[R/assert_DDvTD_wd.R:3:1:](https://github.com/TheoPannetier/DDvTDtools/blob/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/R/get_Kprime.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/get_Kprime.R:7:3:](https://github.com/TheoPannetier/DDvTDtools/blob/da21720d5f73523195bfc0199634da5cd2f454f9/R/get_Kprime.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/get_Kprime.R:8:1:](https://github.com/TheoPannetier/DDvTDtools/blob/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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/da21720d5f73523195bfc0199634da5cd2f454f9/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 )){
    ^
```


Znalzłem taki fajny thread na stacku:

https://stackoverflow.com/questions/26676563/entity-framework-queryable-async

O ile reszta IMO jak najbardziej może być async tak, select po całej tabeli może być średnim pomysłem 😄,

ale to oczywiście to moja opinia, wygląda super !


@sritejakv
Looks good to me so far.
Please also commit the increase of the version number to 0.2-SNAPSHOT, when we merge we set it to 0.2

@rakshitkr The rules are a good reference.