Man pages for hferg/BTprocessR
A set of tools to help with the interpretation and analysis of the output of BayesTraits MCMC analyses.
| autoplot.bt_post | An autoplot (ggplot2) method for objects of class "bt_post".... |
| autoplot.bt_stones | An autoplot method for the class "bt_stones". Plots a bayes... |
| branchColours | branchColours Generates the edge colours to colour edges by... |
| compPosts | compPosts |
| createCounts | createCounts Creates the counts table for the rjpp. |
| funLegend | funLegend Generate some interesting legend labels. |
| generateTrans | generateTrans Generate the transparencies from data and... |
| getAncStates | getAncStates Reads the ancestral states from a posterior... |
| getDescs | getDescs |
| getMRCAbtr | getMRCAbtr |
| getPL | getPL Gets the path length from the root to the position of a... |
| getPostStats | getPostStats |
| getStones | getStones |
| getTaxa | getTaxa |
| getTipNames | getTipNames |
| ggAutoCor | ggAutoCor |
| ggHist | ggHist |
| ggRunmean | ggRunmean |
| ggTrace | ggTrace |
| ilapply | ilapply an invisible version of lapply |
| isapply | isapply an invisible version of sapply |
| legendInfo | legendInfo Generates legend info for colour scale legends |
| loadPosterior | loadPosterior |
| loadRJ | loadRJ |
| makeInfile | makeInfile Takes a tree and some data, ladderizes the tree,... |
| makeKey | sharedBranches |
| makeLegendTitle | makeLegendTitle Generates legend title for scale bars. |
| makeTrans | makeTrans |
| mcmcPlots | mcmcPlots |
| modeStat | modeStat Calculate the mode. |
| multiplyNodes | multiplyNodes Works out the cumulative effect of linear... |
| plot.ancstates | a print method for class ancstates. |
| plot.bt_post | A plot method for the class "bt_post" that invokes the... |
| plot.bt_stones | A plot method for the class "bt_stones" that invokes the... |
| plotPhylo | plotPhylo |
| plot.rjpp | a plot method for class rjpp. |
| plotShapes | plotShapes Generates the node labels, edge.colours and... |
| plotShifts | plotShifts |
| plot.trees_summary | A plot method for the class "trees_summary" - the default... |
| print.ancstates | a plot method for class ancstates |
| print.bt_post | A print method for class bt_post Displays some descriptive... |
| print.rjpp | A print method for the class "rjpp". |
| print.spkey | A print method for the class "spkey" |
| print.trees_summary | Print function for the S3 class trees_summary |
| rjpp | rjpp |
| scalarSearch | scalarSearch Searches through the posterior of an RJ... |
| scaleTree | scaleTree Scales the tree for plotting |
| shapeCols | shapeCols Generates colours for shapes for either node or... |
| sharedBranches | sharedBranches |
| smartBind | smartBind |
| summariseRjpp | summariseRjpp This functions takes the somewhat massive... |
| summariseTrees | summariseTrees |
