[inst/doc/trees_with_root_edge.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:3:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L3) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:9:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L9) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:13:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L13) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:16:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:23:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L23) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:26:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L29) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:31:47:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny1),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:32:13:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:36:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L36) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:38:47:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L38) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny2),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:39:13:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L39) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:43:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L43) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:46:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L46) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:49:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L49) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L57) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:61:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L61) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:64:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L67) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:71:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L71) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:74:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L74) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L77) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:79:47:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L79) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny1),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:80:13:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L80) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:84:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L84) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:86:47:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
  nLTT::get_phylogeny_nltt_matrix(phylogeny2),
                                              ^
```
[inst/doc/vignette_get_average_nltt.R:87:13:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:91:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L91) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:94:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L94) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:96:29:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L96) *style:* **Trailing whitespace is superfluous.**
```r
  c(phylogeny1, phylogeny2),
                            ^
```
[inst/doc/vignette_get_average_nltt.R:97:13:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L97) *style:* **Trailing whitespace is superfluous.**
```r
  dt = 0.20,
            ^
```
[inst/doc/vignette_get_average_nltt.R:100:1:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_average_nltt.R#L100) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_get_nltt_values.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_get_nltt_values.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:8:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_nltt_statistic.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_nltt_statistic.R:4:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L1) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:6:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/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/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L69) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:73:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L73) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:75:27:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L75) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```
[inst/doc/vignette_stretch_nltt_matrix.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L77) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:80:1:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L80) *style:* **lines should not be more than 80 characters.**
```r
stretch_matrix <- nLTT::stretch_nltt_matrix(nltt, dt = 0.05, step_type = "upper")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:81:27:](https://github.com/richelbilderbeek/nLTT/blob/e0e236aff24d63d71c830077828c13ce7c618269/inst/doc/vignette_stretch_nltt_matrix.R#L81) *style:* **Put spaces around all infix operators.**
```r
points(nltt, pch = 19, col="red")
                         ~^~
```


closes #3


@martinwiboe using `.OriginalString` would resurrect [the bug](https://bugzilla.xamarin.com/show_bug.cgi?id=43411) as it would leave whitespace unencoded and the Java URL class performs no encoding on its own (the Java **URI** class does escape the URLs, but I'd rather keep Java API use to minimum for performance reasons) which would lead to error 400 as reported in the bug. Instead, [this PR](https://github.com/xamarin/xamarin-android/pull/222) implements encoding by perusing the `UriBuilder` managed class which does correct work encoding URL query.


Double peak fitting - Peak pos, height, FWHM and area (area rough calculation based on FWHM and peak height)


Ah, OK, so it only fails when resizing the window while editing? I.e. you won't really have any issues if you have a static theme at about  ~560px ?


Hi @eos87 , thanks for this commit, definitely it should be there.


Halleluja

Von meinem iPhone gesendet

> Am 14.09.2016 um 09:07 schrieb Felix Kopp <notifications@github.com>:
>
> Great!!
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>


input_processor_refactor (mbadams5) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: Tests Failed (1817 of 2391 tests passed, 0 test warnings)

 * 508 tests had: AUD diffs.
 * 492 tests had: EIO diffs.
 * 213 tests had: RDD diffs.
 * 470 tests had: Table big diffs.
 * 141 tests had: ERR diffs.
 * 372 tests had: MTD diffs.
 * 271 tests had: DXF diffs.
 * 397 tests had: SHD diffs.
 * 406 tests had: BND diffs.
 * 298 tests had: MDD diffs.
 * 184 tests had: SSZ big diffs.
 * 14 tests had: ESO big diffs.
 * 9 tests had: MTR big diffs.
 * 8 tests had: ZSZ small diffs.
 * 28 tests had: ESO small diffs.
 * 22 tests had: MTR small diffs.
 * 3 tests had: delightin diffs.
 * 3 tests had: delightout diffs.

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-75.99%25-red.svg)


Yes, that seems to have been a mistake or an oversight. This is generally not the case...


Yup
--
Yusuke Yamamoto
@yusukey
http://samuraism.com/

> On Sep 14, 2016, at 17:46, Lalit <notifications@github.com> wrote:
>
> Hi,
> Has this fix been is part of v 4.0.5?
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>


@carolinux

FYI, I started a compatibility layer here for QGIS 2.
In the code all calls will be QGIS 3 compatible and within this file, we will patch the API if QGIS 2 is found. I hope this is suitable not only for this project. Please keep developing with QGIS 2 (as that's what users will also use for the moment).


input_processor_refactor (mbadams5) - x86_64-Linux-Ubuntu-14.04-custom_check: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.svg)


The template have to be defined in module, because module use it in Controller. So if you switch site theme (or using another for admin interface) you will receive an error:
Theme hook campaign_403/campaign_403 not found.


That is good.  I will get rid of `_config_dev.yml` and adjust the `.serve` script to set the `baseurl` parameter there.


Just to be sure, did you try the latest one with `writeXml` method or the one with the `template CORE_EXPORT` code?


can you place this in a distinct file?
This file is a copy https://github.com/2ndQuadrant/audit-trigger/commits/master/audit.sql with some modification to enable schema qualified tables. I would still like to make this changes upstream, so it would be easier to add a submodule later on.


Shnoulle, yes, I removed my comment because I noticed your fix 3 minutes later.


EMS (brianlball) - i386-Windows-7-VisualStudio-12: OK (2314 of 2469 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-93.72%25-yellow.svg)


This should be reverted
Article: http://www.phoronix.com/scan.php?page=news_item&px=MTE4NTg
Commit info: https://github.com/sonyxperiadev/kernel/commit/37407ea7f93864c2cfc03edf8f37872ec539ea2b


TeamCity Todo :: Build [Build 93](http://109.103.226.38:8512/viewLog.html?buildId=38486&buildTypeId=Todo_Build) is now running


hi, can u check your twitter? :)


TeamCity Todo :: Build [Build 94](http://109.103.226.38:8512/viewLog.html?buildId=38487&buildTypeId=Todo_Build) is now running


TeamCity Todo :: Build [Build 93](http://109.103.226.38:8512/viewLog.html?buildId=38486&buildTypeId=Todo_Build) outcome was **SUCCESS**
Summary: Tests passed: 8 Build time: 00:00:38


Hi, the exact opposite occurs for me, With -api works fine, without gives error 400.


TeamCity Todo :: Build [Build 94](http://109.103.226.38:8512/viewLog.html?buildId=38487&buildTypeId=Todo_Build) outcome was **FAILURE**
Summary: Exit code 1 (new) Build time: 00:01:02


TeamCity Todo :: Build [Build 95](http://109.103.226.38:8512/viewLog.html?buildId=38488&buildTypeId=Todo_Build) is now running


TeamCity Todo :: Build [Build 95](http://109.103.226.38:8512/viewLog.html?buildId=38488&buildTypeId=Todo_Build) outcome was **SUCCESS**
Summary: Tests passed: 8 Build time: 00:00:09


dropping photos would leave us without a gallery app


input_processor_refactor (mbadams5) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-IntegrationCoverage-Debug: Tests Failed (1468 of 1785 tests passed, 0 test warnings)

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I used the commit with the template CORE_EXPORT


This answer you ?

https://github.com/opengapps/aosp_build/blob/master/opengapps-packages.mk#L44


Issue in esptool repo: https://github.com/themadinventor/esptool/issues/125


Is it an idea to remove the name from the field, then?


Oops, used the wrong release script 1.2.2 should be fixed


* try to use only `&&` and is cool and I like it but it's not == &&
* no need to compare twice if params[:select_cuisine] is nil it won't equal all


Thanks


ok I found in setup that it should be create if not exist, I guess I just have file permission issue.


please use html beautify if you are using sublime


maybe assign this to a variable
`@cuisine_type = params[:]`


@tomalec did you also update the usages of `connectToRemote`?


add stylings on cascading style sheets


if you assign the value of params[:select_cusiine] to a variable `@foo`
you can then use it here as a value


No worries, thanks.


please download the files and fetch it from local. do not use weblinks


Why there? esp-udev-rules would be a Fedora-specific thing; esptool is a cross-platform tool. Is the esptool upstream even using Fedora?


same comment as above


It's also possible for the mounted devpts to prefer a different UID (see mount(8)).  The reason you'd want to set this is if you, like grantpt, want to have the UID be something you didn't want to hard-code at mount time to apply to all future pseudoterminal slaves.


remove space after hover


standard in css is to break them into different lines


please fetch the file from local donot use web link