d like this to work.


I thought plates were either 1 or 8...


`s/scalaporps.Scalaprops/dog.Dog`


Does this explain why our BIST seemed to be backwards?
On Tue, Apr 19, 2016 at 10:16 AM Colm Ryan <notifications@github.com> wrote:

> @blakejohnson <https://github.com/blakejohnson> we goofed not catching
> this earlier. I spent an hour double checking with debug cores and
> everything because there are so many places to get the byte order wrong but
> the scope tells the story:
> [image: waveform_swapped_samples]
> <https://cloud.githubusercontent.com/assets/1385106/14646705/89259988-0628-11e6-8088-0ebfa21c422b.png>
> [image: waveform_fixed_swapped_samples]
> <https://cloud.githubusercontent.com/assets/1385106/14646712/8c4009b4-0628-11e6-9c56-2c4b73b61246.png>
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly or view it on GitHub
> <https://github.com/BBN-Q/libaps2/commit/b070fa4d620386b6a52239bdbab23c1a709c333c#commitcomment-17163199>
>


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 21810](https://teamcity.mesosphere.io/viewLog.html?buildId=217662&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **SUCCESS**
Summary: Tests passed: 1, ignored: 273 Build time: 00:09:02


FunSuite ?


#2 fixed - modified the Data Base and also the PHP code to check for negative account balance for the customers


The robot test for Plone 5.1 are broken after this change: http://jenkins.plone.org/job/plone-5.1-python-2.7-robot/239/
Could it be related?
I have just started a rebuild, in case it is a temporary glitch. Otherwise you may want to revert this change.


No, I'm shooting in the dark. I have no clue what's going on. I'm still doing almost random trials to try to pin down what causes the issue. I think it's related to the number of times we build the target in a short period of time. My best guess is that Ninja needs to access some log file, and it locks it. Now it could be that for some reason the Windows filesystem does not register the fact that Ninja unlocked the file quickly enough. But that's really far fetched, and there's probably a better explanation.

I'll try to keep reducing the failure until I can see clearer.


I did some more tests today and I think isRcAxisWithinDeadband is off the hook.
I checked the adjustments of RC endpoints and noticed that my yaw midpoint is not centered. Hm. So I raised (both) deadband to 15 and run two tests with Beta 2 as released.
Works like a charm.
No need to fix #21; I can here those short beeps during tuning. I got the ready beeps and it saved a new result.

A long and complicated detour to find out that the original solution was not so bad after all.


Haha you're right. Fixed now. Thanks!


> Should already be a problem with 9.0.1

Just upgraded, still seems to work fine.


@Frandias still working on making classes


Can you please clarify?


Will change.


What is this mitigating?


TeamCity OSS :: Kubernetes Mesos :: 4 - Smoke Tests [Build 21807](https://teamcity.mesosphere.io/viewLog.html?buildId=217652&buildTypeId=Oss_KubernetesMesos_5SmokeTestsDockerMesos&guest=1) outcome was **FAILURE**
Summary: Tests failed: 1 (1 new), passed: 0, ignored: 276 Build time: 00:24:06
### Failed tests
```
null: Kubernetes e2e suite.[k8s.io] Kubectl client [k8s.io] Guestbook application should create and stop a working application [Conformance]: <no details avaliable>

```


Drone.io download seems to not work for elevator controller dev build


Ако добро сфатив мора да ги имам и овие : -using System.Collections.Generic;
 -using System.Linq;
 -using System.Text;
 -using System.Threading.Tasks;
и притоа да ја тргнам класата :manager base Од останатите класи ??
нели тие ја наследват истата?


I too like %_DebuggerFullPath% but I see this as something that can be injected by the build task or targets that invoke the script, as they are the only things which have context into where to stuck the debugger invocation.


@bahuljain Good stuff! 👯


storeCache methods merged to a single one


Thanks.

Looks unrelated, but if it still fails, let's do a revert pull to see if it passes with the revert pull.

On 19. huhtikuuta 2016 klo 19.45 +0300, Maurits van Rees<notifications@github.com>, wrote:
>
> The robot test for Plone 5.1 are broken after this change:http://jenkins.plone.org/job/plone-5.1-python-2.7-robot/239/
> Could it be related?
> I have just started a rebuild, in case it is a temporary glitch. Otherwise you may want to revert this change.
>
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly orview it on GitHub(https://github.com/plone/plone.app.robotframework/commit/1eacb9bda3679837ba7ac34e685494ff537292a4#commitcomment-17163616)
>
>
>


It would load values from your local cache instead of doing a crawl and end up missing some values.


Agreed, was just an oversight.


Gambi.


I see.

Is it always reproducible or rather an erratic behaviour?


I think when done we shouldn't have to keep both, but this is a work-in-progress and is meant to still run the old way on Unix for now.  When this is ready and approved for both .cmd and .sh formats can probably toss the old one (though it's just a property, might come in handy later)


зачем тут нужны @query и @tweets? они вроде не используются, да и в целом не понятно зачем они могут быть нужны


❌ ❌ ❌

@hedojunior

> "mas foi só pra não deixar grande o nome."

Errado e preocupante. O código deve ser legível e não pequeno.


So just stale data?