| gtrigsamples {lorad} | R Documentation |
Sequence data used in gtrig vignette
Description
Sequence data used in gtrig vignette
Usage
gtrigsamples
Format
gtrigsamples
A data frame with 10,001 rows and 35 columns:
- Iteration
MCMC iteration
- Posterior
Log of the unnormalized posterior density
- Likelihood
Log likelihood
- Prior
Log of the prior density
- alpha
Shape parameter of the (mean=1) Gamma distribution of among-site rate heterogeneity
- edge_length_proportions.1.
Proportion of total tree length used by edge 1
- edge_length_proportions.2.
Proportion of total tree length used by edge 2
- edge_length_proportions.3.
Proportion of total tree length used by edge 3
- edge_length_proportions.4.
Proportion of total tree length used by edge 4
- edge_length_proportions.5.
Proportion of total tree length used by edge 5
- edge_length_proportions.6.
Proportion of total tree length used by edge 6
- edge_length_proportions.7.
Proportion of total tree length used by edge 7
- edgelens.1.
Edge length 1
- edgelens.2.
Edge length 2
- edgelens.3.
Edge length 3
- edgelens.4.
Edge length 4
- edgelens.5.
Edge length 5
- edgelens.6.
Edge length 6
- edgelens.7.
Edge length 7
- er.1.
Exchangeability parameter for A to C
- er.2.
Exchangeability parameter for A to G
- er.3.
Exchangeability parameter for A to T
- er.4.
Exchangeability parameter for C to G
- er.5.
Exchangeability parameter for C to T
- er.6.
Exchangeability parameter for G to T
- pi.1.
Nucleotide relative frequency for A
- pi.2.
Nucleotide relative frequency for C
- pi.3.
Nucleotide relative frequency for G
- pi.4.
Nucleotide relative frequency for t
- pinvar
Proportion of invariable sites
- site_rates.1.
Rate for site category 1
- site_rates.2.
Rate for site category 1
- site_rates.3.
Rate for site category 1
- site_rates.4.
Rate for site category 1
- tree_length
Tree length (sum of all edge lengths) in substitutions per site
Source
The program RevBayes (version 1.2.1) was used to obtain a sample from the Bayesian posterior distribution for 5 green plant rbcL sequences under a GTR+I+G model.