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Hi thanks for contributing to this wonderful work in protein co-design, particularly in the novel CTMC mechanism. The code is clean and easy to understand. However, I am little confused about the impl…
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In `antigen`, there is a mutation rate $\mu$. In the original version of `antigen`, which did not model viral sequences, mutations changed a virus's antigenic phenotype. In our updated version, which …
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I think the simulation of ClassicDSD has rounding / precision issues.
When does the issue arise?
When simulation CRN in ClassicDSD where the rate constants are numbers with very different magnitud…
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Out of all functions involving Brownian Motion listed in [the documentation](https://revbayes.github.io/documentation/), only `dnPhyloBrownianMVN` takes a `rootStates` argument, making it so that 1. a…
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Le fichier `bantusubsample.nex` indique qu'il devrait y avoir 108 taxons:
```
#NEXUS
begin data;
dimensions ntax=108 nchar=3859;
```
Or la matrice du fichier ne comporte que 107 lignes. C…
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Dans `01_Import.R` le code `get_nexus_parameters()` plante sur `iecor.nex`:
```
get_nexus_parameters(here("data/real/iecor_ctmc-strict-M1/iecor.nex"))
> Erreur dans cslEscaped[character_num, 2…
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RV 1:
- [ ] the formal notation is a bit sloppy;
\ *can you be more specific?*
- [ ] figures seem low resolution and too small to be fully read.
\ *I have no problem in the pdf version, and …
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Dans 01_Import.R, la fonction `get_tip_ages()` calcule maintenant la moyenne des âges de chaque feuille. Mais il faudrait enlever le burnin non? Et finalement on prend la moyenne ou la médiane?
J'é…
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There's so much fascinating work in this repo, really amazing stuff! It got me thinking about options for Bayesian inference with these data, and here's my attempt at a workflow using the RevBayes pro…
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Bonjour,
Je n'arrive plus à lire aucun fichier .trees depuis mon retour du dejeuner.
`> trees = ape::read.tree(here("data/real/st_ctmc-strict-bd-fossilsRemoved/st_ctmc-strict-bd-fossilRemoved…