Pre- And Post-Processing in Bayesian Evolutionary Analyses

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Documentation for package ‘tbea’ version 1.7.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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