Description: Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.
Packaged: 2019-05-20 11:27:15 UTC; markputtick

Author: Mark Puttick [aut,cre], Pascal Title [ctb]
Packaged: 2019-05-21 19:24:11 UTC; markputtick

Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Authors@R: person("Casey", "Youngflesh", role = c("aut", "cre"), email = "caseyyoungflesh@gmail.com", comment = c(ORCID = "0000-0001-6343-3311"))
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with JAGS, Stan, or other MCMC samplers.
Imports: coda, rstan, grDevices, graphics, stats, overlapping
Packaged: 2018-04-05 15:48:05 UTC; caseyyoungflesh
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>)

Packaged: 2018-05-02 14:59:27 UTC; caseyyoungflesh

person("Casey", "Youngflesh", role = c("aut", "cre"), email = "caseyyoungflesh@gmail.com", comment = c(ORCID = "0000-0001-6343-3311")),
person("Christian", "Che-Castaldo", role = c("ctb")),
person("Tyler", "Hardy", role = c("ctb")))
Packaged: 2018-05-21 22:52:51 UTC; caseyyoungflesh
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>),