Closed drxilu closed 2 years ago
Hi Xavier,
I have managed to see all mcmc stats on the generated phylogeny, the integrated method print.resBactDating
will print out these. Also used capture.output
to save it to a file.
Phylogenetic tree dated using BactDating
Phylogenetic tree with 71 tips and 70 internal nodes.
Tip labels:
16288_4_64, 6999_6_6, 717832, 21903_8_2, 717965, 21903_8_185, ...
Node labels:
Root, n2, n3, n4, n5, n6, ...
Rooted; includes branch lengths.
Probability of root branch=1.00
likelihood=-4.10e+02 [-4.27e+02;-3.97e+02]
prior=-5.04e+02 [-5.64e+02;-4.74e+02]
mu=1.27e+00 [5.54e-01;1.78e+00]
sigma=2.89e-01 [1.33e-01;4.75e-01]
alpha=5.18e+02 [2.85e+02;1.08e+03]
Root date=1645.60 [1234.51;1796.97]
Root date for most likely root=1645.66 [1254.82;1796.97]
Thanks, Xi
Hi Xavier,
I am recently working on plotting MCMCs from Gubbins outputs and after running BactDating. Having some MCMCs traces plots like:![Picture2](https://user-images.githubusercontent.com/52334760/184938742-f0f758d5-5615-4eae-a331-c4664a372dc8.png)
I wonder if there are methods to calculate or plot 95CIs for date of root, clock rate, relaxation parameters etc., in this MCMC traces plot.
Thank you in advance.
Best, Xi