[R/assert_DDvTD_wd.R:10:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_DDvTD_wd.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
assert_DDvTD_wd <- function() {
^~~~~~~~~~~~~~~
```
[R/assert_init_k.R:10:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_init_k.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!init_k %in% arg_init_k()) {
    ^
```
[R/assert_optim.R:3:57:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_optim.R#L3) *warning:* **no visible global function definition for ‘arg_optim’**
```r
    stop(cat("'optim' is invalid. Possible inputs are", arg_optim()))
                                                        ^~~~~~~~~
```
[R/assert_optim.R:9:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_optim.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !(optim %in% arg_optim())){
      ^
```
[R/assert_optim.R:9:33:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_optim.R#L9) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if ( !(optim %in% arg_optim())){
                                ^~
```
[R/assert_para.R:10:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_para.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !(para %in% DDvTDtools::arg_para())){
      ^
```
[R/assert_para.R:10:43:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_para.R#L10) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if ( !(para %in% DDvTDtools::arg_para())){
                                          ^~
```
[R/assert_sim.R:3:57:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_sim.R#L3) *warning:* **no visible global function definition for ‘arg_sim’**
```r
    stop(cat("'optim' is invalid. Possible inputs are", arg_sim()))
                                                        ^~~~~~~
```
[R/assert_sim.R:9:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_sim.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !(sim %in% arg_sim())){
      ^
```
[R/assert_sim.R:9:29:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/assert_sim.R#L9) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if ( !(sim %in% arg_sim())){
                            ^~
```
[R/check_convergence_optim.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/check_convergence_optim.R:13:59:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L13) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
check_convergence_optim <- function(folder = "data/optim/"){
                                                          ^~
```
[R/check_convergence_optim.R:18:6:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(file in files_list){
     ^
```
[R/check_convergence_optim.R:18:25:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L18) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  for(file in files_list){
                        ^~
```
[R/check_convergence_optim.R:22:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(missing_rows) > 0){
      ^
```
[R/check_convergence_optim.R:22:32:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L22) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(length(missing_rows) > 0){
                               ^~
```
[R/check_convergence_optim.R:26:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L26) *style:* **Variable and function name style should be snake_case.**
```r
    notConverged <- which(res$hasConverged == FALSE)
    ^~~~~~~~~~~~
```
[R/check_convergence_optim.R:27:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(notConverged > 0)){
      ^
```
[R/check_convergence_optim.R:27:32:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L27) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(length(notConverged > 0)){
                               ^~
```
[R/check_convergence_optim.R:28:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L28) *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:32:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_convergence_optim.R#L32) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/check_init_pars.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L2) *warning:* **no visible global function definition for ‘assert_optim’**
```r
  assert_optim(optim)
  ^~~~~~~~~~~~
```
[R/check_init_pars.R:16:51:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L16) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
check_init_pars <- function(init_pars, optim, brts){
                                                  ^~
```
[R/check_init_pars.R:18:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L18) *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_init_pars.R:18:28:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L18) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!is.numeric(init_pars)){stop("brts should be a numeric vector.")}
                           ^~
```
[R/check_init_pars.R:18:29:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L18) *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_init_pars.R:18:70:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L18) *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_init_pars.R:19:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L19) *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_init_pars.R:19:23:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L19) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!is.numeric(brts)){stop("init_pars should be a numeric vector.")}
                      ^~
```
[R/check_init_pars.R:19:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.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(brts)){stop("init_pars should be a numeric vector.")}
                       ^
```
[R/check_init_pars.R:19:70:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L19) *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_init_pars.R:20:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(init_pars) != 3){
    ^
```
[R/check_init_pars.R:20:28:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L20) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(length(init_pars) != 3){
                           ^~
```
[R/check_init_pars.R:21:13:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L21) *warning:* **no visible global function definition for ‘get_Kprime’**
```r
  Kprime <- get_Kprime(init_pars)
            ^~~~~~~~~~
```
[R/check_init_pars.R:24:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L24) *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_init_pars.R:24:22:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L24) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(init_pars[1] < 0){ stop("Initial lambda0 has a negative value.") }
                     ^~
```
[R/check_init_pars.R:24:23:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L24) *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_init_pars.R:24:71:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L24) *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_init_pars.R:25:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L25) *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_init_pars.R:25:22:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L25) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(init_pars[2] < 0){ stop("Initial mu0 has a negative value.") }
                     ^~
```
[R/check_init_pars.R:25:23:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L25) *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_init_pars.R:25:67:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L25) *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_init_pars.R:26:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L26) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(init_pars[1] <= init_pars[2]){
    ^
```
[R/check_init_pars.R:26:34:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L26) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(init_pars[1] <= init_pars[2]){
                                 ^~
```
[R/check_init_pars.R:33:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L33) *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_init_pars.R:33:22:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L33) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(init_pars[3] < 1){ stop("Initial K must be greater than 1.")}
                     ^~
```
[R/check_init_pars.R:33:23:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L33) *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_init_pars.R:33:66:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L33) *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_init_pars.R:35:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  N <- length(brts) + 1
  ^
```
[R/check_init_pars.R:36:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  Kprime <- get_Kprime(init_pars)
  ^~~~~~
```
[R/check_init_pars.R:38:26:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_init_pars.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (ceiling(Kprime) < N ) {
                         ^
```
[R/check_results.R:6:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param results a results data frame, as produced by [run_optim()] or accessed by
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_results.R:35:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
#' @param results a results data frame, as produced by [run_optim()] or accessed by
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_results.R:42:55:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L42) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
check_incomplete_rows <- function(results, return_rows){
                                                      ^~
```
[R/check_results.R:45:6:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(results$mc)){
     ^
```
[R/check_results.R:45:33:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L45) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  for(i in seq_along(results$mc)){
                                ^~
```
[R/check_results.R:46:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(anyNA(results[i,])){
      ^
```
[R/check_results.R:46:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L46) *style:* **Commas should always have a space after.**
```r
    if(anyNA(results[i,])){
                       ^
```
[R/check_results.R:46:26:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L46) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(anyNA(results[i,])){
                         ^~
```
[R/check_results.R:50:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L50) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(incomplete_rows > 0)){
    ^
```
[R/check_results.R:50:33:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(length(incomplete_rows > 0)){
                                ^~
```
[R/check_results.R:58:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L58) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_rows){
    ^
```
[R/check_results.R:58:17:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L58) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(return_rows){
                ^~
```
[R/check_results.R:71:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
#' @param results a results data frame, as produced by [run_optim()] or accessed by
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_results.R:78:60:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L78) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
check_loglikelihood_exists <- function(results, return_rows){
                                                           ^~
```
[R/check_results.R:80:60:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L80) *style:* **Commas should always have a space after.**
```r
  missing_loglikelihoods <- which(results$loglik %in% c(NA,-1,-Inf))
                                                           ^
```
[R/check_results.R:80:63:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L80) *style:* **Commas should always have a space after.**
```r
  missing_loglikelihoods <- which(results$loglik %in% c(NA,-1,-Inf))
                                                              ^
```
[R/check_results.R:81:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L81) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(missing_loglikelihoods > 0)){
    ^
```
[R/check_results.R:81:40:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L81) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(length(missing_loglikelihoods > 0)){
                                       ^~
```
[R/check_results.R:89:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L89) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_rows){
    ^
```
[R/check_results.R:89:17:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L89) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(return_rows){
                ^~
```
[R/check_results.R:100:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
#' @param results a results data frame, as produced by [run_optim()] or accessed by
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_results.R:107:51:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L107) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
check_missing_mcs <- function(results, return_rows){
                                                  ^~
```
[R/check_results.R:111:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(missing_mcs > 0)){
    ^
```
[R/check_results.R:111:29:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L111) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(length(missing_mcs > 0)){
                            ^~
```
[R/check_results.R:119:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L119) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(return_rows){
    ^
```
[R/check_results.R:119:17:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L119) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(return_rows){
                ^~
```
[R/check_results.R:126:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L126) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/check_results.R:127:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L127) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/check_results.R:128:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/check_results.R#L128) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/count_errors_logs.R:15:41:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L15) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
count_errors_log <- function(path_to_log){
                                        ^~
```
[R/count_errors_logs.R:37:6:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(log_file)){
     ^
```
[R/count_errors_logs.R:37:31:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L37) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  for(i in seq_along(log_file)){
                              ^~
```
[R/count_errors_logs.R:40:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L40) *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_logs.R:40:65:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L40) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(log_file[[i]] == paste("Running ML for tree", mc + 1, "")){
                                                                ^~
```
[R/count_errors_logs.R:44:8:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(j in seq_along(error_templates)){
       ^
```
[R/count_errors_logs.R:44:40:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L44) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    for(j in seq_along(error_templates)){
                                       ^~
```
[R/count_errors_logs.R:45:9:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(log_file[[i]] == error_templates[j]){
        ^
```
[R/count_errors_logs.R:45:45:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/count_errors_logs.R#L45) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
      if(log_file[[i]] == error_templates[j]){
                                            ^~
```
[R/default_pars2_dd1.R:7:31:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/default_pars2_dd1.R#L7) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
default_pars2_dd1 <- function(){
                              ^~
```
[R/default_pars2_td4.R:7:31:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/default_pars2_td4.R#L7) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
default_pars2_td4 <- function(){
                              ^~
```
[R/fill_missing_rows.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/fill_missing_rows.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L3) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/fill_missing_rows.R:8:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L8) *warning:* **no visible global function definition for ‘%>%’**
```r
    sim <- results$sim %>% as.character() %>% unique()
                       ^~~
```
[R/fill_missing_rows.R:8:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L8) *warning:* **no visible global function definition for ‘%>%’**
```r
    sim <- results$sim %>% as.character() %>% unique()
                       ^~~
```
[R/fill_missing_rows.R:9:28:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L9) *warning:* **no visible global function definition for ‘%>%’**
```r
    optim <- results$optim %>% as.character() %>% unique()
                           ^~~
```
[R/fill_missing_rows.R:9:28:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L9) *warning:* **no visible global function definition for ‘%>%’**
```r
    optim <- results$optim %>% as.character() %>% unique()
                           ^~~
```
[R/fill_missing_rows.R:14:17:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L14) *warning:* **no visible global function definition for ‘get_multi_brts’**
```r
    all_brts <- get_multi_brts(sim = sim, para = para)
                ^~~~~~~~~~~~~~
```
[R/fill_missing_rows.R:16:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L16) *warning:* **local variable ‘new_rows’ assigned but may not be used**
```r
    new_rows <- results_optim_struct()
    ^~~~~~~~
```
[R/fill_missing_rows.R:16:17:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L16) *warning:* **no visible global function definition for ‘results_optim_struct’**
```r
    new_rows <- results_optim_struct()
                ^~~~~~~~~~~~~~~~~~~~
```
[R/fill_missing_rows.R:22:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
    pars <- c(results$crown_age[1], results$true_lambda0[1], results$true_mu0[1], results$true_K[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/fill_missing_rows.R:23:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L23) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(any(para_to_pars(para) != pars)) {
      ^
```
[R/fill_missing_rows.R:29:8:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fill_missing_rows.R#L29) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(mc in missing_rows) {
       ^
```
[R/fix_indexing.R:28:22:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fix_indexing.R#L28) *style:* **Commas should always have a space after.**
```r
      results_copy[i,] <- results[which(results$mc == i),]
                     ^
```
[R/fix_indexing.R:28:58:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/fix_indexing.R#L28) *style:* **Commas should always have a space after.**
```r
      results_copy[i,] <- results[which(results$mc == i),]
                                                         ^
```
[R/format_optim_results_row.R:29:30:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
                             ML_output, num_cycles = 1, methode, optimmethod,
                             ^~~~~~~~~
```
[R/format_optim_results_row.R:30:30:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
                             jobID, cond)
                             ^~~~~
```
[R/format_optim_results_row.R:31:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L31) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/format_optim_results_row.R:46:29:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L46) *style:* **Commas should always have a space after.**
```r
    lambda0_ML = ML_output[,1],
                            ^
```
[R/format_optim_results_row.R:47:25:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L47) *style:* **Commas should always have a space after.**
```r
    mu0_ML = ML_output[,2],
                        ^
```
[R/format_optim_results_row.R:48:23:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L48) *style:* **Commas should always have a space after.**
```r
    K_ML = ML_output[,3],
                      ^
```
[R/format_optim_results_row.R:59:39:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L59) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!is.na(df$K_ML) & df$K_ML == 0) {df$K_ML <- NA}
                                      ^
```
[R/format_optim_results_row.R:59:43:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L59) *style:* **Variable and function name style should be snake_case.**
```r
  if (!is.na(df$K_ML) & df$K_ML == 0) {df$K_ML <- NA}
                                          ^~~~
```
[R/format_optim_results_row.R:59:53:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/format_optim_results_row.R#L59) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!is.na(df$K_ML) & df$K_ML == 0) {df$K_ML <- NA}
                                                    ^
```
[R/get_avg_ltt_table.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_avg_ltt_table.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L3) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_avg_ltt_table.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L4) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_avg_ltt_table.R:15:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L15) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.logical(with_extinct)) {
    ^
```
[R/get_avg_ltt_table.R:16:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L16) *style:* **Only use double-quotes.**
```r
    stop('with_extinct must be a logical')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_avg_ltt_table.R:18:16:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L18) *warning:* **no visible global function definition for ‘para_to_pars’**
```r
  crown_age <- para_to_pars(para)[1]
               ^~~~~~~~~~~~
```
[R/get_avg_ltt_table.R:32:43:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L32) *style:* **Commas should always have a space after.**
```r
    raw_time = as.numeric(avg_ltt_matrix[,1]),
                                          ^
```
[R/get_avg_ltt_table.R:33:44:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_avg_ltt_table.R#L33) *style:* **Commas should always have a space after.**
```r
    raw_avg_n = as.numeric(avg_ltt_matrix[,2]),
                                           ^
```
[R/get_brts.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_brts.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L3) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_brts.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L4) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_brts.R:11:57:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L11) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
get_brts <- function(sim, para, mc, with_extinct = FALSE){
                                                        ^~
```
[R/get_brts.R:12:12:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L12) *warning:* **no visible global function definition for ‘read_sim’**
```r
  trees <- read_sim(sim = sim, para = para)
           ^~~~~~~~
```
[R/get_brts.R:15:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L15) *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:15:39:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L15) *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:15:40:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L15) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!is.numeric(mc) | !mc %in% 1:1000 ){
                                       ^~
```
[R/get_brts.R:16:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L16) *style:* **Only use double-quotes.**
```r
    stop('mc must be a numeric in 1:1000')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:18:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.logical(with_extinct)){
    ^
```
[R/get_brts.R:18:31:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L18) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!is.logical(with_extinct)){
                              ^~
```
[R/get_brts.R:19:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L19) *style:* **Only use double-quotes.**
```r
    stop('with_extinct must be a logical')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:24:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(any(!mc %in% seq_along(trees))){
    ^
```
[R/get_brts.R:24:36:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L24) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(any(!mc %in% seq_along(trees))){
                                   ^~
```
[R/get_brts.R:25:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L25) *style:* **Only use double-quotes.**
```r
    stop('There is no tree is the file for that mc.')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_brts.R:28:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!with_extinct){
    ^
```
[R/get_brts.R:28:19:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L28) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!with_extinct){
                  ^~
```
[R/get_brts.R:29:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L29) *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:29:46:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L29) *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:29:63:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L29) *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:29:65:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L29) *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:31:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L31) *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:31:46:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L31) *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:31:63:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L31) *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:31:65:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_brts.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    brts <- as.numeric( ape::branching.times( trees[[mc]][[2]] ) )
                                                                ^
```
[R/get_default_initpars.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L2) *warning:* **no visible global function definition for ‘assert_optim’**
```r
  assert_optim(optim)
  ^~~~~~~~~~~~
```
[R/get_default_initpars.R:25:56:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L25) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
get_default_initpars <- function(true_pars, optim, brts){
                                                       ^~
```
[R/get_default_initpars.R:27:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L27) *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:27:28:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L27) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!is.numeric(true_pars)){stop("true_pars should be numeric.")}
                           ^~
```
[R/get_default_initpars.R:27:29:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L27) *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:27:66:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L27) *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:28:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L28) *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:28:23:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L28) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(!is.numeric(brts)){stop("brts should be numeric.")}
                      ^~
```
[R/get_default_initpars.R:28:24:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_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(!is.numeric(brts)){stop("brts should be numeric.")}
                       ^
```
[R/get_default_initpars.R:28:56:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L28) *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:30:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  N <- length(brts) + 1
  ^
```
[R/get_default_initpars.R:32:20:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_default_initpars.R#L32) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (optim == "CR"){
                   ^~
```
[R/get_delta_aic.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_delta_aic.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L3) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_delta_aic.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L4) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_delta_aic.R:11:55:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L11) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
get_delta_aic <- function(sim, para, init_k = "true_k"){
                                                      ^~
```
[R/get_delta_aic.R:16:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  res_DD <- read_optim_results(
  ^~~~~~
```
[R/get_delta_aic.R:19:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
  res_TD <- read_optim_results(
  ^~~~~~
```
[R/get_delta_aic.R:23:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
  dAIC <- c()
  ^~~~
```
[R/get_delta_aic.R:28:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
      dAIC <- c(dAIC, NA)
      ^~~~
```
[R/get_delta_aic.R:30:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_delta_aic.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
      dAIC <- c(dAIC, res_DD$AIC[mc] - res_TD$AIC[mc])
      ^~~~
```
[R/get_Kprime.R:8:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_Kprime.R#L8) *style:* **Variable and function name style should be snake_case.**
```r
get_Kprime <- function(pars){
^~~~~~~~~~
```
[R/get_Kprime.R:8:28:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_Kprime.R#L8) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
get_Kprime <- function(pars){
                           ^~
```
[R/get_Kprime.R:9:1:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/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/d2742222e3eb63ca7084292584ece26edc95c8e9/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/d2742222e3eb63ca7084292584ece26edc95c8e9/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:9:41:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_Kprime.R#L9) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```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/d2742222e3eb63ca7084292584ece26edc95c8e9/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/d2742222e3eb63ca7084292584ece26edc95c8e9/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/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_Kprime.R#L11) *style:* **Commented code should be removed.**
```r
  # Kprime = la0 * K / (la0 - mu0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_lr_table.R:9:11:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_table.R#L9) *warning:* **no visible global function definition for ‘get_lr’**
```r
    lr <- get_lr(sim = sim, para = para, init_k = init_k)
          ^~~~~~
```
[R/get_lr_threshold.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_threshold.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_lr_threshold.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_threshold.R#L3) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_lr_threshold.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_threshold.R#L4) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_lr_threshold.R:5:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_threshold.R#L5) *warning:* **no visible global function definition for ‘assert_init_k’**
```r
  assert_init_k(init_k)
  ^~~~~~~~~~~~~
```
[R/get_lr_threshold.R:10:9:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_threshold.R#L10) *warning:* **no visible global function definition for ‘get_lr’**
```r
  lr <- get_lr(sim = sim, para = para, init_k = init_k)
        ^~~~~~
```
[R/get_lr_threshold.R:11:6:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr_threshold.R#L11) *warning:* **no visible global function definition for ‘%>%’**
```r
  lr %>% stats::quantile(probs = percentile, na.rm = TRUE)
     ^~~
```
[R/get_lr.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_lr.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L3) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_lr.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L4) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_lr.R:5:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L5) *warning:* **no visible global function definition for ‘assert_init_k’**
```r
  assert_init_k(init_k)
  ^~~~~~~~~~~~~
```
[R/get_lr.R:14:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  res_DD <- read_optim_results(
  ^~~~~~
```
[R/get_lr.R:17:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  res_TD <- read_optim_results(
  ^~~~~~
```
[R/get_lr.R:22:6:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_lr.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(mc in 1:1000) {
     ^
```
[R/get_multi_brts.R:2:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L2) *warning:* **no visible global function definition for ‘assert_DDvTD_wd’**
```r
  assert_DDvTD_wd()
  ^~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:3:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L3) *warning:* **no visible global function definition for ‘assert_para’**
```r
  assert_para(para)
  ^~~~~~~~~~~
```
[R/get_multi_brts.R:4:3:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L4) *warning:* **no visible global function definition for ‘assert_sim’**
```r
  assert_sim(sim)
  ^~~~~~~~~~
```
[R/get_multi_brts.R:15:12:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L15) *warning:* **no visible global function definition for ‘read_sim’**
```r
  trees <- read_sim(sim = sim, para = para)
           ^~~~~~~~
```
[R/get_multi_brts.R:18:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L18) *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:18:26:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L18) *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:18:44:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L18) *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:19:54:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (!is.numeric(rangemc) | any(!rangemc %in% 1:1000 )) {
                                                     ^
```
[R/get_multi_brts.R:20:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L20) *style:* **Only use double-quotes.**
```r
    stop('mc must be a vector of numeric values between 1 and 1000')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:22:32:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L22) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (!is.logical(with_extinct)){
                               ^~
```
[R/get_multi_brts.R:23:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L23) *style:* **Only use double-quotes.**
```r
    stop('with_extinct must be a logical')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:26:15:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L26) *style:* **Use <-, not =, for assignment.**
```r
  brts_bundle = list()
              ^
```
[R/get_multi_brts.R:30:5:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(any(!rangemc %in% seq_along(trees))){
    ^
```
[R/get_multi_brts.R:30:41:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L30) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(any(!rangemc %in% seq_along(trees))){
                                        ^~
```
[R/get_multi_brts.R:31:10:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L31) *style:* **Only use double-quotes.**
```r
    stop('rangemc out of bounds of the trees list.')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_multi_brts.R:34:31:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L34) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  for (i in seq_along(rangemc)){
                              ^~
```
[R/get_multi_brts.R:36:8:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L36) *style:* **Use <-, not =, for assignment.**
```r
    mc = rangemc[i]
       ^
```
[R/get_multi_brts.R:38:7:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L38) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!with_extinct){
      ^
```
[R/get_multi_brts.R:38:21:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L38) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(!with_extinct){
                    ^~
```
[R/get_multi_brts.R:40:38:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      brts_bundle[[i]] <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                     ^
```
[R/get_multi_brts.R:40:60:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      brts_bundle[[i]] <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                                           ^
```
[R/get_multi_brts.R:40:77:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      brts_bundle[[i]] <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                                                            ^
```
[R/get_multi_brts.R:40:79:](https://github.com/TheoPannetier/DDvTDtools/blob/d2742222e3eb63ca7084292584ece26edc95c8e9/R/get_multi_brts.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      brts_bundle[[i]] <- as.numeric( ape::branching.times( trees[[mc]][[1]] ) )
                                                                              ^
```


Dear Poggit user,

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> I'm not sure if this is appropriate but have you tried to mess with isk - something like:
>
> https://github.com/FrigoEU/psc-ide-vim/pull/146/files

Thanks! I didn't understand what the syntax for `isk` is, but it did the trick! Made a new commit updating the dot-files.

> So "I'm in"! The first upcoming free afternoon I'm going to move to LanguageClient.

Good. I'm pretty sure you'll love it.


@szpeter80
A header-t frissítettem aszerint, ahogy a többi ABP filterben is van, pl itt: https://easylist-downloads.adblockplus.org/easylist.txt vagy itt: https://easylist.to/easylist/easyprivacy.txt
Remélem, hogy ez megoldja azt a gondot is, hogy az Adguard nem akarja nekem manuálisan frissíteni.


Successfully deployed to following URLs:

* https://crawl-a9zqtn3cc.now.sh
* https://crawl.now.sh
* https://crawl.benarthurstuart.now.sh
* https://crawl-git-master.benarthurstuart.now.sh


Commit is not a place for asking support questions. Please use one of [support channels](https://code.djangoproject.com/wiki/TicketClosingReasons/UseSupportChannels).


AQI commit


Successfully deployed to following URLs:

* https://tsps-69u90ezvo.now.sh
* https://tsps.now.sh
* https://tsps.wangchenxu.now.sh
* https://tsps-git-master.wangchenxu.now.sh


Successfully deployed to following URLs:

* https://topics-manager-semi0o20d.now.sh
* https://topics-manager.now.sh
* https://topics-manager.iamstarkov.now.sh
* https://topics-manager-git-master.iamstarkov.now.sh


> ``

@brandonscott1780


Successfully deployed to following URLs:

* https://zeit-now-routing-tests-r7padrqpo.now.sh
* https://zeit-now-routing-tests.now.sh
* https://zeit-now-routing-tests.pristas-peter.now.sh
* https://zeit-now-routing-tests-git-master.pristas-peter.now.sh


yea, the rdn is increasing in each Ps within a line, or the recursion of each Ps, from my debug, there is no reinitialization of rdn and hence causing the value to remain constant or in increasing manner, we need to insert the initialization of rdn in each intra_P call, but i cannot sure on this yet


Successfully deployed to following URLs:

* https://takwimuafrica-8oa5a65vr.now.sh
* https://dev.takwimu.africa
* https://takwimuafrica.takwimu.now.sh
* https://takwimuafrica-git-master.takwimu.now.sh


Successfully deployed to following URLs:

* https://camelidentify-d30mszhhn.now.sh
* https://camelidentify.now.sh
* https://camelidentify.rhiyo.now.sh
* https://camelidentify-git-master.rhiyo.now.sh


Did you test this one? The output should be ValueError: [error message], so I think there is no need to mention ValueError in error message again.


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


Successfully deployed to following URLs:

* https://itchio-godot-scraper-qehng4l1h.now.sh
* https://itchio-godot-scraper.now.sh
* https://itchio-godot-scraper.hiulit.now.sh
* https://itchio-godot-scraper-git-master.hiulit.now.sh


È `pip` installato?


来了来了


`requests`


Successfully deployed to following URLs:

* https://svr2-iupxc6o5u.now.sh
* https://svr2.svodnoeraspisanie.now.sh
* https://svr2-git-master.svodnoeraspisanie.now.sh


yea I think it's on your fork. I can create one here. But I was wondering would it make more sense to make sure that when travis builds and tests owl_ode, it uses the latest version of owl on github (as opposed to opam)


Cambia al branch `step1` ed elenca i file al suo interno.


все делаем красиво, на отдельных строках
messages={this.state.messages}
updateData = {this.updateData}


Successfully deployed to following URLs:

* https://unpaprdapi-9p0tupk8y.now.sh
* https://api.unpaprd.paperplane.ml
* https://unpaprdapi.gargakshit.now.sh
* https://unpaprdapi-git-master.gargakshit.now.sh


This code has Angular with Security , MVC EF , JWT token


Successfully deployed to following URLs:

* https://ui-f15fr4x9n.now.sh
* https://ui.roleypoly.com
* https://ui.roleypoly.now.sh
* https://ui-git-master.roleypoly.now.sh


Successfully deployed to following URLs:

* https://ccc-q3nah79hx.now.sh
* https://ccc.zeit-github-test-dev1.now.sh
* https://ccc-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://next-site-dn2m3uuva.now.sh
* https://next-site-test.now.sh
* https://nextjs.org
* https://www.nextjs.org
* https://next-site.zeit.now.sh
* https://next-site-git-master.zeit.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-without-alias-4vn1pdkvu.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://game-central-9q1mtcg0z.now.sh
* https://game-central.now.sh
* https://game-central.koppawk.now.sh
* https://game-central-git-master.koppawk.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-gdhperydqp.now.sh
* https://z-github-e2e-tests-dev-only.now.sh


Successfully deployed to following URLs:

* https://dreamiumcenter-2bacubkf0.now.sh
* https://dreamium.center
* https://dreamiumcenter.now.sh
* https://dreamiumcenter.zachkrall.now.sh
* https://dreamiumcenter-git-master.zachkrall.now.sh


Deployment failed with the following error:

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


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-with-alias-iwnahag22.now.sh
* https://z-github-e2e-tests-dev-alias-v2-with-alias.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias-git-master.zeit-github-test-dev1.now.sh


Found spelling mistakes in documentation file ANNMODPP.md<<
 annfunc feedforward annfunc ANNfunc ANNfunc ANNfunc ANNfunc
 Found spelling mistakes in documentation file GlossaryPP.md<<
 ANNMOD Multithermal multibaric
 Found spelling mistakes in documentation file ModulesPP.md<<
 annfunc
 Found spelling mistakes in documentation file VESPP.md<<
 Multithermal multibaric
 Found spelling mistakes in documentation file automatic/aaa-master-ISDD-1.txt<<
 ISDD handson
 Found spelling mistakes in documentation file automatic/aaa-master-ISDD-2.txt<<
 ISDD handson ISDD ISDD
 Found spelling mistakes in documentation file automatic/amber18.txt<<
 pmemd pmemd pmemd
 Found spelling mistakes in documentation file automatic/ANN.txt<<
 annfunc annfunc feedforward ann ann th
 Found spelling mistakes in documentation file automatic/gen_example.txt<<
 ppp nobadge
 Found spelling mistakes in documentation file automatic/MAZE_MEMETIC_SAMPLING.txt<<
 memetics
 Found spelling mistakes in documentation file automatic/MAZE_OPTIMIZER_BIAS.txt<<
 Rescaled
 Found spelling mistakes in documentation file automatic/MAZE_RANDOM_ACCELERATION_MD.txt<<
 acceleratiob
 Found spelling mistakes in documentation file automatic/MOLINFO.txt<<
 subprocess subprocess ok ok
 Found spelling mistakes in documentation file automatic/REWEIGHT_TEMP_PRESS.txt<<
 isothermal mathcal mathcal mathcal isothermal mathcal mathcal isothermal NP'T mathcal mathcal isothermal NP'T mathcal mathcal mathcal postprocess postprocess
 Found spelling mistakes in documentation file automatic/TD_MULTICANONICAL.txt<<
 multicanonical TRESHOLD multicanonical multicanonical smooting
 Found spelling mistakes in documentation file automatic/TD_MULTITHERMAL_MULTIBARIC.txt<<
 Multithermal multibaric multithermal multibaric barostat rigurously multicanonical mathcal mathcal TP multicanonical multithermal multibaric multithermal multibaric fcc GPa fcc barostat smooting
 Found spelling mistakes in documentation file automatic/VES_DELTA_F.txt<<
 indipendent MetaD oufile fesA fesA AdaGrad rescale STRIDEs rescaled
 Found spelling mistakes in documentation file ../CHANGES/v2.6.md<<
 sidechain PMEMD Viktor Drobot previosly ADDEXP removerd
 Found spelling mistakes in documentation file tutorials/aaa-master-ISDD-1.txt<<
 ISDD handson
 Found spelling mistakes in documentation file tutorials/aaa-master-ISDD-2.txt<<
 ISDD handson ISDD ISDD


Looks like the Windows box hit a space issue.  I'll clean it up and maybe reboot it.


I actually get the following warning, so maybe it's related:
> [WARNING] The POM for org.jodconverter:jodconverter-local:jar:4.2.3 is missing, no dependency information available


Successfully deployed to following URLs:

* https://candidatspourparis-eb5k2txgr.now.sh
* https://candidats.pour.paris
* https://candidatspourparis.benjamintd.now.sh
* https://candidatspourparis-git-master.benjamintd.now.sh


Successfully deployed to following URLs:

* https://cinemaddict-react-app-2q5fjcy8x.now.sh
* https://cinemaddict-react-app.now.sh
* https://cinemaddict-react-app.zhukovaxenia.now.sh
* https://cinemaddict-react-app-git-master.zhukovaxenia.now.sh


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Successfully deployed to following URLs:

* https://basis-kr6vbf8q8.now.sh
* https://basis.now.sh
* https://basis.basis.now.sh
* https://basis-git-master.basis.now.sh


Could we not delete this heading please? Instead a line saying "There are no contributing mentors yet" underneath (presuming that to be correct)


Successfully deployed to following URLs:

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* https://veneman.dev
* https://bartvenemangithubio.bartveneman.now.sh
* https://bartvenemangithubio-git-master.bartveneman.now.sh


The slacks should have ` around them


> Yes, but sed and some other GNU utilities are. In the pack of them that coming with GIT there is unzip.exe as well.

I would not have a problem to use unzip if it was declared to be necessary for the build, but it (nor any package containing it) was not so far.


Failed to assign a domain to your deployment due to the following error:

~~~
The domain r5vmnophkk.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/9j15mi6or) or [visit](https://github-e2e-test-dev-domain-issues-9j15mi6or.now.sh) the non-aliased deployment)