Package index • neotrans

All functions
`AllProjects()`	List all projects
`AnalysisDir()`	Directory containing analysis output
`AsHMS()`	Convert time to H:M:S format
`BurnOff()`	Remove burnin
`Collect()`	Process analyses that have completed on remote server
`ComparisonTrees()`	Sample of 128 posterior trees for comparison with well-corroborated tree
`Config()`	Configuration settings
`ConnectSSH()`	Connect to remote server via SSH
`ConvergenceFile()`	Path to convergence-diagnostic file
`Cores()`	Predict number of cores required
`DeZZ()`	Unify tip label format
`Decrypt()`	Human-readable label for internal metadata variable
`DiffDepth()`	Explore whether differences in tree topology are deep or shallow
`DiskFile()`	Path to temporary disk-usage log
`Dispersion()`	Summarize dispersion of tree distances within and between samples
`DistanceFile()`	Path to tree-distance results
`DummyFile()`	Path to dummy input matrix for testing
`ESS()`	Effective sample size
`EnqueueMC()`	Queue projects for MCMC analysis
`EnqueueML()`	Queue projects for marginal likelihood estimation
`EpsLine()`	Mark meaningful differences
`EvaluatePartitioning()`	Evaluate t parameter
`ExistingResults()`	Existing results Read results that have already been cached using `UpdateRecords()`.
`ExtendRun()`	Submit a continuation job
`FetchLogIfMissing()`	Fetch log file from simulation study
`FetchResults()`	Fetch results from remote server
`HasConverged()`	Has an analysis converged?
`HetNPlot()`	Plot values of n from heterogeneous models
`InfNeo()`	Informative neomorphic cells
`InformationGain()`	Increase in information density in prior vs posterior.
`KiProjects()`	List projects suitable for _ki analyses
`MakeRepo()`	Create a new RevBayes analysis repository
`MakeSlurm()`	Create a slurm job Constructs and submits a slurm job to complete an analysis
`MarginalDiffs()`	Difference between marginal likelihood estimates obtained by stepping stone and path sampling analyses.
`MarginalFile()`	Path to marginal-likelihood output
`MatrixFile()`	Path to matrix file
`MemFile()`	Path to memory-usage log
`Metadata()`	Project metadata
`ModelBF()`	Bayes factor support for each model, relative to best fitting
`ModelCol()`	Model colour Return the colour used to plot results of this model
`ModelHeatmap()`	Heatmap of model comparisons
`ModelIsHeterogeneous()` `ModelIsStationary()`	Type of model
`ModelLabel()`	Model label Translates a model script identifier to a human-readable label
`ModelLabelExpr()`	Axis-ready model labels Wraps `ModelLabel` output in `phantom("\|")` on each side, ensuring a consistent bounding-box height for horizontal (`las = 1`) axis labels.
`OutputDir()` `RepoDir()` `SlurmDir()` `RemoteDir()` `RBScriptDir()`	Path to directories in which files are stored locally.
`OutputPlot()`	Output a plot to file or graphics device
`PDFFile()`	Path to PDF comparison file
`PFiles()`	List RevBayes log-file paths
`PPSamplerFile()`	Path to posterior-predictive sample file
`PSRF()`	Potential scale reduction factor (PSRF)
`Panel()`	Add label for plot region
`ParameterFile()`	Path to stored parameter summary
`ParsEvalFile()`	Path to parsimony-evaluation results
`ParsimonyFile()`	Path to parsimony-score results
`PastRuns()`	Previous attempts to run an analysis
`Peek()`	View tail of job output
`PlotParamViolin()`	Violin plot of posterior parameter medians with exp-scale y-axis
`PosteriorTreeSteps()`	Parsimony lengths of trees in posterior distribution
`PrecisionIncrease()`	Calculate proportional improvement in precision
`PredictWith()`	Depict predictive power of variable for output
`PrepareMatrix()`	Prepare matrices for phylogenetic analysis
`PriorVsPost()`	Compare prior and posterior distributions
`QueueSim()`	Queue simulation for remote analysis
`ReadTrees()`	Read trees from cache
`ResultsDir()`	Directory containing stored results
`RevBayes()`	Prepare and submit a new RevBayes analysis job
`RewindRepo()`	Restore MCMC files in a git repo to a previous state
`SCancel()`	scancel
`SQ()`	squeue Output the current slurm queue on the remote host
`ScriptBase()`	Construct base name for a script
`ScriptFile()`	Path to RevBayes script
`Simulated01s()`	Retrieve counts of 0s and 1s from simulation output
`SlurmFile()`	Path to generated SLURM script
`SlurmLog()`	Read log of completed SLURM jobs
`SlurmQueue()`	Read current slurm queue on remote host
`SlurmTemplate()`	Path to SLURM submission template
`SpindleCompare()`	Comparative spindle plot of model Bayes factors
`SpindlePlot()`	Spindle plot
`SshSession()`	Start ssh session with remote server
`StoneFile()`	Path to stepping-stone results
`StoneOrigin()`	Path to stepping-stone origin file
`TaxonCol()`	Taxon colour Return an appropriate colour for each higher taxon
`TimeFile()`	Path to time-usage log
`TreeDistances()`	Compute pairwise tree distances between two model samples
`TreeFiles()`	List tree-file paths
`TreeLengths()`	Compute total tree lengths for all trees in a sample
`TreeSampleFile()`	Path to combined tree sample
`TreeSearch()`	Queue parsimony search on Slurm remote
`TreeSimBox()` `TreeSimPlot()`	Box plot of tree similarity
`TreeSimSpindle()`	Spindle plot of tree similarity
`TreeSimSpindleRow()`	Plot a row of tree similarity spindles
`TreeSimilarities()`	Compare trees with well corroborated tree
`UpdateRecords()`	Fetch ML and MCMCMC results from GitHub.
`.DiffErr()`	Combine two error terms
`.MeanAcc()`	Mean accuracy across all tips and characters for one replicate
`.NCoded()`	Number of characters with non-ambiguous state
`.OutwithError()`	Outwith error
`.PoolRuns()`	Pool runs within each replicate, then summarise per replicate Each cell of `accuracy` is a list of nTip vectors (one per tip); c() concatenates the two runs' values for the same tip.
`incompleteBeta()` `fnDiscretizeBeta()`	Discretized beta distribution R implementation of the RevBayes function fnDiscretizeBeta

Reference

All functions