[inst/doc/trees_with_root_edge.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L1) *style:* **Commented code should be removed.**
```r
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[inst/doc/trees_with_root_edge.R:6:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L6) *style:* **Commented code should be removed.**
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[inst/doc/trees_with_root_edge.R:10:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L10) *style:* **Commented code should be removed.**
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[inst/doc/trees_with_root_edge.R:14:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L14) *style:* **Commented code should be removed.**
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[inst/doc/trees_with_root_edge.R:18:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L18) *style:* **Commented code should be removed.**
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[inst/doc/trees_with_root_edge.R:22:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L22) *style:* **Commented code should be removed.**
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[inst/doc/trees_with_root_edge.R:25:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L25) *style:* **Commented code should be removed.**
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[inst/doc/trees_with_root_edge.R:27:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/trees_with_root_edge.R#L27) *style:* **Trailing blank lines are superfluous.**
```r

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```
[inst/doc/vignette_get_average_nltt.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L1) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:49:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L49) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L57) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:61:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L61) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:64:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L64) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:67:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L67) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:71:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L71) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:74:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L74) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L77) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:84:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L84) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:91:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L91) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:94:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_average_nltt.R#L94) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_average_nltt.R:100:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L1) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:8:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L8) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:19:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L19) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:22:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L22) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:26:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L26) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:33:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L33) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:37:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L37) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:40:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L40) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:44:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L44) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:51:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L51) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:57:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L57) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:63:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L63) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:67:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L67) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:70:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L70) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:74:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L74) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:77:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L77) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:84:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L84) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:90:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L90) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:99:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L99) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:103:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L103) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:106:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L106) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:110:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L110) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:114:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L114) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:117:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L117) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:121:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L121) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:127:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L127) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:133:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L133) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:137:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L137) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:141:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L141) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:144:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L144) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:151:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L151) *style:* **Commented code should be removed.**
```r
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[inst/doc/vignette_get_nltt_values.R:157:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L157) *style:* **Commented code should be removed.**
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[inst/doc/vignette_get_nltt_values.R:169:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L169) *style:* **Commented code should be removed.**
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 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:173:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L173) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:179:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L179) *style:* **Commented code should be removed.**
```r
## ------------------------------------------------------------------------
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/vignette_get_nltt_values.R:184:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_get_nltt_values.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/vignette_stretch_nltt_matrix.R:1:2:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/inst/doc/vignette_stretch_nltt_matrix.R#L91) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/ABC_SMC.R:19:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
  	#Just checking
  ^
```
[R/ABC_SMC.R:20:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
  	stop("mcmc_nltt: ",
  ^
```
[R/ABC_SMC.R:21:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
  	 "initial parameter values have to be above zero\n",
  ^
```
[R/ABC_SMC.R:22:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
  	 "but mu was ",parameters[2]," instead")
  ^
```
[R/ABC_SMC.R:67:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L67) *style:* **Use two spaces to indent, never tabs.**
```r
	        new_pp        <- likelihood_function(parameters, phy)
^
```
[R/ABC_SMC.R:68:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L68) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[R/ABC_SMC.R:69:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L69) *style:* **Use two spaces to indent, never tabs.**
```r
	        #accept or reject
^
```
[R/ABC_SMC.R:70:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L70) *style:* **Use two spaces to indent, never tabs.**
```r
	        if ( is.finite(new_pp) &&
^
```
[R/ABC_SMC.R:71:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L71) *style:* **Use two spaces to indent, never tabs.**
```r
	          is.finite(hr) &&
^
```
[R/ABC_SMC.R:72:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L72) *style:* **Use two spaces to indent, never tabs.**
```r
	          new_pp - pp + hr > log(stats::runif(1, 0, 1)) ) {
^
```
[R/ABC_SMC.R:73:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L73) *style:* **Use two spaces to indent, never tabs.**
```r
	          pp <- new_pp
^
```
[R/ABC_SMC.R:74:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L74) *style:* **Use two spaces to indent, never tabs.**
```r
	        } else {
^
```
[R/ABC_SMC.R:75:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L75) *style:* **Use two spaces to indent, never tabs.**
```r
	          parameters[j] <- eta
^
```
[R/ABC_SMC.R:76:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L76) *style:* **Use two spaces to indent, never tabs.**
```r
	        }
^
```
[R/ABC_SMC.R:77:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L77) *style:* **Use two spaces to indent, never tabs.**
```r
	    } else {
^
```
[R/ABC_SMC.R:78:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L78) *style:* **Use two spaces to indent, never tabs.**
```r
	    		parameters[j] <- eta
^
```
[R/ABC_SMC.R:78:6:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L78) *style:* **Use two spaces to indent, never tabs.**
```r
	    		parameters[j] <- eta
     ^~
```
[R/ABC_SMC.R:79:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L79) *style:* **Use two spaces to indent, never tabs.**
```r
	    }
^
```
[R/ABC_SMC.R:280:26:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L280) *style:* **Trailing whitespace is superfluous.**
```r
  #check data type of phy
                         ^
```
[R/ABC_SMC.R:287:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L287) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:293:5:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L293) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(parameters[2] < 0) {
    ^
```
[R/ABC_SMC.R:295:23:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
  	stop("mcmc_nltt: ",
                      ^
```
[R/ABC_SMC.R:340:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L340) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/ABC_SMC.R:341:11:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L341) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(parameters[j] >= 0 & parameters[1] > 0) {
          ^
```
[R/ABC_SMC.R:341:52:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L341) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        if(parameters[j] >= 0 & parameters[1] > 0) {
                                                   ^
```
[R/ABC_SMC.R:341:53:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L341) *style:* **Trailing whitespace is superfluous.**
```r
        if(parameters[j] >= 0 & parameters[1] > 0) {
                                                    ^~~~~~~~
```
[R/ABC_SMC.R:342:31:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L342) *style:* **Put spaces around all infix operators.**
```r
	        new_pp        <- likelihood_function(parameters, phy)
                             ~^~~
```
[R/ABC_SMC.R:343:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L343) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/ABC_SMC.R:345:20:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L345) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	        if ( is.finite(new_pp) &&
                   ^
```
[R/ABC_SMC.R:347:26:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L347) *style:* **Put spaces around all infix operators.**
```r
	          new_pp - pp + hr > log(stats::runif(1, 0, 1)) ) {
                         ^~
```
[R/ABC_SMC.R:347:31:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L347) *style:* **Put spaces around all infix operators.**
```r
	          new_pp - pp + hr > log(stats::runif(1, 0, 1)) ) {
                              ^~
```
[R/ABC_SMC.R:347:36:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L347) *style:* **Put spaces around all infix operators.**
```r
	          new_pp - pp + hr > log(stats::runif(1, 0, 1)) ) {
                                  ~^~
```
[R/ABC_SMC.R:348:22:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/R/ABC_SMC.R#L348) *style:* **Put spaces around all infix operators.**
```r
	          pp <- new_pp
                    ~^~~
```
[tests/testthat/test_calculate_weight.R:2:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/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/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_calculate_weight.R#L27) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[tests/testthat/test_mcmc_nltt.R:3:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L3) *style:* **Use two spaces to indent, never tabs.**
```r
	set.seed(1) #just to be safe
^
```
[tests/testthat/test_mcmc_nltt.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L4) *style:* **Use two spaces to indent, never tabs.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
^
```
[tests/testthat/test_mcmc_nltt.R:5:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L5) *style:* **Use two spaces to indent, never tabs.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
^
```
[tests/testthat/test_mcmc_nltt.R:5:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L5) *style:* **Use two spaces to indent, never tabs.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
^
```
[tests/testthat/test_mcmc_nltt.R:6:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
^
```
[tests/testthat/test_mcmc_nltt.R:7:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	LL_BD <- function(params, phy) {
^
```
[tests/testthat/test_mcmc_nltt.R:7:11:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Put spaces around all infix operators.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
         ~^~~
```
[tests/testthat/test_mcmc_nltt.R:7:35:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Put spaces around all infix operators.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                 ~^~
```
[tests/testthat/test_mcmc_nltt.R:7:43:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Put spaces around all infix operators.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                         ~^~
```
[tests/testthat/test_mcmc_nltt.R:7:50:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Put spaces around all infix operators.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                                ~^~
```
[tests/testthat/test_mcmc_nltt.R:7:61:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Put spaces around all infix operators.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                                           ~^~
```
[tests/testthat/test_mcmc_nltt.R:7:68:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L7) *style:* **Put spaces around all infix operators.**
```r
	p <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                                                  ~^~
```
[tests/testthat/test_mcmc_nltt.R:8:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	LL_BD <- function(params, phy) {
^
```
[tests/testthat/test_mcmc_nltt.R:8:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
		lnl <- TESS::tess.likelihood(phy[[1]], lambda = params[1], mu = params[2],
^~
```
[tests/testthat/test_mcmc_nltt.R:8:11:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Put spaces around all infix operators.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
         ~^~~
```
[tests/testthat/test_mcmc_nltt.R:8:35:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Put spaces around all infix operators.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                 ~^~
```
[tests/testthat/test_mcmc_nltt.R:8:43:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Put spaces around all infix operators.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                         ~^~
```
[tests/testthat/test_mcmc_nltt.R:8:50:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Put spaces around all infix operators.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                                ~^~
```
[tests/testthat/test_mcmc_nltt.R:8:61:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Put spaces around all infix operators.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                                           ~^~
```
[tests/testthat/test_mcmc_nltt.R:8:68:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L8) *style:* **Put spaces around all infix operators.**
```r
	q <- TESS::tess.sim.taxa(n=1,nTaxa=50,max=100,lambda=1.0,mu=0.0)[[1]]
                                                                  ~^~
```
[tests/testthat/test_mcmc_nltt.R:9:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
		lnl <- TESS::tess.likelihood(phy[[1]], lambda = params[1], mu = params[2],
^~
```
[tests/testthat/test_mcmc_nltt.R:9:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
	 							  samplingProbability = 1, log = TRUE)
^
```
[tests/testthat/test_mcmc_nltt.R:9:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
	 							  samplingProbability = 1, log = TRUE)
  ^~~~~~~
```
[tests/testthat/test_mcmc_nltt.R:10:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
	 							  samplingProbability = 1, log = TRUE)
^
```
[tests/testthat/test_mcmc_nltt.R:10:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior1 <- dunif( params[1], 0, 100, log = TRUE)
^
```
[tests/testthat/test_mcmc_nltt.R:10:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
	 							  samplingProbability = 1, log = TRUE)
  ^~~~~~~
```
[tests/testthat/test_mcmc_nltt.R:10:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior1 <- dunif( params[1], 0, 100, log = TRUE)
  ^
```
[tests/testthat/test_mcmc_nltt.R:10:15:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L10) *style:* **Put spaces around all infix operators.**
```r
	LL_BD <- function(params, phy) {
             ~^~~
```
[tests/testthat/test_mcmc_nltt.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior1 <- dunif( params[1], 0, 100, log = TRUE)
^
```
[tests/testthat/test_mcmc_nltt.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior2 <- dunif( params[2], 0, 100, log = TRUE)
^
```
[tests/testthat/test_mcmc_nltt.R:11:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior1 <- dunif( params[1], 0, 100, log = TRUE)
  ^
```
[tests/testthat/test_mcmc_nltt.R:11:3:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior2 <- dunif( params[2], 0, 100, log = TRUE)
  ^
```
[tests/testthat/test_mcmc_nltt.R:11:21:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L11) *style:* **Put spaces around all infix operators.**
```r
		lnl <- TESS::tess.likelihood(phy[[1]], lambda = params[1], mu = params[2],
                   ~^~~
```
[tests/testthat/test_mcmc_nltt.R:11:63:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L11) *style:* **Put spaces around all infix operators.**
```r
		lnl <- TESS::tess.likelihood(phy[[1]], lambda = params[1], mu = params[2],
                                                             ~^
```
[tests/testthat/test_mcmc_nltt.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L12) *style:* **Use two spaces to indent, never tabs.**
```r
	 	prior2 <- dunif( params[2], 0, 100, log = TRUE)
^
```
[tests/testthat/test_mcmc_nltt.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/9b4c2cbe54997ef29e493eef0586a4d32d5b122c/tests/testthat/test_mcmc_nltt.R#L12) *style:* **Use two spaces to indent, never tabs.**
```r
	 	return(lnl + prior1 + prior2)
^
```


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