R We There Yet? Visualizing MCMC Convergence in Phylogenetics
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Documentation for package ‘rwty’ version 1.0.3
Help Pages
| analyze.rwty | analyze.rwty, the main interface for rwty analyses and plots. |
| check.chains | Function for checking suitability of chains for rwty analyses, auto-generating labels, etc |
| clade.freq | Returns clade names and frequencies |
| combine.ptables | Function for merging p tables for multiple MCMC chains |
| cumulative.freq | Cumulative means of clade split frequencies. |
| estimate.autocorr.m | Calculate sampling interval based on exponential semivariogram model. |
| fungus | MrBayes output from analysis of Hibbett et al. data |
| load.multi | Load all matching files from a directory into a list of rwty.chain objects |
| load.trees | Custom functions to load tree lists so that rwty can do basic processing on the way in. |
| makeplot.acsf.cumulative | Plot the Change in Split Frequencies (CSF) in sliding windows over the course of an MCMC. |
| makeplot.acsf.sliding | Plot the Chaing in Split Frequencies (CSF) in sliding windows over the course of an MCMC. |
| makeplot.all.params | Plotting all parameters |
| makeplot.asdsf | Plot the Standard Deviation of Split Frequencies over the course of an MCMC. |
| makeplot.autocorr | Make autocorrelation plots of tree topologies from MCMC analyses |
| makeplot.pairs | Plotting parameters against each other |
| makeplot.param | Plotting parameters |
| makeplot.pseudo.ess | Plot the pseudo ESS of tree topologies from MCMC chains. |
| makeplot.splitfreq.matrix | Plots a matrix of split frequency comparisons between multiple MCMC chains. |
| makeplot.splitfreqs.cumulative | Plot cumulative split frequencies over the course of an MCMC |
| makeplot.splitfreqs.sliding | Plot split frequencies in sliding windows over the course of an MCMC |
| makeplot.topology | Plotting parameters |
| makeplot.treespace | Plot chains in treespace. |
| parse.clades | Rename clades for easy recall |
| parse.slide.clades | Rename clades for easy recall |
| print.rwty.chain | Function for printing rwty.chain objects |
| salamanders | MrBayes output from analysis of Williams et al. data |
| slide.freq | Sliding window measurements of clade split frequencies. |
| topological.approx.ess | Calculate the approximate Effective Sample Size (ESS) of tree topologies |
| topological.autocorr | Calculate data for autocorrelation plots of tree topologies from MCMC analyses |
| topological.pseudo.ess | Calculate the pseudo Effective Sample Size (ESS) of tree topologies |
| tree.dist.matrix | Tree distance matrix calculation |
| treespace | MDS scaling of treespace for a single tree list. |