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After recursively cloning the repo and installing the required R packages, I ran runTestSuite.sh and got the following:
```
fabusard@Nagisa:~/git/Kaphi$ sh runTestSuite.sh
R version 3.2.3 (2015…
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@thijsjanzen deprecated the `nltt_diff` function, over using the `nltt_diff_exact` function.
There are three ways to go:
* [ ] 1. Remove `nltt_diff` in the next version
* [ ] 2. Let `nltt_di…
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The last Peregrine run, there was a hiccup (see #3)
* [ ] Measure which parameter files have failed, using #4
* [ ] redo those
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From the vignette `trees_with_root_edge.Rmd`:
![issue](https://cloud.githubusercontent.com/assets/2098230/18436268/c9150618-78f7-11e6-890d-1eda7b67b3f9.png)
@thijsjanzen : do you agree this behavior…
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```
nltt_stats_raw
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For every simulation, I run at least two BEAST2 runs per alignment. It would be a good idea to check if these differ using statistics.
Because if they do not differ, I can just remove these replicate…
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To quote [the NERN site](https://www.nern.nl/CT2016):
```
Deadline for submissions of abstracts for a presentation in one of the parallel sessions: Tuesday 13 December 2016
```
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At the end of the worked-out example 1, it shows two different nLTT lines: (1) the 'true' nLTT line, and (2) the average posterior nLTT line. The nLTT statistic equals the surface between these two li…
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This works:
```
dplyr::summarise(
dplyr::group_by(nltt_stats, filename, sti, ai, pi),
mean = mean(nltt_stat)
)
```
This does not:
```
dplyr::summarise(
dplyr::group_by(nltt_stats, filename, s…
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- [x] create parameters
- [x] check
- [x] create PDF: analyse_files (now as Markdown)
- [x] add pbd_sim output
- [x] check
- [x] create PDF: analyse_n_taxa (now as Markdown)
- [x] add_species_trees
- …