[inst/doc/trees_with_root_edge.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_average_nltt.R#L29) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:36:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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:43:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_average_nltt.R#L77) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_average_nltt.R:84:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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:91:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_average_nltt.R#L96) *style:* **Trailing whitespace is superfluous.**
```r
  c(phylogeny1, phylogeny2),
                            ^
```
[inst/doc/vignette_get_average_nltt.R:100:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L15) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:19:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L26) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:33:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L33) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:37:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L37) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:40:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L40) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:44:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L44) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:51:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L51) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L57) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:63:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L63) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:67:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L67) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:70:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L70) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:74:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L74) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L77) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:84:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L84) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:90:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L90) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:99:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L99) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:103:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L103) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:106:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L106) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:110:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L110) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:114:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L114) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:117:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L117) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:121:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L121) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:127:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L127) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:133:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L133) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:137:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L137) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:141:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L141) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:144:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L144) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:146:54:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L146) *style:* **Trailing whitespace is superfluous.**
```r
  t, nltt, data = df, geom = "point", ylim = c(0, 1),
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:151:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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:152:103:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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:155:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L155) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:164:53:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L164) *style:* **Trailing whitespace is superfluous.**
```r
phylogenies <- c(phylogeny1, phylogeny2, phylogeny3,
                                                    ^
```
[inst/doc/vignette_get_nltt_values.R:167:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L167) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:171:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L171) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:172:58:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L172) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0, 1),
                                                         ^
```
[inst/doc/vignette_get_nltt_values.R:177:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L177) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:178:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L178) *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:178:103:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L178) *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:180:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_get_nltt_values.R#L180) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_nltt_statistic.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L6) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:12:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/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/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L19) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:23:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L23) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:30:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L30) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:35:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L35) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:41:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L41) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:44:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L44) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:48:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L48) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:52:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L52) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:59:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L59) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:64:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L64) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:72:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L72) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:75:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L75) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:79:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L79) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:83:2:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L83) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_stretch_nltt_matrix.R:91:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/inst/doc/vignette_stretch_nltt_matrix.R#L91) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:2:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L2) *style:* **Use two spaces to indent, never tabs.**
```r
	weights <- rep(1, 2);
^
```
[tests/testthat/test_calculate_weight.R:3:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L3) *style:* **Use two spaces to indent, never tabs.**
```r
	particles <- list();
^
```
[tests/testthat/test_calculate_weight.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L4) *style:* **Use two spaces to indent, never tabs.**
```r
	for(i in 1:2) {
^
```
[tests/testthat/test_calculate_weight.R:5:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L5) *style:* **Use two spaces to indent, never tabs.**
```r
		particles[[i]] <- c(10, 10)
^~
```
[tests/testthat/test_calculate_weight.R:5:17:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L5) *style:* **Put spaces around all infix operators.**
```r
	weights <- rep(1, 2);
               ~^
```
[tests/testthat/test_calculate_weight.R:6:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	}
^
```
[tests/testthat/test_calculate_weight.R:6:19:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L6) *style:* **Put spaces around all infix operators.**
```r
	particles <- list();
                 ~^~~
```
[tests/testthat/test_calculate_weight.R:7:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	sigma <- 1;
^
```
[tests/testthat/test_calculate_weight.R:7:12:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L7) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	for(i in 1:2) {
           ^
```
[tests/testthat/test_calculate_weight.R:8:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	prior_density_function <- function(x) {
^
```
[tests/testthat/test_calculate_weight.R:9:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
		dunif(x[1], min=0, max=1000) *
^~
```
[tests/testthat/test_calculate_weight.R:10:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
		dunif(x[2], min=0, max=1000) }
^~
```
[tests/testthat/test_calculate_weight.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:11:32:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L11) *style:* **Put spaces around all infix operators.**
```r
	prior_density_function <- function(x) {
                              ~^~~
```
[tests/testthat/test_calculate_weight.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L12) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(
^
```
[tests/testthat/test_calculate_weight.R:13:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L13) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
^~
```
[tests/testthat/test_calculate_weight.R:13:46:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L13) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
		dunif(x[2], min=0, max=1000) }
                                             ^
```
[tests/testthat/test_calculate_weight.R:14:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L14) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(20, 20), sigma, prior_density_function), #so these should be equal, because jumping densities are symmetric (dnorm)
^~
```
[tests/testthat/test_calculate_weight.R:14:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L14) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:15:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L15) *style:* **Use two spaces to indent, never tabs.**
```r
		tolerance = 0.0001
^~
```
[tests/testthat/test_calculate_weight.R:16:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L16) *style:* **Use two spaces to indent, never tabs.**
```r
	)
^
```
[tests/testthat/test_calculate_weight.R:16:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L16) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:16:61:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L16) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
                                                           ~^~
```
[tests/testthat/test_calculate_weight.R:16:90:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L16) *style:* **Commented code should be removed.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
                                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:17:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L17) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:17:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L17) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(20, 20), sigma, prior_density_function), #so these should be equal, because jumping densities are symmetric (dnorm)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:17:61:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L17) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(20, 20), sigma, prior_density_function), #so these should be equal, because jumping densities are symmetric (dnorm)
                                                           ~^~
```
[tests/testthat/test_calculate_weight.R:18:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L18) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(
^
```
[tests/testthat/test_calculate_weight.R:19:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
^~
```
[tests/testthat/test_calculate_weight.R:20:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(5.0, 5.0), sigma, prior_density_function),
^~
```
[tests/testthat/test_calculate_weight.R:20:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:21:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
		tolerance = 0.0001
^~
```
[tests/testthat/test_calculate_weight.R:22:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
	)
^
```
[tests/testthat/test_calculate_weight.R:22:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L22) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:22:61:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L22) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
                                                           ~^~
```
[tests/testthat/test_calculate_weight.R:22:88:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
                                                                                ^
```
[tests/testthat/test_calculate_weight.R:23:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L23) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:23:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L23) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(5.0, 5.0), sigma, prior_density_function),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:23:61:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L23) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(5.0, 5.0), sigma, prior_density_function),
                                                            ^~
```
[tests/testthat/test_calculate_weight.R:24:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:26:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L26) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:27:1:](https://github.com/richelbilderbeek/nLTT/blob/ca9b901a79e95041d44b12fb22f96793259952f6/tests/testthat/test_calculate_weight.R#L27) *style:* **Trailing whitespace is superfluous.**
```r

^
```


That was producing tons of warnings here. They could be sorted out but I think the later approach should also work, so if you have the chance to test it, that will be much appreciated :)


That's certainly possible. But the inconsistency bothers me, and is the encounter function really important? There's no more Shuckle to be a Rock Smash–only Pokémon, and there are no random fossils available like in HG/SS. Thoughts?


nice !


added business.css


Is this a standard way of doing PAM parameters? Typically "\0" would be used for string safety in C, but if the password is any byte sequence including all unreadable characters this doesn't work without encoding. The trim() is potentially fatal, too.


to clarify, you won't need $sqlconf.
(for example, the sqlStatement call below means your database connection is already set up and working by OpenEMR via the globals.php include)


vbm,./


sounds good


We should probably bundle these images with the application code, instead of relying on them being available at these URLs..


@grendello thanks for your reply :) So you assume that the caller gives a complete url without any escaping? How does that work for url parameters with ampersands? Like http://example.com/?param1=test&hello&param2=test

The example above is impossible to parse correctly (the first ampersand should be encoded, the latter not). I think the caller will need to escape the url parameters correctly and your class should do no encoding. But also, not use Uri.ToString() as that will undo escaping by the caller.


Looks good to me, thank you


removed


hello ,the first comment!please help me!


There is none. ;)
Are you interested in a specific issue resolution or is this just a general question?


Sounds good. Will watch this issue develop as the code matures.


I think you have now -j two times.


is `text` a text format?

Then you should maybe use a `simple_format`?


this fix #10


[inst/doc/trees_with_root_edge.R:27:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/trees_with_root_edge.R#L27) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_get_average_nltt.R:38:47:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:86:47:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:96:29:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_average_nltt.R#L96) *style:* **Trailing whitespace is superfluous.**
```r
  c(phylogeny1, phylogeny2),
                            ^
```
[inst/doc/vignette_get_average_nltt.R:100:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_average_nltt.R#L100) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_get_nltt_values.R:146:54:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_nltt_values.R#L146) *style:* **Trailing whitespace is superfluous.**
```r
  t, nltt, data = df, geom = "point", ylim = c(0, 1),
                                                     ^
```
[inst/doc/vignette_get_nltt_values.R:152:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:152:103:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:164:53:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_nltt_values.R#L164) *style:* **Trailing whitespace is superfluous.**
```r
phylogenies <- c(phylogeny1, phylogeny2, phylogeny3,
                                                    ^
```
[inst/doc/vignette_get_nltt_values.R:172:58:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_nltt_values.R#L172) *style:* **Trailing whitespace is superfluous.**
```r
qplot(t, nltt, data = df, geom = "point", ylim = c(0, 1),
                                                         ^
```
[inst/doc/vignette_get_nltt_values.R:178:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_nltt_values.R#L178) *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:178:103:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_nltt_values.R#L178) *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:180:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_get_nltt_values.R#L180) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_nltt_statistic.R:21:22:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_nltt_statistic.R#L23) *style:* **Trailing whitespace is superfluous.**
```r
  species_tree,
               ^
```
[inst/doc/vignette_nltt_statistic.R:39:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:54:27:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:62:38:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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:69:14:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_nltt_statistic.R#L76) *style:* **Trailing whitespace is superfluous.**
```r
  df$method,
            ^
```
[inst/doc/vignette_nltt_statistic.R:82:13:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/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/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_nltt_statistic.R#L89) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_stretch_nltt_matrix.R:91:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/inst/doc/vignette_stretch_nltt_matrix.R#L91) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:2:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L2) *style:* **Use two spaces to indent, never tabs.**
```r
	weights <- rep(1, 2);
^
```
[tests/testthat/test_calculate_weight.R:3:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L3) *style:* **Use two spaces to indent, never tabs.**
```r
	particles <- list();
^
```
[tests/testthat/test_calculate_weight.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L4) *style:* **Use two spaces to indent, never tabs.**
```r
	for(i in 1:2) {
^
```
[tests/testthat/test_calculate_weight.R:5:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L5) *style:* **Use two spaces to indent, never tabs.**
```r
		particles[[i]] <- c(10, 10)
^~
```
[tests/testthat/test_calculate_weight.R:5:17:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L5) *style:* **Put spaces around all infix operators.**
```r
	weights <- rep(1, 2);
               ~^
```
[tests/testthat/test_calculate_weight.R:6:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	}
^
```
[tests/testthat/test_calculate_weight.R:6:19:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L6) *style:* **Put spaces around all infix operators.**
```r
	particles <- list();
                 ~^~~
```
[tests/testthat/test_calculate_weight.R:7:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	sigma <- 1;
^
```
[tests/testthat/test_calculate_weight.R:7:12:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L7) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	for(i in 1:2) {
           ^
```
[tests/testthat/test_calculate_weight.R:8:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	prior_density_function <- function(x) {
^
```
[tests/testthat/test_calculate_weight.R:9:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
		dunif(x[1], min=0, max=1000) *
^~
```
[tests/testthat/test_calculate_weight.R:10:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
		dunif(x[2], min=0, max=1000) }
^~
```
[tests/testthat/test_calculate_weight.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:11:32:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L11) *style:* **Put spaces around all infix operators.**
```r
	prior_density_function <- function(x) {
                              ~^~~
```
[tests/testthat/test_calculate_weight.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L12) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(
^
```
[tests/testthat/test_calculate_weight.R:13:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L13) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
^~
```
[tests/testthat/test_calculate_weight.R:13:46:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L13) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
		dunif(x[2], min=0, max=1000) }
                                             ^
```
[tests/testthat/test_calculate_weight.R:14:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L14) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(20, 20), sigma, prior_density_function), #so these should be equal, because jumping densities are symmetric (dnorm)
^~
```
[tests/testthat/test_calculate_weight.R:14:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L14) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:15:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L15) *style:* **Use two spaces to indent, never tabs.**
```r
		tolerance = 0.0001
^~
```
[tests/testthat/test_calculate_weight.R:16:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L16) *style:* **Use two spaces to indent, never tabs.**
```r
	)
^
```
[tests/testthat/test_calculate_weight.R:16:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L16) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:16:61:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L16) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
                                                           ~^~
```
[tests/testthat/test_calculate_weight.R:16:90:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L16) *style:* **Commented code should be removed.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function), #log(5) - log(10) == -1 * (log(20) - log(10))
                                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:17:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L17) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:17:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L17) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(20, 20), sigma, prior_density_function), #so these should be equal, because jumping densities are symmetric (dnorm)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:17:61:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L17) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(20, 20), sigma, prior_density_function), #so these should be equal, because jumping densities are symmetric (dnorm)
                                                           ~^~
```
[tests/testthat/test_calculate_weight.R:18:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L18) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(
^
```
[tests/testthat/test_calculate_weight.R:19:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
^~
```
[tests/testthat/test_calculate_weight.R:20:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
		calculate_weight(weights, particles, current=c(5.0, 5.0), sigma, prior_density_function),
^~
```
[tests/testthat/test_calculate_weight.R:20:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:21:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
		tolerance = 0.0001
^~
```
[tests/testthat/test_calculate_weight.R:22:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
	)
^
```
[tests/testthat/test_calculate_weight.R:22:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L22) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:22:61:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L22) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
                                                           ~^~
```
[tests/testthat/test_calculate_weight.R:22:88:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
		calculate_weight(weights, particles, current=c(5, 5), sigma, prior_density_function),
                                                                                ^
```
[tests/testthat/test_calculate_weight.R:23:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L23) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:23:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L23) *style:* **lines should not be more than 80 characters.**
```r
		calculate_weight(weights, particles, current=c(5.0, 5.0), sigma, prior_density_function),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_calculate_weight.R:23:61:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L23) *style:* **Put spaces around all infix operators.**
```r
		calculate_weight(weights, particles, current=c(5.0, 5.0), sigma, prior_density_function),
                                                            ^~
```
[tests/testthat/test_calculate_weight.R:24:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[tests/testthat/test_calculate_weight.R:26:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L26) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_calculate_weight.R:27:1:](https://github.com/richelbilderbeek/nLTT/blob/15538ccc313ab3af967838fac7e5ff1ac2f5987a/tests/testthat/test_calculate_weight.R#L27) *style:* **Trailing whitespace is superfluous.**
```r

^
```


Would be better to use mor concise splitting. Split() may be able to limit its substring count, 2 is what you want here. Does "password=" also return 2? If service is added, defaults need to be set or empty service rejected.


Czy ten commit mógłby mieć zastosowanie również w 'nodeinfo' ?


where is the test for this? :)


这里有 bug，应该传递 callback


I meant explode() 😊


Are there any chances of using an external package with this library rather than bundling it directly with the application ode?


Hello World


stuff


Этот момент я вынесу в отдельный метод, т.к. он используется не только здесь, а реализация однообразная


@kwonn It's great! But you can see that your name was removed here. Perhaps you resolved using theirs/your version option? SourceTree allows you to sort of merge manually, in which you choose which lines to discard and which lines to keep. After that, you can mark it as resolved and commit the changes.


As far as I get your code, I didn't have to as it just forwards `bootstrap` callback. Plus, all tests excepts outdated ones (https://github.com/PuppetJs/PuppetJs/issues/103) were passing.


I think that if you decide to copy-paste CSS from a library then it's better to keep customizations in a separate file. This one may be a bit unexpected and overlooked by someone who is (for example) willing to replace the file with a newer version.


I think it is convenient because the one it puts in `~/.leksah-0.16` on startup is a copy of the one installed from the data dir.  On systems installed from binaries the admin could modify the the prefs on a shared machine and each user would start with a copy of that modified version.

We should try to make it so there is only one copy though.  We could:

* Generate `data/prefs.lkshp` somehow at build time using this code.
* Use template haskell to load in `data/prefs.lkshp` at compile time (to replace this code).
* Remove this code and change the behaviour when `~/.leksah-0.16/prefs.lkshp` fails to load, so that instead of using this code it tries to load the `prefs.lkshp` file from the leksah data dir.  If that fails it could print an error and exit.

I think the last option is nicest (but I have no strong opinion).


Cross platform method: `os.homedir()` https://nodejs.org/api/os.html#os_os_homedir


as


a


巡鹰高尔夫开发笔记


I've modified the code to use `O_CREAT`.

About the lock/retry it's supported in the `BlockingLockFile` class which extends `LockFile`.


This is certainly not the place to ask questions. Go on the Discord API server and ask there (linked in the README)


Thankes. Now the base Ini is enough. and our ini can write.
sdlang will maybe to use. but now it does not have  demand, and json is enough.


Yes , but
![qq 20160914172950](https://cloud.githubusercontent.com/assets/21981102/18506980/eae5ea46-7aa0-11e6-8de1-1477bfa7d467.png)


After testing your code, it seems to work (but it does ignore erroneous ampersands).

The original bug was regarding a well-formed (escaped) url causing a problem. Why not just require that consumers escape their url parameters correctly rather than attempt to do it inside AndroidClientHandler?