R: Pre- And Post-Processing in Bayesian Evolutionary Analyses

# Pre- And Post-Processing in Bayesian Evolutionary Analyses

## Documentation for package ‘tbea’ version 1.7.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

andes | Divergence-time estimation data for cis-trans-Andean pairs
concatNexus | concatNexus: Function for concatenation of nexus matrices both morphological and molecular
conflate | conflate: Calculate the conflation of multiple distributions pdfs, plot = TRUE, from, to, n, add = FALSE
crossplot | crossplot: Plot the mean/median and HPD interval bars for pairs of distributions
cynodontidae.posterior | Posterior samples for the family Cynodontidae
cynodontidae.prior | Prior samples for the family Cynodontidae
c_truncauchy | c_truncauchy: Estimate the c parameter for the truncated cauchy L distribution to be used in MCMCTree
density_fun | density_fun: A way to represent distributions to be conflated
fasta2nexus | fasta2nexus (deprecated): Function for converting molecular alignments from fasta to nexus format
findParams | Function for estimation of probability density function parameters through quadratic optimization
laventa | Geochronology samples from the Honda Group in Colombia
lognormalBeast | Constructing a curve for the user-specified lognormal prior using Beast2 parameters
measureSimil | Calculate the Intersection Between Two Densities
mswd.test | Reduced chi-square test or mean square weighted deviation (mswd) test
quantile_conflation | quantile_conflation: Calculate the quantile for a given probabiliy under a conflated distribution
stratCI | stratCI: Estimate the confidence intervals of endpoints in stratigraphic intervals
summaryBrlen | summaryBrlen: Summarise branch lengths on trees with identical topology
table2nexus | table2nexus: Read a data matrix in delimited format and convert into a data matrix in nexus format
tnt2newick | tnt2newick: Function for converting from TNT tree format to newick parenthetical format
topoFreq | Frequency of topologies in a tree sample
xintercept | xintercept: Estimate the x-intercept of an empirical cdf