[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 )){
    ^
```


todo


This doesn't sound correct. `HAVE_ALLOCA` is always available. `ZEND_ALLOCA_MAX_SIZE` is also far more than is needed for a path.

Why is there a memory leak, free_alloca missing somewhere?

Thanks.


Another optimization we could do here is to completely drop the fallback codepath if we know that the value can only be MAY_BE_LONG / MAY_BE_STRING.


Seem to remember that -E is what allows sudoedit to use vim instead of vi


the blog is not working, is it still operational?


so where is the pencil please?


Yes. Then there was a fight about the one true style and, well, there still is not `.clang-format` file.


Fixed the chat community link at the top because the last one expired.


I think that was the wrong one :D


I find it easier to let appveyor build the Windows _artifact_ as opposed to the complication of gathering all the requisite files for a general use Win 10 environment (assuming that would even be possible).  While I don't recommend every user of RcloneBrowser clone their own repo to produce a Wndows artifact, the bigger issue is that RcloneBrower.exe is effectively useless without the Qt5 support files which would be present on a machine that had built the executable.

Provided in this document is the method by which to procure those missing files and use the RcloneBrowser.exe artifact without installing Qt5.


@MrChico did you mean to include this change?


why not:
```
quotes[pair] = quote
```
?


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* https://react-slidy.midu.dev
* https://react-slidy-git-master.midudev.now.sh


Oh yes.

So the functions are going to be automatically renamed, or..?


IT IS JUST A TRAI IDK WHAT IS RESULT


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


They are, yes


Looks like this obsoletes #521.


Ok, I'll just remove the overflow checks.


Nice!


Thanks for noticing and fixing this!


@mp911de the same for me. A locally maven test runs without errors and also the CI-Build with Concourse (https://ci.spring.io/builds/74364) is successful.


Indeed, i forgot to remove that ! my bad :)


The function lets users to view their incomes by account type, type of incomes and date.


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* https://demo-sync-moltin-to-zendesk-git-master.particular.now.sh
* https://particular-demo-sync-moltin-to-zendesk.now.sh


Successfully aliased the URL <https://demo-sync-moltin-to-shippo-v8gimxdc8.now.sh> to the following aliases.

* https://demo-sync-moltin-to-shippo-git-master.particular.now.sh
* https://particular-demo-sync-moltin-to-shippo.now.sh


Fix #55.


The function lets users to view their expenses by account type, type of money and date.


@cnuke: ignore the first request, and add please this one to staging


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* https://www.timdeschryver.dev
* https://timdeschryverdev-git-master.timdeschryver.now.sh


Wouldn't it be clearer to ignore the error?

```
from kitty.constants import str_version  # noqa: E402
```


Most of the LookupXXX() functions return a slice of results.
Not all accept a single "name" string though.
I tried to give as much value without making the API too abstract and too hard to use.
I think it's good enough for most users


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

`task.dependencies` references non-existing tasks:
 * FVJCza24Tn2yqClsuXO5Kw,
All taskIds in `task.dependencies` **must** exist
before the task is created.

---

* method:     createTask
* errorCode:  InputError
* statusCode: 400
* time:       2019-04-24T13:12:14.605Z

</details>


Yep, I'll replace the occurences by the issue URL while cleaning and creating the Xprocspec and xpec tests


I would prefer to have 2 spaces everywhere in the plugin, since it's the code style of IntelliJ.


Got it.


It's basically the same, except maybe a documentation that we may want to consider a later context propagation here. I didn't have a complete idea of what I want, so...


it's not, it's bad refactoring ;)


good


I dont much like supressing errors in that fashion, I can later never remember what that is for at a glance.


Start with the same as the container element: `entry__content`


Absolutely fantastic job on the assignment Karim! You successfully implemented all of the tasks by building out the HTML structure using semantic HTML and you styled the elements successfully to match the design file. Your attention to detail is amazing!

You have also gone above and beyond and have completed every single one of the stretch goals! Your commit messages are clear and descriptive.

Overall great job. Phenomenal first day! 🚀💪


Closes #1108


Potential container inside `.entry__footer`, but I haven't looked at the card design / content requirements here too closely.


do you need both pry-byebug and pry rails?


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

InterpreterError at template.tasks[0]: object keys must be strings

</details>


And


Remove comments


Note that this code will not affect multi-configuration generators/IDEs[1], but that is already the case for the line `if (CMAKE_BUILD_TYPE MATCHES Rel)`, so this is okay.

[1] https://stackoverflow.com/a/24470998


The function lets users view their monthly incomes, expenses and the percentage of particular expenses and incomes.


Начинать комент с большой буквы, и нужно еще добавить строчку `@param {FormGroup}` для определения типа переменной.


@alex-ab done, thanks for the offline notification - I would have missed it otherwise (using github with two different e-mail addresses still works wonderful not).


Thanks! Fixed in commit 9c63fbb2d20e72992e3c9dd5b5c1a5b33bb568cd.


Нужно писать тип возвращаемого значения возле каждой функции, если ничего не возвращает - `void`


Oh my god, this issue tooks our two days' time to solve!!!


Better be sure `this.pos` is set :laughing:


I agree. Fixed it here and at every other controller methods, see 9c63fbb2d20e72992e3c9dd5b5c1a5b33bb568cd.


Yup. There's also a partial fix for a test that broke some time ago in commit 8defc5e65aa311d88ce8d66f68151e6014d7d9f6. Couldn't figure out why the last bit failed.


PARTS:
	Register(load=rload, in=loriorr, out=regout, out=out);	// Increment
	Inc16(in=regout, out=incout);							// Throw away overflow
	Mux16(sel=load, a=incout, b=in, out=lori);				// Load
	Mux16(sel=reset, a=lori, b=false, out=loriorr);			// Reset
	Nand(a=true, b=load, out=aout);
	Nand(a=true, b=inc, out=bout);
	Nand(a=true, b=reset, out=cout);
	Nand(a=aout, b=bout, out=about);
	Nand(a=true, b=about, out=abnot);
	Nand(a=abnot, b=cout, out=rload); 						// load + inc + reset


То же самое, нужно вставлять тип параметра, например `@param {string} userLogin`


The function warns users not to exceed the budget.


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/255](https://github.com/JuliaRegistries/General/pull/255)

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 v2.1.3 -m "<description of version>" 9c89b2aa02225cc9757493bffd82adbad410a82b
git push origin v2.1.3
```


What was the problem with the old approach here?


Awesome! May I continue to be a pain and ask if you could add some documentation examples?  :-)


415. 字符串相加 https://leetcode-cn.com/problems/add-strings/
类似方法求解


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* https://vue-paintable-git-master.ph1p.now.sh
* https://vue-paintable.now.sh


hi bro, can you please send the report on this project to my email... oyafunke_temitayo@yahoo.com


Hello World


This file talks about different functions included in our accounting system.


good work


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The function lets the users exchange certain amount of HKD to some other currencies.


Registration pull request updated: [JuliaRegistries/General/255](https://github.com/JuliaRegistries/General/pull/255)

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 v2.1.3 -m "<description of version>" 40236eccc61ce3eb9911c91284693c9e456546bc
git push origin v2.1.3
```


working progress....


W fasadzie nie powinno być czyszczenia, to się powinno odbyć w teście (podobnie jak inicjalizacja danych)


fixed, thanks @julienrf


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @chiahaoliu was added to conda-forge. Welcome to conda-forge!
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This commit started to fail builds on IB/CMSSW_10_6_X/gcc9.


Si funziona


Problems:
- The Programm is lagging after some time, the timers won't be closed. Now I search for a fix for this Problem.


acces link


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This feature has been merged to `master` now, you should be able to rebase this branch (`git fetch --all; git rebase upstream/master`) to take advantage of it without it being cherry picked into this feature branch.


简约部分代码


草
这写的什么垃圾


This is upstreamed, I think this feature branch can be pruned.


CUDA does not support GCC 9


Thanks for the contribution. This has made its way into `master` now, I think this branch can be pruned.


This is the main function including some features, like adding or deleting income and expense records, calling other functions to achieve certain goals. For example, the users can view their incomes and expenses by different categories, view statistical report ,exchange currency and set budget warning.


This is just for fun.


plop worked with a smile :-) tx!

A last hint what to change to build SCIP+OR-Tools for .Net Framework 4.7? Currently looking through template files.... will test lp_test.cc hopefully tomorrow!


@nikic if you like - implement this.


Another comment here


Would this clear out existing values as well?


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**作業2：**

**想像你經營一個自由載客車隊，你希望能透過數據分析以提升業績，請你思考並描述你如何規劃整體的分析/解決方案：**
**1. 核心問題為何 (tips：如何定義 「提升業績 & 你的假設」)**
提升業績：應以完整交易量做為提升目標

**2. 資料從何而來 (tips：哪些資料可能會對你想問的問題產生影響 & 資料如何蒐集)**
從app、訂車網站、車隊客服而來：由app及網站的資料可能多為年輕客群，若能將客服資訊也記錄下來可以擴大資料來源和年齡層。缺點為客服數據若由人員手動輸入有紀錄錯誤的風險。
須記錄所需載客時間、上車地點、下車地點、路程遠近(km)、路程時間(min)、交易金額($)、付款方式及乘車人數

**3. 蒐集而來的資料型態為何**
載客時間：date, 上車地點、下車地點：string, 路程遠近：float, 路程時間：float, 交易金額：int, 付款方式：category, 乘車人數：int

**4. 你要回答的問題，其如何評估 (tips：你的假設如何驗證)**
是先畫出各項解釋變數與交易金額的趨勢圖、解釋變數與解釋變數的相關性，再試圖整理出找有關聯性的並分類。如在什麼時間點什麼上車地點的需求量較大，即可增加派車輛。 或者因路程遠交易金額高使得付款方式改變，可新增車上的刷卡功能，吸引年輕族群使用。


I'm currently having trouble to test SCIP on windows see
https://stackoverflow.com/questions/55831443/problem-installing-scip-6-0-1-on-windows-cmake-based-build

So first need to fix it, then i'll test the .Net Framework 4.7

AFAIK if we are using SCIP as .lib static library it should "just work"
IMHO...

On Wed, Apr 24, 2019 at 3:38 PM TornadoJo <notifications@github.com> wrote:

> plop worked with a smile :-) tx!
>
> A last hint what to change to build SCIP+OR-Tools for .Net Framework 4.7?
> Currently looking through template files.... will test lp_test.cc hopefully
> tomorrow!
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/google/or-tools/commit/7f45691e0b29e68f630ce5d24ce5c54d11aa003e#commitcomment-33292469>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AA6X6GUK5Y7P4ZDQWLEY7VTPSBPFTANCNFSM4HIDGN3Q>
> .
>


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* https://react-slidy.midu.dev
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Even better, you can add `revert()` in it to really say no.
That's what the compiler does by default now. So in effect, by defining it like this you "opened" the fallback.


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @micknudsen was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

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      Use branches in your fork for any changes and send a PR.
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Hello Pavel,

Could you please give me a short example explaining the last three commits?

Thank you.
BR


Perhaps slightly uneconomical but safety comes first here. Did you know that Ethereum balances can be higher than `2^256 - 1`, even if a contract would not be able to handle it.
Use `SafeMath` library.


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owo


2. Problem:

- If you're fully out of ammo, it could be possible that a bullet spawns at the left up corner and don't move


K, currently trying....

@cmake: super nice somehow but didn't work out for me.... made everything with msys2 x64.


> owo

u rart


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This code implies that if `msg.value % 2 > 0`, then `msg.value % 2 == 1`, am I right?
Your assumption is true now, yes. It would not be if it were `% 3`. I am no fan of implicit assumptions. I prefer explicit. Look at that:

```solidity
uint dust = msg.value % 2;
if (dust > 0) {
    _balances[owner()] += dust;
}
```
No implicit assumption.
Of course, you would use `SafeMath`. Plus, considering the discussion in Slack about the new gas cost (200) of `+= 0`, the trade-off of the `if` between cheap / clarity is probably not warranted now.


pierwsza wersja dzielenia, 7 reprezentacji, zapis do .npz


:tada:


Delete only mWakeUpPref. Don't delete mRestorePref.


If `msg.sender` emits an event on reception, then the 2 events will look "out of natural order", no?


Haxx


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Corrected the range of the numbers in test case.


Don't you also want to prevent withdraw when it is paused?


`, 0)`? Why?


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