| densityOU | Calculate the density of OU process for a given (x,t) pair |
| expectedValOU | Expected value of OU process at times t starting at x0 at... |
| getBranchingTimes | Calculate the branching times of a tree (based on getx()... |
| getDayDate | Convert date from year + fraction to normal date (day, month... |
| getHPD | Get HPD of a posterior sample |
| getLeafTimes | Calculate the leaf heights of a tree |
| getMatrixHPD | Get HPD of a matrix of values e.g. a skyline |
| getMonths | Return start and end date, with all months in between |
| getPrior | Return a function with parameters that can be evaluated using... |
| getSkylineSubset | Extract all matching parameters from the logfile |
| getSurface | Return datastructure with the meshed likelihood surface as... |
| getTreeIntervals | Calculate the branching times and leaf heights of a tree |
| getWeeks | From the first week BEFORE start up to end (strict) |
| getYearDate | Convert from date to decimal fraction of year |
| gridSkyline | Interpolates skyline on a time grid (returns a matrix) |
| gridSkylineDates | Grid the skyline between two dates |
| gridSkylineVec | Version using apply, but it is slower for some enigmatic... |
| labelPlot | Label plot in top left corner |
| likOU | Calculates the likelihood of observing a trajectory under a... |
| logLikOU | Calculates the log-likelihood of observing a trajectory under... |
| NewFig | Need to follow with dev.off() |
| paddedrange | Get range and pad by some percentage of the range on either... |
| pal.dark | Palette of diverging dark colours (Paired palette from... |
| pal.light | Palette of diverging light colours (Paired palette from... |
| plotBeanPlot | Plot beans |
| plotBMProcessPriors | This function does not really plot the true quantiles -... |
| plotCrossSection | Plot cross section of the likelihood surface of par1, for... |
| plotHPDs | Plot distributions using beans |
| plotJellyBeanHPDs | Get HPDs and plot jelly beans |
| plotJellyBeans | Plot jelly beans |
| plotOUDensity | Plot the density of an OU-process with parameters x0, mu,... |
| plotOUDensityEmpirical | Plot the density of ntraj OU-processes simulated to time dt,... |
| plotOUProcessFlexibility | Plot a summary of the flexibility of an OU-process with... |
| plotOUProcessFlexibilityEmpirical | Plot a summary of the flexibility of an OU-process with... |
| plotOUProcessHPD | Plot expected 95 conditioning on values of x0, mu, sigma, nu |
| plotOUProcessHPDEmpirical | Plot empirical 95 from simulating nTraj replicates, which can... |
| plotOUProcessPriors | This function does not really plot the true quantiles -... |
| plotPrior | Plot a parametric distribution where the distribution is... |
| plotQuantileGradient | Plot the quantiles for OU or BM process as a gradient across... |
| plotRoundedBars | Plot a rounded bar (jelly bean) |
| plotSkyline | Plot a Skyline. |
| plotSkylinePretty | Plot a pretty skyline. Contains default options for drawing... |
| quantilesBM | Calculate quantiles of BM process at different timepoints |
| quantilesOU | Calculate quantiles of OU process at different timepoints |
| readLogfile | Read in BEAST2 logfile |
| removeInfinite | Remove all rows containing non-finite values |
| revMatrix | Reverses each column (margin=2) or row (margin=1) of a matrix |
| simulateBM | Simulate BM trajectory |
| simulateDiscreteOU | Functions for simulating Ornstein-Uhlenbeck processes and... |
| simulateOU | Simulate OU trajectory using the analytical solution obtained... |
| simulateOUslow | Simulate OU trajectory using the analytical solution obtained... |
| standardDevOU | Standard deviation of OU process at times t starting at x0 at... |
| timer | Wrapper for timing a function |
