[R/assert_DDvTD_wd.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_DDvTD_wd.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' Most functions in DDvTDtools rely on a relative path from DDvTD folder to access data and save files.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assert_DDvTD_wd.R:9:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_DDvTD_wd.R#L9) *style:* **Variable or function name should be snake_case.**
```r
assert_DDvTD_wd <- function(){
^~~~~~~~~~~~~~~
```
[R/assert_DDvTD_wd.R:12:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_DDvTD_wd.R#L12) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(substr(working_dir, nchar_path-4, nchar_path) != "DDvTD"){
    ^
```
[R/assert_DDvTD_wd.R:12:36:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_DDvTD_wd.R#L12) *style:* **Put spaces around all infix operators.**
```r
  if(substr(working_dir, nchar_path-4, nchar_path) != "DDvTD"){
                                  ~^~
```
[R/assert_DDvTD_wd.R:13:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_DDvTD_wd.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Please set working dir to root of DDvTD folder before using DDvTDtools")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assert_optim.R:9:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_optim.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !(optim %in% get_optim_names())){
      ^
```
[R/assert_optim.R:10:57:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_optim.R#L10) *warning:* **no visible global function definition for ‘get_optim_names’**
```r
    stop(cat("'optim' is invalid. Possible inputs are", get_optim_names()))
                                                        ^~~~~~~~~~~~~~~
```
[R/assert_para.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_para.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param para numeric or character. A four-digits code specifying a set of parameter values.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assert_para.R:10:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_para.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !(para %in% DDvTDtools::get_para_values())){
      ^
```
[R/assert_sim.R:9:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_sim.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !(sim %in% get_sim_names())){
      ^
```
[R/assert_sim.R:10:57:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/assert_sim.R#L10) *warning:* **no visible global function definition for ‘get_sim_names’**
```r
    stop(cat("'optim' is invalid. Possible inputs are", get_sim_names()))
                                                        ^~~~~~~~~~~~~
```
[R/check_convergence_optim.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/check_convergence_optim.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' The function reads results files output from run_ML calls and prints whether some
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_convergence_optim.R:5:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/check_convergence_optim.R:6:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param folder the folder where the results files are stored. All .rds files in the folder are read.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_convergence_optim.R:7:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/check_convergence_optim.R:9:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L9) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/check_convergence_optim.R:13:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L13) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/check_convergence_optim.R:14:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L14) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/check_convergence_optim.R:16:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L16) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/check_convergence_optim.R:17:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(file in files_list){
     ^
```
[R/check_convergence_optim.R:19:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L19) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/check_convergence_optim.R:21:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(missing_rows) > 0){
      ^
```
[R/check_convergence_optim.R:24:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L24) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/check_convergence_optim.R:25:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L25) *style:* **Variable or function name should be snake_case.**
```r
    notConverged <- which(res$hasConverged == FALSE)
    ^~~~~~~~~~~~
```
[R/check_convergence_optim.R:26:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L26) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(notConverged > 0)){
      ^
```
[R/check_convergence_optim.R:27:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
      cat(paste("File", file, ": optimisation has not converged for", length(notConverged), "trees\n"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_convergence_optim.R:31:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_convergence_optim.R#L31) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/check_duplicated_rows.R:4:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_duplicated_rows.R#L4) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(duplicated_rows > 0)){
    ^
```
[R/check_duplicated_rows.R:12:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_duplicated_rows.R#L12) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_out){
    ^
```
[R/check_incomplete_rows.R:4:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_incomplete_rows.R#L4) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(res$mc)){
     ^
```
[R/check_incomplete_rows.R:5:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_incomplete_rows.R#L5) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(anyNA(res[i,])){
      ^
```
[R/check_incomplete_rows.R:5:20:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_incomplete_rows.R#L5) *style:* **Commas should always have a space after.**
```r
    if(anyNA(res[i,])){
                   ^
```
[R/check_incomplete_rows.R:9:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_incomplete_rows.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(incomplete_rows > 0)){
    ^
```
[R/check_incomplete_rows.R:17:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_incomplete_rows.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_out){
    ^
```
[R/check_initpars.R:18:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L18) *warning:* **no visible global function definition for ‘assert_optim’**
```r
  assert_optim(optim)
  ^~~~~~~~~~~~
```
[R/check_initpars.R:19:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L19) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(init_pars)){stop("brts should be a numeric vector.")}
    ^
```
[R/check_initpars.R:19:29:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.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.numeric(init_pars)){stop("brts should be a numeric vector.")}
                            ^
```
[R/check_initpars.R:19:70:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L19) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(!is.numeric(init_pars)){stop("brts should be a numeric vector.")}
                                                                     ^
```
[R/check_initpars.R:20:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(brts)){stop("init_pars should be a numeric vector.")}
    ^
```
[R/check_initpars.R:20:24:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L20) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(!is.numeric(brts)){stop("init_pars should be a numeric vector.")}
                       ^
```
[R/check_initpars.R:20:70:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L20) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(!is.numeric(brts)){stop("init_pars should be a numeric vector.")}
                                                                     ^
```
[R/check_initpars.R:21:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(optim == "CR" & length(init_pars) != 2){
    ^
```
[R/check_initpars.R:24:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(optim %in% c("DD","TD") & length(init_pars) != 3){
    ^
```
[R/check_initpars.R:24:24:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L24) *style:* **Commas should always have a space after.**
```r
  if(optim %in% c("DD","TD") & length(init_pars) != 3){
                       ^
```
[R/check_initpars.R:28:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(init_pars[1] < 0){ stop("Initial lambda0 has a negative value.") }
    ^
```
[R/check_initpars.R:28:23:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(init_pars[1] < 0){ stop("Initial lambda0 has a negative value.") }
                      ^
```
[R/check_initpars.R:28:71:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(init_pars[1] < 0){ stop("Initial lambda0 has a negative value.") }
                                                                      ^
```
[R/check_initpars.R:29:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L29) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(init_pars[2] < 0){ stop("Initial mu0 has a negative value.") }
    ^
```
[R/check_initpars.R:29:23:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L29) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(init_pars[2] < 0){ stop("Initial mu0 has a negative value.") }
                      ^
```
[R/check_initpars.R:29:67:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L29) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(init_pars[2] < 0){ stop("Initial mu0 has a negative value.") }
                                                                  ^
```
[R/check_initpars.R:30:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(init_pars[1] <= init_pars[2]){
    ^
```
[R/check_initpars.R:35:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L35) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(optim %in% c("DD","TD")){
    ^
```
[R/check_initpars.R:35:24:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L35) *style:* **Commas should always have a space after.**
```r
  if(optim %in% c("DD","TD")){
                       ^
```
[R/check_initpars.R:37:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(init_pars[3] < 1){ stop("Initial K must be greater than 1.")}
      ^
```
[R/check_initpars.R:37:25:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(init_pars[3] < 1){ stop("Initial K must be greater than 1.")}
                        ^
```
[R/check_initpars.R:37:68:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if(init_pars[3] < 1){ stop("Initial K must be greater than 1.")}
                                                                   ^
```
[R/check_initpars.R:39:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L39) *style:* **Variable or function name should be snake_case.**
```r
    N <- length(brts) + 1
    ^
```
[R/check_initpars.R:40:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L40) *style:* **Variable or function name should be snake_case.**
```r
    Kprime = init_pars[1] / (init_pars[1] - init_pars[2]) * init_pars[3]
    ^~~~~~
```
[R/check_initpars.R:40:12:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L40) *style:* **Use <-, not =, for assignment.**
```r
    Kprime = init_pars[1] / (init_pars[1] - init_pars[2]) * init_pars[3]
           ^
```
[R/check_initpars.R:42:28:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if (ceiling(Kprime) < N ){
                           ^
```
[R/check_initpars.R:45:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L45) *style:* **Variable or function name should be snake_case.**
```r
      Kprime = init_pars[1] / (init_pars[1] - init_pars[2]) * init_pars[3]
      ^~~~~~
```
[R/check_initpars.R:45:14:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_initpars.R#L45) *style:* **Use <-, not =, for assignment.**
```r
      Kprime = init_pars[1] / (init_pars[1] - init_pars[2]) * init_pars[3]
             ^
```
[R/check_loglikelihood_exists.R:3:56:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_loglikelihood_exists.R#L3) *style:* **Commas should always have a space after.**
```r
  missing_loglikelihoods <- which(res$loglik %in% c(NA,-1,-Inf))
                                                       ^
```
[R/check_loglikelihood_exists.R:3:59:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_loglikelihood_exists.R#L3) *style:* **Commas should always have a space after.**
```r
  missing_loglikelihoods <- which(res$loglik %in% c(NA,-1,-Inf))
                                                          ^
```
[R/check_loglikelihood_exists.R:4:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_loglikelihood_exists.R#L4) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(missing_loglikelihoods > 0)){
    ^
```
[R/check_loglikelihood_exists.R:12:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_loglikelihood_exists.R#L12) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_out){
    ^
```
[R/check_missing_mcs.R:5:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_missing_mcs.R#L5) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(missing_mcs > 0)){
    ^
```
[R/check_missing_mcs.R:13:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_missing_mcs.R#L13) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_out){
    ^
```
[R/check_missing_mcs.R:20:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/check_missing_mcs.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/compare_method_bd.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' This function runs bd_ML() three times for the 50 first trees in the dataset selected by the arguments.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/compare_method_bd.R:4:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' Each time a different \code{method} argument is used, among \code{"lsoda"}, \code{"ode45"}, \code{"lsodes"}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/compare_method_bd.R:13:40:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
compare_method_bd <- function(sim, para ){
                                       ^
```
[R/compare_method_bd.R:15:17:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L15) *style:* **Use <-, not =, for assignment.**
```r
  method_vector = c("lsoda","ode45","lsodes")
                ^
```
[R/compare_method_bd.R:15:29:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L15) *style:* **Commas should always have a space after.**
```r
  method_vector = c("lsoda","ode45","lsodes")
                            ^
```
[R/compare_method_bd.R:15:37:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L15) *style:* **Commas should always have a space after.**
```r
  method_vector = c("lsoda","ode45","lsodes")
                                    ^
```
[R/compare_method_bd.R:16:11:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L16) *style:* **Use <-, not =, for assignment.**
```r
  rangemc = 1:50
          ^
```
[R/compare_method_bd.R:17:9:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L17) *style:* **Use <-, not =, for assignment.**
```r
  optim = "TD"
        ^
```
[R/compare_method_bd.R:20:18:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L20) *warning:* **no visible global function definition for ‘get_multi_brts’**
```r
  brts_bundle <- get_multi_brts("data/sim/", sim, para, rangemc)
                 ^~~~~~~~~~~~~~
```
[R/compare_method_bd.R:35:14:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L35) *style:* **Use <-, not =, for assignment.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
             ^
```
[R/compare_method_bd.R:35:43:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L35) *style:* **Commas should never have a space before.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
                                         ~^
```
[R/compare_method_bd.R:35:51:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L35) *style:* **Commas should never have a space before.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
                                                 ~^
```
[R/compare_method_bd.R:35:52:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L35) *style:* **Commas should always have a space after.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
                                                   ^
```
[R/compare_method_bd.R:37:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(mc in rangemc){
     ^
```
[R/compare_method_bd.R:41:17:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L41) *style:* **Use <-, not =, for assignment.**
```r
    initparsopt = para_to_pars(para)[2:4]
                ^
```
[R/compare_method_bd.R:41:19:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L41) *warning:* **no visible global function definition for ‘para_to_pars’**
```r
    initparsopt = para_to_pars(para)[2:4]
                  ^~~~~~~~~~~~
```
[R/compare_method_bd.R:42:20:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L42) *style:* **Use <-, not =, for assignment.**
```r
    initparsopt[3] = length(brts) + 1
                   ^
```
[R/compare_method_bd.R:44:8:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:3){
       ^
```
[R/compare_method_bd.R:45:15:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L45) *style:* **Use <-, not =, for assignment.**
```r
      methode = method_vector[i]
              ^
```
[R/compare_method_bd.R:49:18:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L49) *style:* **Use <-, not =, for assignment.**
```r
      timerstart = proc.time()
                 ^
```
[R/compare_method_bd.R:51:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L51) *style:* **Variable or function name should be snake_case.**
```r
      ML_output <- DDD::bd_ML(
      ^~~~~~~~~
```
[R/compare_method_bd.R:53:42:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_bd.R#L53) *style:* **Commas should always have a space after.**
```r
        initparsopt = c(initparsopt[1:2],150),
                                         ^
```
[R/compare_method_dd.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' This function runs dd_ML() three times for the 50 first trees in the dataset selected by the arguments.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/compare_method_dd.R:4:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' Each time a different \code{method} argument is used, among \code{"lsoda"}, \code{"ode45"}, \code{"analytical"}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/compare_method_dd.R:13:40:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
compare_method_dd <- function(sim, para ){
                                       ^
```
[R/compare_method_dd.R:15:17:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L15) *style:* **Use <-, not =, for assignment.**
```r
  method_vector = c("lsoda","ode45","analytical")
                ^
```
[R/compare_method_dd.R:15:29:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L15) *style:* **Commas should always have a space after.**
```r
  method_vector = c("lsoda","ode45","analytical")
                            ^
```
[R/compare_method_dd.R:15:37:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L15) *style:* **Commas should always have a space after.**
```r
  method_vector = c("lsoda","ode45","analytical")
                                    ^
```
[R/compare_method_dd.R:16:11:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L16) *style:* **Use <-, not =, for assignment.**
```r
  rangemc = 1:50
          ^
```
[R/compare_method_dd.R:17:9:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L17) *style:* **Use <-, not =, for assignment.**
```r
  optim = "DD"
        ^
```
[R/compare_method_dd.R:20:18:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L20) *warning:* **no visible global function definition for ‘get_multi_brts’**
```r
  brts_bundle <- get_multi_brts("data/sim/", sim, para, rangemc)
                 ^~~~~~~~~~~~~~
```
[R/compare_method_dd.R:35:14:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L35) *style:* **Use <-, not =, for assignment.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
             ^
```
[R/compare_method_dd.R:35:43:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L35) *style:* **Commas should never have a space before.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
                                         ~^
```
[R/compare_method_dd.R:35:51:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L35) *style:* **Commas should never have a space before.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
                                                 ~^
```
[R/compare_method_dd.R:35:52:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L35) *style:* **Commas should always have a space after.**
```r
  outputfile = paste0("method-", sim, "-" , optim ,"-", para, ".RData")
                                                   ^
```
[R/compare_method_dd.R:37:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(mc in rangemc){
     ^
```
[R/compare_method_dd.R:41:17:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L41) *style:* **Use <-, not =, for assignment.**
```r
    initparsopt = para_to_pars(para)[2:4]
                ^
```
[R/compare_method_dd.R:41:19:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L41) *warning:* **no visible global function definition for ‘para_to_pars’**
```r
    initparsopt = para_to_pars(para)[2:4]
                  ^~~~~~~~~~~~
```
[R/compare_method_dd.R:42:20:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L42) *style:* **Use <-, not =, for assignment.**
```r
    initparsopt[3] = length(brts) + 1
                   ^
```
[R/compare_method_dd.R:44:8:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:3){
       ^
```
[R/compare_method_dd.R:45:15:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L45) *style:* **Use <-, not =, for assignment.**
```r
      methode = method_vector[i]
              ^
```
[R/compare_method_dd.R:49:18:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L49) *style:* **Use <-, not =, for assignment.**
```r
      timerstart = proc.time()
                 ^
```
[R/compare_method_dd.R:51:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L51) *style:* **Variable or function name should be snake_case.**
```r
      ML_output <- DDD::bd_ML(
      ^~~~~~~~~
```
[R/compare_method_dd.R:53:42:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/compare_method_dd.R#L53) *style:* **Commas should always have a space after.**
```r
        initparsopt = c(initparsopt[1:2],150),
                                         ^
```
[R/count_errors.R:6:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param log_filename a log file to search the errors in. Can be a \code{.txt} or
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_errors.R:16:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
  if(!is.character(log_filename) | !tools::file_ext(log_filename) %in% c("txt", "log")){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_errors.R:16:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.character(log_filename) | !tools::file_ext(log_filename) %in% c("txt", "log")){
    ^
```
[R/count_errors.R:20:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
  no_conv_error <- "Optimization has not converged. Try again with different initial values."
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_errors.R:36:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(log_file)){
     ^
```
[R/count_errors.R:39:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(log_file[[i]] == paste("Running ML for tree", mc + 1, "")){
      ^
```
[R/count_errors.R:43:8:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L43) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(j in seq_along(error_templates)){
       ^
```
[R/count_errors.R:44:9:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/count_errors.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(log_file[[i]] == error_templates[j]){
        ^
```
[R/get_brts.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' Read the dataset at specified location and returns branching times for specified tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:5:61:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#' @param sim character, the name of a simulation model. See
                                                            ^
```
[R/get_brts.R:7:76:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' @param para numeric or character. A four-digits code specifying a set of
                                                                           ^
```
[R/get_brts.R:10:78:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#' @param with_extinct logical. \code{with_extinct = F} for the reconstructed
                                                                             ^
```
[R/get_brts.R:19:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L19) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_brts.R:20:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L20) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_brts.R:21:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L21) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_brts.R:22:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(mc) | !mc %in% 1:1000 ){
    ^
```
[R/get_brts.R:22:39:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if(!is.numeric(mc) | !mc %in% 1:1000 ){
                                      ^
```
[R/get_brts.R:23:10:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L23) *style:* **Only use double-quotes.**
```r
    stop('mc must be a numeric in 1:1000')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:25:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.logical(with_extinct)){
    ^
```
[R/get_brts.R:26:10:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L26) *style:* **Only use double-quotes.**
```r
    stop('with_extinct must be a logical')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:29:12:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L29) *warning:* **no visible global function definition for ‘read_trees’**
```r
  trees <- read_trees(sim = sim, para = para)
           ^~~~~~~~~~
```
[R/get_brts.R:31:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L31) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(any(!mc %in% seq_along(trees))){
    ^
```
[R/get_brts.R:32:10:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L32) *style:* **Only use double-quotes.**
```r
    stop('There is no tree is the file for that mc.')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:35:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L35) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!with_extinct){
    ^
```
[R/get_brts.R:37:24:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                       ^
```
[R/get_brts.R:37:46:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                             ^
```
[R/get_brts.R:37:63:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                                              ^
```
[R/get_brts.R:37:65:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                                                ^
```
[R/get_brts.R:40:24:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[2]] ) )
                       ^
```
[R/get_brts.R:40:46:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[2]] ) )
                                             ^
```
[R/get_brts.R:40:63:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[2]] ) )
                                                              ^
```
[R/get_brts.R:40:65:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[2]] ) )
                                                                ^
```
[R/get_dAIC_DDvTD.R:4:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param para numeric or character. A four-digits code specifying a set of parameter values. See \code{get_para_values()} for possible values.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:9:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L9) *style:* **Variable or function name should be snake_case.**
```r
get_dAIC_DDvTD <- function(sim, para){
^~~~~~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:10:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L10) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:11:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L11) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:12:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L12) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:14:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L14) *style:* **Variable or function name should be snake_case.**
```r
  res_DD <- read_optim_table(sim = sim, para = para, optim = "DD")
  ^~~~~~
```
[R/get_dAIC_DDvTD.R:14:13:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L14) *warning:* **no visible global function definition for ‘read_optim_table’**
```r
  res_DD <- read_optim_table(sim = sim, para = para, optim = "DD")
            ^~~~~~~~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:15:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L15) *style:* **Variable or function name should be snake_case.**
```r
  res_TD <- read_optim_table(sim = sim, para = para, optim = "TD")
  ^~~~~~
```
[R/get_dAIC_DDvTD.R:15:13:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L15) *warning:* **no visible global function definition for ‘read_optim_table’**
```r
  res_TD <- read_optim_table(sim = sim, para = para, optim = "TD")
            ^~~~~~~~~~~~~~~~
```
[R/get_dAIC_DDvTD.R:17:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  dAIC <- c()
  ^~~~
```
[R/get_dAIC_DDvTD.R:18:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(mc in 1:1000){
     ^
```
[R/get_dAIC_DDvTD.R:19:72:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if (any(c(res_DD$AIC[mc], res_TD$AIC[mc]) %in% c(Inf, -Inf, NA, -1) )){
                                                                       ^
```
[R/get_dAIC_DDvTD.R:20:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L20) *style:* **Variable or function name should be snake_case.**
```r
      dAIC <- c(dAIC, NA)
      ^~~~
```
[R/get_dAIC_DDvTD.R:22:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_dAIC_DDvTD.R#L22) *style:* **Variable or function name should be snake_case.**
```r
      dAIC <-  c(dAIC, res_DD$AIC[mc] - res_TD$AIC[mc])
      ^~~~
```
[R/get_default_initpars.R:30:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L30) *warning:* **no visible global function definition for ‘assert_optim’**
```r
  assert_optim(optim)
  ^~~~~~~~~~~~
```
[R/get_default_initpars.R:31:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L31) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(true_pars)){stop("true_pars should be numeric.")}
    ^
```
[R/get_default_initpars.R:31:29:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L31) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(!is.numeric(true_pars)){stop("true_pars should be numeric.")}
                            ^
```
[R/get_default_initpars.R:31:66:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L31) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(!is.numeric(true_pars)){stop("true_pars should be numeric.")}
                                                                 ^
```
[R/get_default_initpars.R:32:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(brts)){stop("brts should be numeric.")}
    ^
```
[R/get_default_initpars.R:32:24:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L32) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(!is.numeric(brts)){stop("brts should be numeric.")}
                       ^
```
[R/get_default_initpars.R:32:56:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L32) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(!is.numeric(brts)){stop("brts should be numeric.")}
                                                       ^
```
[R/get_default_initpars.R:34:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_default_initpars.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(brts) + 1
  ^
```
[R/get_empty_optim_df.R:32:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_empty_optim_df.R#L32) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/get_Kprime.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/get_Kprime.R:7:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/get_Kprime.R:8:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L8) *style:* **Variable or function name should be snake_case.**
```r
get_Kprime <- function(pars){
^~~~~~~~~~
```
[R/get_Kprime.R:9:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
  if(!is.numeric(pars)|length(pars) != 3){stop("Invalid input. Please check pars argument")}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_Kprime.R:9:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(pars)|length(pars) != 3){stop("Invalid input. Please check pars argument")}
    ^
```
[R/get_Kprime.R:9:23:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L9) *style:* **Put spaces around all infix operators.**
```r
  if(!is.numeric(pars)|length(pars) != 3){stop("Invalid input. Please check pars argument")}
                     ~^~
```
[R/get_Kprime.R:9:42:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L9) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(!is.numeric(pars)|length(pars) != 3){stop("Invalid input. Please check pars argument")}
                                         ^
```
[R/get_Kprime.R:9:92:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L9) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if(!is.numeric(pars)|length(pars) != 3){stop("Invalid input. Please check pars argument")}
                                                                                ^
```
[R/get_Kprime.R:11:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_Kprime.R#L11) *style:* **Commented code should be removed.**
```r
  # Kprime = la0 * K / (la0 - mu0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_likelihood_along_K.R:21:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L21) *style:* **Variable or function name should be snake_case.**
```r
get_likelihood_along_K <- function(optim,
^~~~~~~~~~~~~~~~~~~~~~
```
[R/get_likelihood_along_K.R:25:29:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L25) *style:* **Variable or function name should be snake_case.**
```r
                            K_seq = seq(10, 1000, by = 10)) {
                            ^~~~~
```
[R/get_likelihood_along_K.R:26:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L26) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/get_likelihood_along_K.R:28:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L28) *warning:* **no visible global function definition for ‘assert_optim’**
```r
  assert_optim(optim)
  ^~~~~~~~~~~~
```
[R/get_likelihood_along_K.R:41:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L41) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/get_likelihood_along_K.R:45:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L45) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/get_likelihood_along_K.R:49:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L49) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/get_likelihood_along_K.R:51:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L51) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/get_likelihood_along_K.R:71:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_likelihood_along_K.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/get_LR_DDvTD.R:4:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param para numeric or character. A four-digits code specifying a set of parameter values. See \code{get_para_values()} for possible values.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_LR_DDvTD.R:8:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L8) *style:* **Variable or function name should be snake_case.**
```r
get_LR_DDvTD <- function(sim, para){
^~~~~~~~~~~~
```
[R/get_LR_DDvTD.R:9:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L9) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_LR_DDvTD.R:10:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L10) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_LR_DDvTD.R:11:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L11) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_LR_DDvTD.R:13:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  res_DD <- read_optim_table(sim = sim, para = para, optim = "DD")
  ^~~~~~
```
[R/get_LR_DDvTD.R:13:13:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L13) *warning:* **no visible global function definition for ‘read_optim_table’**
```r
  res_DD <- read_optim_table(sim = sim, para = para, optim = "DD")
            ^~~~~~~~~~~~~~~~
```
[R/get_LR_DDvTD.R:14:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L14) *style:* **Variable or function name should be snake_case.**
```r
  res_TD <- read_optim_table(sim = sim, para = para, optim = "TD")
  ^~~~~~
```
[R/get_LR_DDvTD.R:14:13:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L14) *warning:* **no visible global function definition for ‘read_optim_table’**
```r
  res_TD <- read_optim_table(sim = sim, para = para, optim = "TD")
            ^~~~~~~~~~~~~~~~
```
[R/get_LR_DDvTD.R:16:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  LR <- c()
  ^~
```
[R/get_LR_DDvTD.R:17:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(mc in 1:1000){
     ^
```
[R/get_LR_DDvTD.R:18:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
    if (any(c(res_DD$loglik[mc], res_TD$loglik[mc]) %in% c(Inf, -Inf, NA, -1) )){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_LR_DDvTD.R:18:78:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if (any(c(res_DD$loglik[mc], res_TD$loglik[mc]) %in% c(Inf, -Inf, NA, -1) )){
                                                                             ^
```
[R/get_LR_DDvTD.R:19:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L19) *style:* **Variable or function name should be snake_case.**
```r
      LR <- c(LR, NA)
      ^~
```
[R/get_LR_DDvTD.R:21:7:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_LR_DDvTD.R#L21) *style:* **Variable or function name should be snake_case.**
```r
      LR <-  c(LR, res_DD$loglik[mc] - res_TD$loglik[mc])
      ^~
```
[R/get_multi_brts.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' Read the dataset at specified location and returns branching times for multiple trees specified by indices.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:5:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sim character, the name of a simulation model. See \code{get_sim_names()} for possible values.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:6:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param para numeric or character. A four-digits code specifying a set of parameter values. See \code{get_para_values()}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:7:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param rangemc numeric vector. The indices of the trees to return branching times from.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:8:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param with_extinct logical. \code{with_extinct = F} for the reconstructed tree, \code{with_extinct = T} for the complete tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:10:1:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a list of numerical vectors containing the branching times of the specified trees.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:16:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L16) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:17:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L17) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_multi_brts.R:18:3:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L18) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_multi_brts.R:19:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L19) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if( is.null(rangemc)) { rangemc <- 1:1000 }
    ^
```
[R/get_multi_brts.R:19:6:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if( is.null(rangemc)) { rangemc <- 1:1000 }
     ^
```
[R/get_multi_brts.R:19:25:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.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.null(rangemc)) { rangemc <- 1:1000 }
                        ^
```
[R/get_multi_brts.R:19:45:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L19) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if( is.null(rangemc)) { rangemc <- 1:1000 }
                                            ^
```
[R/get_multi_brts.R:20:5:](https://github.com/TheoPannetier/DDvTDtools/blob/a24bc88ee2f1ec1aaa129891868c1cbe3194397b/R/get_multi_brts.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.numeric(rangemc) | any(!rangemc %in% 1:1000 )){
    ^
```


## Words

| Changed   |   Status |
|:----------|---------:|
| `lat`     |      -14 |

*[Hook UI build recap](http://ci.perseids.org/repo/PerseusDL/canonical-latinLit/4964)*


We shouldn't display Artist Events if we don't have their main information


Successfully aliased the URL <https://itberries-frontend-afpg9zw3s.now.sh> to the following aliases.

* https://itberries-frontend.now.sh
* https://itberries-frontend-git-master.it-berries1.now.sh


Yes, it could do that despite the prefix. Another solution could be that I extend SessionRegistryImpl and make it a component so that it is piked up automatically by Spring and then there's no need for the bean definition method, but I think that would be an overkill.


ok


nice correction


`github.com` and `gist.github.com` have `fill: currentColor` set on the `.octicon` class which is coming from [here](https://github.com/primer/octicons/blob/6fe5475945d5633818b49ce55619ec039789b1c8/lib/octicons_node/index.scss), but on the other subdomains it's not guaranteed to be set. Some sites like `help.github.com` don't have it set while `developer.github.com` does but this one is using an Octicons font instead of svgs 🤷♂

Adding `fill: currentColor` as a blanket rule breaks the styling in some spots which is why I had removed it, but we needed to add it back in for some of these other sites which is why there's exclusions.


great change


Add build config stuff


Created multidev environment [hscrb#ci-975](https://dashboard.pantheon.io/sites/06f9bf1c-27cc-4fe9-8eda-f88f153eb347#ci-975).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-975-hscrb.pantheonsite.io/)


TeamCity Bvcms / Build [Build 1159](https://builds.tpsdb.com/viewLog.html?buildId=4721&buildTypeId=Bvcms_Build) is now running


Should it be explicitly specified that the next byte should be zero ?


Thank you! You rock!


IIRC, you can do `vec![self.s, other_str.s].join("")`, but now I look at it, allocating a `vec` is wasteful. So ignore my comment.


[This breaks building on linux / clang](https://travis-ci.org/inexorgame/entity-system/builds/517936142)


@AlexPl292 I would put this code into `VimPlugin.updateState()` to have a single place for updating the state.


TeamCity Bvcms / Build [Build 1159](https://builds.tpsdb.com/viewLog.html?buildId=4721&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Running Build time: 00:04:20


adding indigo to master


I noticed a strange behavior a long time ago, with the Event Manager,
an unwanted behavior was always triggered when i clicked ok, it had to
do with translating variables that were evaluated, once i removed
gettext from those variables, the issue was gone.

I found an identical issue in the ppm.. a long time ago, and i also
removed the gettext from those variables. I guess this is what some
people saw, "ppm stopped working".

The issue with the ppm is events somehow being triggered in some cases
causing a loop, with a properly compiled and working GtkDialog. Some
people noted gtkdialog issues in some distros, it doesn't behave
exactly the same in all of them, the biggest problem: some specific
events.

But i guess the biggest problem here is the code itself, a package
manager is less reliable when it uses too many external apps. It needs
to be more self-contained.

I personally don't need it, wine runs all the apps i use, and when i
want to update something, i just download the latest exe, no need to
compile it or download it from somewhere and deal with the dependency
hell. It seems the easy way out.


должно быть два пробела, а не табы,исправь везде


что бы не было красной стрелки оставляй пустую строку в конце


d


very nice!


Added a generator for it in https://github.com/StylishThemes/GitHub-Dark/commit/852f2038479cb5862459ef38e13015b2a8fe0aa3. It's only covering `.octicon`. So if someone encounters more black svgs on other site, please add a site-specific rule like I did here.


Вынеси базовое т.е. `@carriages << carriage if speed.zero? ` это в родительский класс
и вызывай тут super
`super if carriage.type == "cargo"`


Cool! I'm assuming `hasNextPage` winds up being enough to determine if there is more to show (i think that might be how `relay.hasMore()` works?).

Each node has a cursor, where `endCursor` here is just a shortcut to the cursor of the last node, and that does _seem_ necessary to page to the next set, but I'm assuming the Relay pagination container winds up managing that for us (esp if this all still works!).


I aggree. It's okay this way then


Think about the purpose of why you want to add the sleep.
Then check the Javadoc of the sleep method and see if these calls to sleep will do what you expect.


первый и второй очень похожи, если постараться можно вынести скоротить


Maybe I'm getting something wrong but looks like you overwriting existing value initialized with `Collections.emptyList()` on itself


Closes #280


The same. See comment https://github.com/oyeli/swagger-validator-maven-plugin/commit/487fab94256cf7d8ae65d3120a4f2811132c9bba?diff=split#r33279583


But it's `kotlin` file. Should we use 2 spaces indent also for kotlin?


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/d91aa068-9246-4f13-b1c4-65154b216dc1?env_id=ibm%3Ayp%3Aus-south "demo-SDKfNod"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/d556bcfe-3a03-4484-9303-6751f172a78f?env_id=ibm%3Ayp%3Aus-south "demo-SDKfNod") deployed [holamundo](https://github.com/jlpv1976/holamundo/releases/tag/deploy-ibm-yp-us-south-jperez-integssoft.com-dev-20190423-171605 "deploy-ibm-yp-us-south-jperez-integssoft.com-dev-20190423-171605") to [dev](https://console.bluemix.net/apps/efb25855-9e53-4957-bbf5-d78fb39cf118?env_id=ibm:yp:us-south "ibm:yp:us-south:jperez@integssoft.com:dev"), including this commit


Love it. Updating!


Yeah, me too, but `VimPlugin.updateState()` doesn't have an instance of `element`.


You don't need this line of code


@allcontributors[bot] please add @markerikson for content


Rats, was hoping that would work here.


Thanks!

By the way,
Are you considering to include the `revise-thumbnail` branch in 8.8?:
https://github.com/libvips/libvips/compare/master...revise-thumbnail

I've tried this branch on our test server and it seems to work (in most cases):
https://t0.nl/?url=downloads.webmproject.org/webp/images/dancing-banana.gif&pages=-1 (original 990x1050) - works
https://t0.nl/?url=downloads.webmproject.org/webp/images/dancing-banana.gif&pages=-1&w=495 (990 / 2) - works
https://t0.nl/?url=downloads.webmproject.org/webp/images/dancing-banana.gif&pages=-1&w=550 (990 / 1.8) - needs some revising (due to:
https://github.com/libvips/libvips/blob/f06a01ccbef778b0e9428408f5c37b238ad94bfb/libvips/resample/thumbnail.c#L653-L654)


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/d91aa068-9246-4f13-b1c4-65154b216dc1?env_id=ibm%3Ayp%3Aus-south "demo-SDKfNod"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/d556bcfe-3a03-4484-9303-6751f172a78f?env_id=ibm%3Ayp%3Aus-south "demo-SDKfNod") deployed [holamundo](https://github.com/jlpv1976/holamundo/releases/tag/deploy-ibm-yp-us-south-jperez-integssoft.com-dev-20190423-171859 "deploy-ibm-yp-us-south-jperez-integssoft.com-dev-20190423-171859") to [dev](https://console.bluemix.net/apps/efb25855-9e53-4957-bbf5-d78fb39cf118?env_id=ibm:yp:us-south "ibm:yp:us-south:jperez@integssoft.com:dev"), including this commit


Created multidev environment [hscrb#ci-977](https://dashboard.pantheon.io/sites/06f9bf1c-27cc-4fe9-8eda-f88f153eb347#ci-977).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-977-hscrb.pantheonsite.io/)


Yay! :)


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/7f384fc2-6269-4b2c-a18e-830dd00bf15c?env_id=ibm%3Ayp%3Aeu-gb "ForTestBranchNott"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/796927db-7cac-4759-b536-24b8d38bc2c7?env_id=ibm%3Ayp%3Aeu-gb "ForTestBranchNott") deployed [NottsMissingMaps](https://github.com/Carbsta/NottsMissingMaps/releases/tag/deploy-ibm-yp-eu-gb-ibmclouduni-gmail.com-dev-20190423-171955 "deploy-ibm-yp-eu-gb-ibmclouduni-gmail.com-dev-20190423-171955") to [dev](https://console.bluemix.net/apps/79b554b9-4488-40c5-9ff8-e062569b5674?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:ibmclouduni@gmail.com:dev"), including this commit


If wrap is mandatory, then do a literal wrap

```html
<cxl-lesson-card>
  <div class="wrap">
  </div>
</cxl-lesson-card>
```


Puzzle `1-e8a239fe` discovered in   [`Code/Runner.py`](  https://github.com/supakornbabe/data_mining_project/blob/master/Code/Runner.py)   and submitted as #1. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


"that be executed"  -> "that can be executed". Did you mean that?


Solved Camera bug, sorry for the typo


Successfully aliased the URL <https://aremycolorsaccessible-qrx8n2yt7.now.sh> to the following aliases.

* https://aremycolorsaccessible.com
* https://aremycoloursaccessible.com
* https://www.aremycoloursaccessible.com
* https://www.aremycolorsaccessible.com
* https://aremycolorsaccessible-git-master.sitaggart.now.sh


I'm aware of what this specific call does.

It's more about "are there any other magic attributes needed" to replicate semantics of a native element?


changes to the module-info


Successfully aliased the URL <https://photoinmedia-fbi9x4viq.now.sh> to the following aliases.

* https://photoinmedia-git-master.rodchenkoartschool.now.sh
* https://photoin.media


@vfarcic `charts/javascript` should not be here


## Jenkins Build Summary

Built from [this commit](https://github.com/ximinez/rippled/commit/e3c5d797bf4071bb7706515584035d70176f2c72)

Built at __20190423 - 17:22:58__

### Test Results

Build Type | Log | Result | Status
---------- | --- | ------ | ------
msvc.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/msvc.Debug.txt) | 1159 cases, 0 failed, t: 599s | PASS :white_check_mark:
gcc.Release
-Dassert=ON,
MANUAL_TESTS=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Release_Dassert_ON_MANUAL_TESTS_true.txt) | 915 cases, 0 failed, t: 5m10s | PASS :white_check_mark:
docs,
TARGET=docs | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/docs_TARGET_docs.txt) | 1 cases, 0 failed, t: 0m1s | PASS :white_check_mark:
gcc.Debug
-Dcoverage=ON,
TARGET=coverage_report,
SKIP_TESTS=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Debug_Dcoverage_ON_TARGET_coverage_report_SKIP_TESTS_true.txt) | 1159 cases, 0 failed, t: 17m6s | PASS :white_check_mark:
clang.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/clang.Debug.txt) | 1159 cases, 0 failed, t: 2m59s | PASS :white_check_mark:
msvc.Debug,
NINJA_BUILD=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/msvc.Debug_NINJA_BUILD_true.txt) | 1159 cases, 0 failed, t: 633s | PASS :white_check_mark:
gcc.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Debug.txt) | 1159 cases, 0 failed, t: 3m8s | PASS :white_check_mark:
clang.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/clang.Debug_Dunity_OFF.txt) | 1158 cases, 0 failed, t: 10m26s | PASS :white_check_mark:
rpm | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/rpm.txt) | 1159 cases, 0 failed, t: n/a | PASS :white_check_mark:
clang.Release
-Dassert=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/clang.Release_Dassert_ON.txt) | 1159 cases, 0 failed, t: 4m56s | PASS :white_check_mark:
gcc.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Debug_Dunity_OFF.txt) | 1158 cases, 0 failed, t: 11m19s | PASS :white_check_mark:
msvc.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/msvc.Debug_Dunity_OFF.txt) | 1158 cases, 0 failed, t: 1167s | PASS :white_check_mark:
gcc.Debug
-Dstatic=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Debug_Dstatic_OFF.txt) | 1159 cases, 0 failed, t: 3m5s | PASS :white_check_mark:
gcc.Release
-Dassert=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Release_Dassert_ON.txt) | 1159 cases, 0 failed, t: 5m13s | PASS :white_check_mark:
msvc.Release | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/msvc.Release.txt) | 1159 cases, 0 failed, t: 422s | PASS :white_check_mark:
gcc.Debug,
NINJA_BUILD=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Debug_NINJA_BUILD_true.txt) | 1159 cases, 0 failed, t: 3m0s | PASS :white_check_mark:
gcc.Debug
-Dstatic=OFF -DBUILD_SHARED_LIBS=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/gcc.Debug_Dstatic_OFF_DBUILD_SHARED_LIBS_ON.txt) | 1159 cases, 0 failed, t: 3m6s | PASS :white_check_mark:
clang.Debug
-Dunity=OFF -Dsan=address,
PARALLEL_TESTS=false,
DEBUGGER=false | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/clang.Debug_Dunity_OFF_Dsan_address_PARALLEL_TESTS_false_DEBUGGER_false.txt) | 1158 cases, 0 failed, t: 10m54s | PASS :white_check_mark:
clang.Debug
-Dunity=OFF -Dsan=undefined,
PARALLEL_TESTS=false | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/41//artifact/clang.Debug_Dunity_OFF_Dsan_undefined_PARALLEL_TESTS_false.txt) | 1158 cases, 0 failed, t: 12m13s | PASS :white_check_mark:


Actually, it was more informative when property was called as CreateDate. So, you need to change property name in Models Folder


Now could not deploy this pull request since the `now.json` file is empty.
It should be a valid JSON file.

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


I recognize and really appreciate all your recent simplifications, @protonspring.  You've made an incredible series of contributions cleaning up the SF code base.

But I really don't think anything that adds `passed_pawn_span` here can possibly be a simplification, for reasons I outlined previously...


у нас в `@trains` объекты а не хэш и что это сравнение с `@routes`, тебе нужно сделать метод получения роута

Лучше сделай два метода
первый показывает роуты пусть будет `show_routes`

А чтобы у нас у роута было еще название, давай сделаем метод name который показывает название первой и последней станции

```ruby
  def show_routes
    @routes.each.with_index(1) { |route, x| puts "#{x}. #{route.station.name}" }
  end
```
тут мы выводим роуты с индексом начиная от одного что бы было удобно, и используем наш созданный метод `name`

и второй выбирает роут, пусть будет select_route
```ruby
def select_route
    puts 'Выберите маршрут'
    show_routes # показываем роуты
    @routes[gets.to_i - 1] # выбираем роут по индексу, запрашиваем ввод от пользователя
end
```

Таким образом мы можем тут вызвать `route = select_route`
и у нас будет локальная переменная route с выбранным роутом

Так же можно делать и с поездами и со станциями


Тут тоже самое, с super


Nice meme


Когда ты делаешь add_route станция не знает что поезд прибыл


Crud, I completely missed the fact that I didn't make a feature branch for this. Whoops. 😬


Когда мы делаем move_next станция не знает что поезд уехал со своей станции, и следующая станция не знает что к ней приехал поезд


Тут тоже самое


используй сразу next_station


Разбивай на методы


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


OK.  I was thinking removing the RANK_5, shifting, and more_than_one would offset (if you look at everything), but I certainly see your point.  I'm always pushing the lines on these.


Created multidev environment [hscrb#ci-981](https://dashboard.pantheon.io/sites/06f9bf1c-27cc-4fe9-8eda-f88f153eb347#ci-981).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-981-hscrb.pantheonsite.io/)


## Words

| Changed   |   Status |
|:----------|---------:|
| `lat`     |      -14 |

*[Hook UI build recap](http://ci.perseids.org/repo/PerseusDL/canonical-latinLit/4966)*


Should wr use `Optional<CircuitBreakerConfig>`


Maybe a whole new set of icons?
[color_icons_for_sigil.zip](https://github.com/Sigil-Ebook/Sigil/files/3108802/color_icons_for_sigil.zip)

[Default mode](https://i.imgur.com/CJ4B0yy.png)
[Dark mode](https://i.imgur.com/WFxYvIo.png)

BTW:
[Combobox with headers](https://i.imgur.com/3jVHIJj.png)


no you swallow


This is the same ui component as when there's hidden comments on an issue, but for some reason they're using different classes on that one and the one when there's over 10 suggested edits in a row.

![image](https://user-images.githubusercontent.com/831974/56602630-f08c3e00-65cb-11e9-85a7-351026139479.png)


This was a rather VERY annoying change!

Please DO NOT remove defcustom variables without at least marking them as deprecated for a full release cycle!

It would also be really helpful if there was a NEWS file which mentioned major changes too!


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

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

// 20190423122115
// https://gist.githubusercontent.com/gmrsagar/1afe89f363e470215bacd548b6c628fd/raw/4a906324359d6395e0075be30a6752ac12431e47/for-our-react-repo.json

{
  "version": 2,
  "name": "create-react-app",
  "builds": [
    {
      "src": "package.json",
      "use": "@now/static-build"
    }
  ],
  "routes": [
    {
      "src": "^/static/(.*)",
      "dest": "/static/$1"
    },
    {
      "src": "^/favicon.ico",
      "dest": "/favicon.ico"
    },
    {
      "src": "^/asset-manifest.json",
      "dest": "/asset-manifest.json"
    },
    {
      "src": "^/manifest.json",
      "dest": "/manifest.json"
    },
    {
      "src": "^/service-worker.js",
      "headers": {
        "cache-control": "s-maxage=0"
      },
      "dest": "/service-worker.js"
    },
    {
      "src": "^/precache-manifest.(.*)",
      "dest": "/precache-manifest.$1"
    },
    {
      "src": "^/(.*)",
      "dest": "/index.html"
    }
  ]
}

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


That seems to be the case - though I will have to make sure I didn't break the app with this change 😕


I would guess the cowsay and other implementations are the same as the wapm packages, which have build instructions and links to github on their pages: https://wapm.io/package/cowsay
@syrusakbary can you confirm?


@janhieber I guess this commit is not a complete implementation of imx6 MarS Board support for OpenELEC.

Is there any chance you can commit missing pieces?


fixed #5 and #6


q: Can't we just upstream a lot of these fixes? I imagine it's going to be beneficial for others and less annoying for us to keep cherry picking onto new versions.


@srumyantsev Yes, there are many issues with Wrike's documentation. My client code is based on the information provided in the documentation so it also has many issues like this one I guess.

Please forgive me that I could not understand what you are suggesting with ValidateOptionalParameters setting. I would appreciate if you could provide a code sample, that would help a lot.


Successfully aliased the URL <https://sklinkusch-vbbmicro-idor8ksel.now.sh> to the following alias.

* https://sklinkusch-vbbmicro.now.sh


Added Contents


Puzzle `2-f378450a` discovered in   [`Code/Runner.py`](  https://github.com/supakornbabe/data_mining_project/blob/master/Code/Runner.py)   and submitted as #2. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


Puzzle `3-723ae97f` discovered in   [`Code/Runner.py`](  https://github.com/supakornbabe/data_mining_project/blob/master/Code/Runner.py)   and submitted as #3. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


@nitayneeman `classnames` dependency is ok, it's just the usage of it which is incorrect.
it should be `import * as classNames from 'classnames';`


Dodaj proszę jeszcze jeden test gdy tablica jest pusta


accidentally here, looking at policy parms. tmtomh.

erm, windows/en-US/firefox.adml line **39**:

  **_<string id="RememberPasswords"Rember Passwords<\/string>\_**

        _I 'rember... back inna day win I wuz a pogammer..._

 Old programmers never die, they just OC1.


How is this a fix... as shown also here https://bugs.python.org/msg329463 ?
Following the Python RFC should check for parsedFrom == ('', '') and same for parsedTo == ('', '')


vughbghjbg


Thank you!


It looks like the change from https://github.com/StackStorm/st2cd/pull/369 didn't work. I will look into why.


Successfully aliased the URL <https://magento-venia-ypmsqqroon.now.sh> to the following aliases.

* https://magento-venia.now.sh
* https://veniapwa.com


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2613143)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/32bit-dialogs/d90dad962fbfb524e4766940281df8f0933734d2/2613143/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>66 tests failed, 205 tests skipped, 317 tests passed.</summary>

## Failed tests

 * apitest/Mac Unified 32-bit/NonSystem: Failed (Test run failed.)
 * apitest/Mac Unified XM45 32-bit/NonSystem: Failed (Test run failed.)
 * monotouch-test/iOS Unified 64-bits - device/Debug: Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/Debug: Crashed
 * mscorlib/iOS Unified 64-bits - device/Debug: Crashed
 * System.Net.Http/iOS Unified 64-bits - device/Debug: Crashed
 * System.Xml/iOS Unified 64-bits - device/Debug: Crashed
 * System.IO.Compression/iOS Unified 64-bits - device/Debug: Crashed
 * System.ServiceModel/iOS Unified 64-bits - device/Debug: Crashed
 * dont link/iOS Unified 64-bits - device/Debug: Crashed
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/Debug: Crashed
 * [xUnit] Mono BCL tests group 4/iOS Unified 64-bits - device/Debug: Crashed
 * [xUnit] Mono BCL tests group 5/iOS Unified 64-bits - device/Debug: Crashed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * monotouch-test/iOS Unified 64-bits - device/Release: Crashed
 * monotouch-test/iOS Unified 64-bits - device/Release (all optimizations): Crashed
 * monotouch-test/iOS Unified 64-bits - device/Debug (interpreter): Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/Release: Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * mscorlib/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * mscorlib/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * mscorlib/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * mscorlib/iOS Unified 64-bits - device/Debug (interpreter -mscorlib): Crashed
 * mscorlib/iOS Unified 64-bits - device/Release (interpreter -mscorlib): Crashed
 * System.Data/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * System.Net.Http/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * System.Web.Services/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * System.Web.Services/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * System.Xml/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * System.Xml/iOS Unified 64-bits - device/Release: Crashed
 * Mono.Data.Sqlite/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * Mono.Data.Sqlite/iOS Unified 64-bits - device/Release: Crashed
 * System.IO.Compression/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * System.ServiceModel/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * System.ServiceModel/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * System.IdentityModel/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * System.IdentityModel/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * dont link/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * dont link/iOS Unified 64-bits - device/Release: Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/Release: Crashed
 * mono-native-unified/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * mono-native-unified/iOS Unified 64-bits - device/Release: Crashed
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/Release: Crashed
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/Release: TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * [xUnit] Mono BCL tests group 3/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * [xUnit] Mono BCL tests group 3/iOS Unified 64-bits - device/Release: Crashed
 * [xUnit] Mono BCL tests group 4/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * [xUnit] Mono BCL tests group 4/iOS Unified 64-bits - device/Release: Crashed
 * [xUnit] Mono BCL tests group 4/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * [xUnit] Mono BCL tests group 5/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * [xUnit] Mono BCL tests group 5/iOS Unified 64-bits - device/Release: Crashed
 * [xUnit] Mono BCL tests group 5/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
</details>


CopyOnWriteArrayList


hello world


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/239](https://github.com/JuliaRegistries/General/pull/239)

After the above pull request is merged, it is recommended that you create
a tag on this repository for the registered package version:
```
git tag -a v0.0.1 -m "<description of version>" 47999f9f600d1dad9d997273085e575259fbd405
git push origin v0.0.1
```


Hi @SwapneelM ,
Can we please also add to the instructions that the user must logout after each installation process for the changes to be in-effect.
Thanks


does this really work? should be `if (ret.size() == 0)`, right?


This is causing the battle to fail


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


Here it is:
https://github.com/DL4Jets/DeepJetCore/blob/master/TrainData.py


Don't you want to check mailFrom != parsedFrom  and mailTo != parsedTo as stated in "This rejects any requests where the parsed email address does not match the raw input." ?


Let's return an optional


## Jenkins Build Summary

Built from [this commit](https://github.com/ximinez/rippled/commit/1b5ed27ac5c9b348889e33ce978da845cf3dfb27)

Built at __20190423 - 17:46:41__

### Test Results

Build Type | Log | Result | Status
---------- | --- | ------ | ------
rpm | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/rpm.txt) | no test results, t: n/a | FAIL :red_circle:
msvc.Debug | [console](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//console) | no test results, t: n/a | FAIL :red_circle:
msvc.Debug,
NINJA_BUILD=true | [console](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//console) | no test results, t: n/a | FAIL :red_circle:
msvc.Debug
-Dunity=OFF | [console](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//console) | no test results, t: n/a | FAIL :red_circle:
msvc.Release | [console](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//console) | no test results, t: n/a | FAIL :red_circle:
gcc.Release
-Dassert=ON,
MANUAL_TESTS=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Release_Dassert_ON_MANUAL_TESTS_true.txt) | no test results, t: 196s | FAIL :red_circle:
docs,
TARGET=docs | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/docs_TARGET_docs.txt) | 1 cases, 0 failed, t: 0m1s | PASS :white_check_mark:
gcc.Debug
-Dcoverage=ON,
TARGET=coverage_report,
SKIP_TESTS=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Debug_Dcoverage_ON_TARGET_coverage_report_SKIP_TESTS_true.txt) | no test results, t: 128s | FAIL :red_circle:
clang.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/clang.Debug.txt) | no test results, t: 92s | FAIL :red_circle:
gcc.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Debug.txt) | no test results, t: 118s | FAIL :red_circle:
clang.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/clang.Debug_Dunity_OFF.txt) | no test results, t: 348s | FAIL :red_circle:
clang.Release
-Dassert=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/clang.Release_Dassert_ON.txt) | no test results, t: 179s | FAIL :red_circle:
gcc.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Debug_Dunity_OFF.txt) | no test results, t: 413s | FAIL :red_circle:
gcc.Release
-Dassert=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Release_Dassert_ON.txt) | no test results, t: 189s | FAIL :red_circle:
gcc.Debug
-Dstatic=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Debug_Dstatic_OFF.txt) | no test results, t: 118s | FAIL :red_circle:
gcc.Debug
-Dstatic=OFF -DBUILD_SHARED_LIBS=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Debug_Dstatic_OFF_DBUILD_SHARED_LIBS_ON.txt) | no test results, t: 115s | FAIL :red_circle:
gcc.Debug,
NINJA_BUILD=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/gcc.Debug_NINJA_BUILD_true.txt) | no test results, t: 107s | FAIL :red_circle:
clang.Debug
-Dunity=OFF -Dsan=address,
PARALLEL_TESTS=false,
DEBUGGER=false | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/clang.Debug_Dunity_OFF_Dsan_address_PARALLEL_TESTS_false_DEBUGGER_false.txt) | no test results, t: 362s | FAIL :red_circle:
clang.Debug
-Dunity=OFF -Dsan=undefined,
PARALLEL_TESTS=false | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/x-strong-fee-typing/42//artifact/clang.Debug_Dunity_OFF_Dsan_undefined_PARALLEL_TESTS_false.txt) | no test results, t: 378s | FAIL :red_circle:


I've tested, it breaks. I'll make a fix


[bot] 自动构建 [auto-dragalia-fc11358a.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/123/artifacts/0/home/circleci/project/artifacts/auto-dragalia-fc11358a.zip)


We have these because without them, assigning a long long to variant of ambiguous in Clang.


@MiguelCastillo2019
MIguel cuando entento registrar un nuevo participante no me funciona, favor de reevisar el codigo en linea 170.  me avisas


The questions were proposed in the discipline of microcontrollers, and I used the PIC16F628A for didactic reasons. Enjoy it.


Yep, "can be" it is! Thanks for spotting that!


Successfully aliased the URL <https://hello-world-nlfoozwjl.now.sh> to the following aliases.

* https://hello-world-git-master.nova38.now.sh
* https://nowjs.csnovas.com
* https://now.csnovas.com


Extra divs on each of these screens we didn't need


Moved components we use on multiple screens to their own file


nope. ci is passing


Using generic component names


A file with similar / related components


Notice how we export the components we want to use on other screens, but not all are exported


The CI is passing because it's not using long longs. My local test case has them, and if you try to assign one, *it will fail*.


Above are exported to be used on other screens, but these are just internally referenced by Button


@kisvegabor Not sure if GitHub will automatically notify you of comments on commits.


Generic name where we had this copied before and given a contextual name. Instead, since it's the same style we just copy and pasted it into a new js file and gave it a common name and reused.