Pre- And Post-Processing in Bayesian Evolutionary Analyses
c_truncauchy: Estimate the c parameter for the truncated cauchy L dist...
concatNexus: Function for concatenation of nexus matrices both morphol...
conflate: Calculate the conflation of multiple distributions pdfs, plo...
crossplot: Plot the median and HPD interval bars for pairs of distribu...
density_fun: A way to represent distributions to be conflated
fasta2nexus (deprecated): Function for converting molecular alignments...
Function for estimation of probability density function parameters thr...
Constructing a curve for the user-specified lognormal prior using Beas...
Calculate the Intersection Between Two Densities
Reduced chi-square test or mean square weighted deviation (mswd) test
stratCI: Estimate the confidence intervals of endpoints in stratigraph...
summaryBrlen: Summarise branch lengths on trees with identical topolog...
table2nexus: Read a data matrix in delimited format and convert into a...
tbea: Pre- And Post-Processing in Bayesian Evolutionary Analyses
tnt2newick: Function for converting from TNT tree format to newick par...
Frequency of topologies in a tree sample
xintercept: Estimate the x-intercept of an empirical cdf
Functions are provided for prior specification in divergence time estimation using fossils as well as other kinds of data. It provides tools for interacting with the input and output of Bayesian platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes', or 'MCMCTree'. It Implements a simple measure similarity between probability density functions for comparing prior and posterior Bayesian densities, as well as code for calculating the combination of distributions using conflation of Hill (2008). Functions for estimating the origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and stratigraphic intervals (Marshall 2010) are also available. Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. <doi:10.48550/arXiv.0808.1808>, Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. <DOI:10.1002/9781118625590>, Marshall, C. R. 2010. "Using confidence intervals to quantify the uncertainty in the end-points of stratigraphic ranges". Quantitative Methods in Paleobiology, 291--316. <DOI:10.1017/S1089332600001911>.