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