gtrigsamples: Sequence data used in gtrig vignette
In lorad: Lowest Radial Distance Method of Marginal Likelihood Estimation

gtrigsamples

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.

lorad documentation built on May 29, 2024, 1:30 a.m.