[inst/doc/trees_with_root_edge.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/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/ebd8646dcd6d75c6889e61d5edf30a10fde666e4/inst/doc/vignette_stretch_nltt_matrix.R#L69) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Related to: backdrop/backdrop-issues#1705


Did you add lock screen spectrogram? Can we turn it off?


this cannot work, as driveletter is not set


I'm not completely sure why but I think this latest lodash update is breaking things.

[Here](https://github.com/tjunnone/npm-check-updates/blob/master/lib/versionmanager.js#L343) that `_.partialRight(_.pick, _.identity)` thing (which I believe to [Remove empty properties / falsy values from Object](http://stackoverflow.com/questions/14058193/remove-empty-properties-falsy-values-from-object-with-underscore-js#comment41184386_23708667)?) doesn't behave the same anymore with lodash update.

I put a small code to debug what it was doing (or why it wasn't working)

    // .then(_.partialRight(_.pick, _.identity));
    .then(_.partialRight(_.pick, x => {
        console.log('x:', x);
        const fn = _.partialRight(_.pick, _.identity);
        console.log('_.pick:', _.pick);
        const y = fn(x);
        console.log('y:', y);
        return y;
    }));

Here's the result (with the latest lodash)

    x: { 'babel-core': '6.14.0' }
    _.pick: function () {
            var args = arguments,
                index = -1,
                length = nativeMax(args.length - start, 0),
                array = Array(length);

            while (++index < length) {
              array[index] = args[start + index];
            }
            index = -1;
            var otherArgs = Array(start + 1);
            while (++index < start) {
              otherArgs[index] = args[index];
            }
            otherArgs[start] = array;
            return apply(func, this, otherArgs);
          }
    y: {}

The result `y` should be unchanged but it's empty.

For comparison here's the same result from before the lodash update

    x: { 'babel-core': '6.14.0' }
    _.pick: function () {
            var args = arguments,
                index = -1,
                length = nativeMax(args.length - start, 0),
                rest = Array(length);

            while (++index < length) {
              rest[index] = args[start + index];
            }
            switch (start) {
              case 0: return func.call(this, rest);
              case 1: return func.call(this, args[0], rest);
              case 2: return func.call(this, args[0], args[1], rest);
            }
            var otherArgs = Array(start + 1);
            index = -1;
            while (++index < start) {
              otherArgs[index] = args[index];
            }
            otherArgs[start] = rest;
            return func.apply(this, otherArgs);
          }
    y: { 'babel-core': '6.14.0' }


Related to: backdrop/backdrop-issues#1231


done


@fosterlynn would be great to add a quick description at the top outlining what this list of files is capturing.


Also added fonts and hex inner text formatting


make a test to see if the path exists (mediainfo) -- if not, throw an error


typo here -- you have an extra caps A n XMLP[A]th


I agree that this API-change is unnecessary. I will remove the function.


fkjfj


Cool!
However, it doesn't work with /Library/Fonts/Skia.ttf any more... (Skia v10.0d4e1 from Yosemite)
I tried both the pre-compiled app, and compiling from source.


Hi,

I tested 3.1 and it should work in 3.3


No I didn't add.


That's the problem with displaying firing buttons (selecting a weapon for an attack). The goal is to select a different unit, during combat, and if it "can fire", display the correct buttons. The first conditions (in red) were not correct, because even if the PS of the unit is different from the PS of the firing units (skillturn), this unit can still fire sometimes (Dengar for instance). This correction was not sufficient. A unit must be able to fire, and no action is pending (like actions triggered at the beginning of the combat phase).


Details


Removed here: https://github.com/h5p/h5p-editor-php-library/commit/4f3bce523876621513432e9777c417857bf720de


Yes looks like you are correct, these all need flipping to 'false'


Yes, it closes it. Closed.


Nice one :) Can't get enough of getting rid of those nasty C-style casts ^^


Moses against Pharoa


done


I had a suggestion but the patch got merged before i could discuss it.
Anyways here are the little changes in the original patch..

https://github.com/SAOSP-N/platform_packages_apps_Settings/commit/1f98a4e6003c8dea536e4777551aea25234670a0


**[unitTests_php_branches run failed](http://jenkins.wikia-prod:8080/job/unitTests_php_branches/35334/testReport/) for this commit**


yes, will change to []


Related to: backdrop/backdrop-issues#2169


When this API was added in 2015 it wasn't supported by any browser... Browsers now are implementing it so I guess splitting it into the supported and unsupported features is a maintenance burden.


Thanks,it works!


is a test/live check. Could make this a config variable.


Mazi: why don't you try do port it? It's not that hard.


true, will look into it.


oops. i released this. thanks.


base 下 scss 公用设置 提取 以及 tap 组件 增补


@ssj17vegeta since C++11 theres excplicit type cast (Old C Style cast) which does interesting things. Only cast it doednt cover is dynamic_cast


thanks for the response, I have implemented it on 3.3 and not coming right,  will you be able to assist me?


Thanks, I'll change that.


Perfect! I build successfully! thanks @m-kuhn !


so what is the fabled MP fix here? bDontShowRewardPopup?


Here the static instance was always created (not depending on using it)


@SamanthaNguyen Please revert. This is mostly broken, because:

1. save for the `$wgArticlePath` definition and the commented-out `$wgCaptchaDirectory` definition, all the double quotes here are both intentional and **necessary** for functionality! Without the double quotes, [$IP](https://www.mediawiki.org/wiki/Manual:$IP) in these definitions will **not** get properly expanded. $IP is a global variable and on our setup it's set to `/var/www/core`. So PHP will "translate" `require_once "$IP/extensions/Echo/Echo.php";` at run-time to `require_once "/var/www/core/extensions/Echo/Echo.php";` so that it knows what file to load. When you change it to single quotes (`require_once '$IP/extensions/Echo/Echo.php';`) you are telling PHP to load a file from a directory that is literally named `$IP` (but obviously since there isn't such a directory, it'll fail and you'll get fatals all over the place).
2. you forgot to remove the foreach loop associated with the CAPTCHA questions (`foreach ( $arr as $key => $value ) {`, lines 89-91). Because you however _did_ remove the `$arr` variable that this foreach loop attempts to use, this will result in a bunch of annoying E_NOTICEs about undefined variables.


I always thought the "ignition" signal could be obtained without problems from the so-called "clamp-15", which many car electronics manufacturer's refer to in their equipment manuals.

Did you try to use board package v1.0.4 and see if debug_print() hangs the device?


This way the bean was still initialized with `SystemProperties.getDefault()` since the constructor is called prior to fields autowiring.


Because I do not want to break stuff and prefer to let the expert do such work.


Yes, I adjusted .gitignore to ignore some of the source code directories which were not deleted when I switched branches.  Of course, now that I think of it, if you have files in those subdirectories:
+emscripten
 +tools
 +include
which are in the gh-pages branch, then that is why they were not deleted.  (but that would be confusing to be putting gh-pages content in those directories).

The .serve script is handy for running a local copy of the website with jekyll from the command-line.  The baseurl parameter needed to be cleared from _config.yml, so I added _config_dev.yml which removes it when serving locally (_config.yml is read first, and then _config_dev.yml is read, allowing parameters to be changed for the "development" mode).


I guess this was done because the message beeing displayed for empty mandatory WYSIWYG-fields was something else that found in requiredProperty. But, I did change the message, and I see they now communicate the same message, so I agree with you. I will fix.


Also translated hard coded events #1 and #2 into code for two new Events objects.


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Учитывай, что при ORM запросе  Multilingual навесит свой Join, где помимо прочего в условиях будет `language_id`, который всегда по умолчанию берется из Multilingual. Соответсна, запрос будет по таким-то заданным тобой контекстам, но по `language_id` из Multilingual


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