Man pages for laduplessis/beastio
Functions for pre- and post-processing of BEAST and BEAST2 files.
| applyMCMC | Apply a function to an mcmc or mcmc.list object, e.g. median |
| checkESS | Check if any parameters in an mcmc chain have an ESS value <... |
| checkESSl | Check that all parameters in an mcmc chain have an ESS value... |
| constantPars | Identify parameters in the mcmc chain that have not been... |
| constantParsMCMC | Like constantPars, but for a single mcmc object (private... |
| effectiveSize | Overwrites coda::effectiveSize Avoids numerical underflow by... |
| getBranchingTimes | Branching (coalescent) times of a phylogenetic tree |
| getCladeHeight | Height of a clade in a phylogenetic tree |
| getCladeMonophyly | Monophyly statistics of a clade in a list of trees |
| getHPD.boa | Calculate HPD of a parameter |
| getHPDMedian | Calculate the HPD interval and median and return in a single... |
| getLineages | Internal function to get the number of lineages during an... |
| getLogFileSubset | Extract a subset of parameters from a log file |
| getMatrixHPD.boa | Calculate HPD of a set of parameters |
| getMonths | Generate a sequence of months |
| getSamplingTimes | Sampling times of a phylogenetic tree |
| getTreeIntervals | Intervals of a phylogenetic tree |
| getTreeIntervalsSlow | Intervals of a phylogenetic tree |
| getWeeks | Generate a sequence of weeks |
| hello | Hello, World! |
| pairwiseCorrelations | Calculate pairwise correlations between parameters |
| plotESS | Plot barplot of ESS values |
| readLog | Read BEAST log files |
| readSingleLog | Read a single BEAST log file |
| readTreeLog | Read BEAST trees file |
| sampledPars | The opposite to constantPars, that is returns all parameters... |
| treeDFSSlow | Internal function for depth first traversal of a tree in... |
| writeLog | Save BEAST/Tracer log file |
