[inst/doc/trees_with_root_edge.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:6:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L6) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:10:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L10) *style:* **Commented code should be removed.**
```r
## ----fig.width = 3, fig.height = 3---------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:14:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L14) *style:* **Commented code should be removed.**
```r
## ----fig.width = 3, fig.height = 3---------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:18:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L18) *style:* **Commented code should be removed.**
```r
## ----fig.width = 7, fig.height = 7---------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:22:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L22) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:25:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L25) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:27:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/trees_with_root_edge.R#L27) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_get_average_nltt.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:3:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L3) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:9:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L9) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:13:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L13) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:16:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L16) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:19:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:23:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L23) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:26:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L26) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:29:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L29) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:31:47:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny1),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:32:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:36:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L36) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:38:47:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L38) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny2),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:39:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L39) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:43:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L43) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:46:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L46) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:49:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L49) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L57) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:61:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L61) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:64:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L64) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:67:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L67) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:71:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L71) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:74:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L74) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L77) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:79:47:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L79) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny1),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:80:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L80) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:84:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L84) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:86:47:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny2),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:87:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:91:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L91) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:94:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L94) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:96:29:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L96) *style:* **Trailing whitespace is superfluous.**
```r
  c(phylogeny1, phylogeny2),
                            ^
```
[inst/doc/vignette_get_average_nltt.R:97:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L97) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:100:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_average_nltt.R#L100) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_get_nltt_values.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:8:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L8) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:15:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L15) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:17:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L17) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:19:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:22:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L22) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:26:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L26) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:28:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L28) *style:* **lines should not be more than 80 characters.**
```r
qplot(time, N, data = df, geom = "step", ylim = c(0,1), direction = "vh", main = "NLTT plot of phylogeny 1")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:28:53:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L28) *style:* **Commas should always have a space after.**
```r
qplot(time, N, data = df, geom = "step", ylim = c(0,1), direction = "vh", main = "NLTT plot of phylogeny 1")
                                                    ^
```
[inst/doc/vignette_get_nltt_values.R:30:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L30) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:32:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L32) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:34:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L34) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:37:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L37) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:41:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L41) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:43:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L43) *style:* **lines should not be more than 80 characters.**
```r
qplot(time, N, data = df, geom = "step", ylim = c(0,1), direction = "vh", main = "NLTT plot of phylogeny 2")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:43:53:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L43) *style:* **Commas should always have a space after.**
```r
qplot(time, N, data = df, geom = "step", ylim = c(0,1), direction = "vh", main = "NLTT plot of phylogeny 2")
                                                    ^
```
[inst/doc/vignette_get_nltt_values.R:45:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L45) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:46:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L46) *style:* **lines should not be more than 80 characters.**
```r
t <- nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny1), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:49:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L49) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:50:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L50) *style:* **lines should not be more than 80 characters.**
```r
t <- nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny2), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:53:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L53) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L57) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:60:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L60) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:61:41:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L61) *style:* **Commas should always have a space after.**
```r
t <- nLTT::get_nltt_values(c(phylogeny1,phylogeny2), dt = 0.2)
                                        ^
```
[inst/doc/vignette_get_nltt_values.R:64:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L64) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:65:42:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L65) *style:* **Commas should always have a space after.**
```r
df <- nLTT::get_nltt_values(c(phylogeny1,phylogeny2), dt = 0.01)
                                         ^
```
[inst/doc/vignette_get_nltt_values.R:67:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L67) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:68:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L68) *style:* **lines should not be more than 80 characters.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:68:54:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L68) *style:* **Commas should always have a space after.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:68:129:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L68) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
                                                                                ^
```
[inst/doc/vignette_get_nltt_values.R:71:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L71) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:72:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L72) *style:* **lines should not be more than 80 characters.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:72:54:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L72) *style:* **Commas should always have a space after.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:72:102:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L72) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
                                                                                ^
```
[inst/doc/vignette_get_nltt_values.R:75:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L75) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:77:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L77) *style:* **lines should not be more than 80 characters.**
```r
newick2 <- "((((XD:1,ZD:1):1,CE:2):1,(FE:2,EE:2):1):4,((AE:1,BE:1):1,(WD:1,YD:1):1):5);"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:82:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L82) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:84:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L84) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:86:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L86) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:89:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L89) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:93:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L93) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:95:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L95) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:97:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L97) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:100:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L100) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:104:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L104) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:105:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L105) *style:* **lines should not be more than 80 characters.**
```r
t <- nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny1), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:108:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L108) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:109:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L109) *style:* **lines should not be more than 80 characters.**
```r
t <- nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny2), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:112:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L112) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:116:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L116) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:117:41:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L117) *style:* **Commas should always have a space after.**
```r
t <- nLTT::get_nltt_values(c(phylogeny1,phylogeny2), dt = 0.2)
                                        ^
```
[inst/doc/vignette_get_nltt_values.R:120:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L120) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:121:42:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L121) *style:* **Commas should always have a space after.**
```r
df <- nLTT::get_nltt_values(c(phylogeny1,phylogeny2), dt = 0.01)
                                         ^
```
[inst/doc/vignette_get_nltt_values.R:123:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L123) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:124:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L124) *style:* **lines should not be more than 80 characters.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:124:54:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L124) *style:* **Commas should always have a space after.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:124:129:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L124) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
                                                                                ^
```
[inst/doc/vignette_get_nltt_values.R:127:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L127) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:128:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L128) *style:* **lines should not be more than 80 characters.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:128:54:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L128) *style:* **Commas should always have a space after.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:128:102:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L128) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
                                                                                ^
```
[inst/doc/vignette_get_nltt_values.R:131:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L131) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:140:53:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L140) *style:* **Trailing whitespace is superfluous.**
```r
phylogenies <- c(phylogeny1, phylogeny2, phylogeny3,
                                                    ^
```
[inst/doc/vignette_get_nltt_values.R:143:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L143) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:147:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L147) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:148:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L148) *style:* **lines should not be more than 80 characters.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:148:54:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L148) *style:* **Commas should always have a space after.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:148:129:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L148) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0,1), main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)) +
                                                                                ^
```
[inst/doc/vignette_get_nltt_values.R:151:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L151) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:152:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L152) *style:* **lines should not be more than 80 characters.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:152:54:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L152) *style:* **Commas should always have a space after.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:152:102:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L152) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "blank", ylim = c(0,1), main = "Average nLTT plot of phylogenies") +
                                                                                ^
```
[inst/doc/vignette_get_nltt_values.R:154:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_get_nltt_values.R#L154) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_nltt_statistic.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:4:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L4) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:7:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L7) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:10:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L10) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:13:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L13) *style:* **Commented code should be removed.**
```r
## ----fig.width = 7, fig.height = 4---------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:19:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:21:22:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
  ape::rcoal(n = 10),
                     ^
```
[inst/doc/vignette_nltt_statistic.R:22:22:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
  ape::rcoal(n = 10),
                     ^
```
[inst/doc/vignette_nltt_statistic.R:23:16:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L23) *style:* **Trailing whitespace is superfluous.**
```r
  species_tree,
               ^
```
[inst/doc/vignette_nltt_statistic.R:27:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L27) *style:* **Commented code should be removed.**
```r
## ----fig.width = 7, fig.height = 10--------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:35:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L35) *style:* **Commented code should be removed.**
```r
## ----fig.width = 7, fig.height = 7---------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:39:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L39) *style:* **lines should not be more than 80 characters.**
```r
rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4], col = colors()[240])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:39:20:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L39) *style:* **Commas should always have a space after.**
```r
rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4], col = colors()[240])
                   ^
```
[inst/doc/vignette_nltt_statistic.R:39:34:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L39) *style:* **Commas should always have a space after.**
```r
rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4], col = colors()[240])
                                 ^
```
[inst/doc/vignette_nltt_statistic.R:39:48:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L39) *style:* **Commas should always have a space after.**
```r
rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4], col = colors()[240])
                                               ^
```
[inst/doc/vignette_nltt_statistic.R:45:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L45) *style:* **lines should not be more than 80 characters.**
```r
  nLTT::nltt_lines(p, lwd = 3, lty = 2, col = grDevices::heat.colors(n = 4)[col_index])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:49:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L49) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:54:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L54) *style:* **Variable and function names should be all lowercase.**
```r
  nltt_stats_exact[i]  <- nLTTstat_exact(species_tree, p)
                          ^~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:55:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L55) *style:* **Variable and function names should be all lowercase.**
```r
  nltt_stats_approx[i] <- nLTTstat(species_tree, p)
                          ^~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:59:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L59) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:62:38:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L62) *style:* **Trailing whitespace is superfluous.**
```r
  nltt_stat_exact = nltt_stats_exact,
                                     ^
```
[inst/doc/vignette_nltt_statistic.R:67:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L67) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:69:14:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L69) *style:* **Trailing whitespace is superfluous.**
```r
  nltt_stats,
             ^
```
[inst/doc/vignette_nltt_statistic.R:70:21:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L70) *style:* **Trailing whitespace is superfluous.**
```r
  id.vars = c("id"),
                    ^
```
[inst/doc/vignette_nltt_statistic.R:76:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L76) *style:* **Trailing whitespace is superfluous.**
```r
  df$method,
            ^
```
[inst/doc/vignette_nltt_statistic.R:80:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L80) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:82:13:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L82) *style:* **Trailing whitespace is superfluous.**
```r
  data = df,
            ^
```
[inst/doc/vignette_nltt_statistic.R:89:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_nltt_statistic.R#L89) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_stretch_nltt_matrix.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:6:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L6) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:10:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L10) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:12:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L12) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:15:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L15) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:19:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:21:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L21) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:23:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L23) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:25:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L25) *style:* **lines should not be more than 80 characters.**
```r
stretch_matrix <- nLTT::stretch_nltt_matrix(nltt, dt = 0.25, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:28:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L28) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:30:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L30) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:31:37:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L31) *style:* **Put spaces around all infix operators.**
```r
points(stretch_matrix, pch = 19, col="blue")
                                   ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:33:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L33) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:37:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:39:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L39) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:42:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L42) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:46:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L46) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:48:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L48) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:50:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L50) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:52:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L52) *style:* **lines should not be more than 80 characters.**
```r
stretch_matrix <- nLTT::stretch_nltt_matrix(nltt, dt = 0.25, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:55:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L55) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:57:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L57) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:58:37:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L58) *style:* **Put spaces around all infix operators.**
```r
points(stretch_matrix, pch = 19, col="blue")
                                   ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:60:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L60) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:61:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L61) *style:* **lines should not be more than 80 characters.**
```r
newick <- "((((XD:1,ZD:1):1,CE:2):1,(FE:2,EE:2):1):4,((AE:1,BE:1):1,(WD:1,YD:1):1):5);"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:64:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L64) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:66:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L66) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:69:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L69) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:73:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L73) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:75:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L75) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L77) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:80:1:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L80) *style:* **lines should not be more than 80 characters.**
```r
stretch_matrix <- nLTT::stretch_nltt_matrix(nltt, dt = 0.05, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:81:27:](https://github.com/richelbilderbeek/nLTT/blob/92b95883cc96a1b3e32d5dde97d57e4334b73707/inst/doc/vignette_stretch_nltt_matrix.R#L81) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```


yes thanks, will start tracking there repos too


Since our manifest ... Is tracking all stuff needed ... I think you don't need track it


sounds good


Aren't these already in 7.0 NEWS? If so, why do you add them to 7.1? I thought that we add a news info to the lowest branch only..?