[inst/doc/trees_with_root_edge.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:3:9:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L3) *style:* **Variable and function names should be all lowercase.**
```r
library(nLTT)
        ^~~~
```
[inst/doc/vignette_get_average_nltt.R:6:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L6) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:12:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L12) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:14:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L14) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:16:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:22:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L22) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:24:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L24) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:26:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L29) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:32:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L32) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:33:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L33) *style:* **lines should not be more than 80 characters.**
```r
nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny1), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:35:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L35) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:36:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L36) *style:* **lines should not be more than 80 characters.**
```r
nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny2), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:38:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L38) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:41:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:44:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L44) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:46:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L46) *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_average_nltt.R:50:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L50) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:52:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L52) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:54:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L54) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L57) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:60:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L60) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:62:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L62) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
add.scale.bar()
^~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:64:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L67) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:70:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L70) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:71:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L71) *style:* **lines should not be more than 80 characters.**
```r
nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny1), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:73:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L73) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:74:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L74) *style:* **lines should not be more than 80 characters.**
```r
nLTT::stretch_nltt_matrix(nLTT::get_phylogeny_nltt_matrix(phylogeny2), dt = 0.20, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:76:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L76) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:79:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L79) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:81:1:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_average_nltt.R#L81) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_get_nltt_values.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_nltt_values.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:4:9:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_get_nltt_values.R#L4) *style:* **Variable and function names should be all lowercase.**
```r
library(nLTT)
        ^~~~
```
[inst/doc/vignette_get_nltt_values.R:8:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_nltt_statistic.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:2:9:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_nltt_statistic.R#L2) *style:* **Variable and function names should be all lowercase.**
```r
library(nLTT)
        ^~~~
```
[inst/doc/vignette_nltt_statistic.R:4:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_stretch_nltt_matrix.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:3:9:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_stretch_nltt_matrix.R#L3) *style:* **Variable and function names should be all lowercase.**
```r
library(nLTT)
        ^~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:6:2:](https://github.com/richelbilderbeek/nLTT/blob/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/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/569f0fb794b68cb41eb05cd28cd01a162600c98a/inst/doc/vignette_stretch_nltt_matrix.R#L69) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


I'll stick to what motivated the change:

"This is an overall more user-friendly layout.
Fortunatelly Xiaomi didn't put any patterns over the buttons,
so this change can be done without causing an aesthetic problem."


Thank you for your advice and feed back.I will learn it more and fix it as soon as possible.


Hi,
Has this fix been is part of v 4.0.5?


Typo It's pom.xml


uni su tigdagdag ko


同上上


additional dummy texts


Related to: backdrop/backdrop-issues#1373


aa


Partially reverted in https://github.com/LimeSurvey/LimeSurvey/commit/b39ad5f0c9092dc004d82dde7389d6f12c30a81f .

@maziminke : you delete your comment ? You're tracked ;)


OK. I have two clones, one for the program code and one for the gh-pages. This avoids the problem of directories not being deleted.

For running it locally, you can pass baseurl as parameter. I do
```
jekyll serve --watch --baseurl="" --trace
```