Man pages for laduplessis/bdskytools
BDSKY Tools

densityOUCalculate the density of OU process for a given (x,t) pair
expectedValOUExpected value of OU process at times t starting at x0 at...
getBranchingTimesCalculate the branching times of a tree (based on getx()...
getDayDateConvert date from year + fraction to normal date (day, month...
getHPDGet HPD of a posterior sample
getLeafTimesCalculate the leaf heights of a tree
getMatrixHPDGet HPD of a matrix of values e.g. a skyline
getMonthsReturn start and end date, with all months in between
getPriorReturn a function with parameters that can be evaluated using...
getSkylineSubsetExtract all matching parameters from the logfile
getSurfaceReturn datastructure with the meshed likelihood surface as...
getTreeIntervalsCalculate the branching times and leaf heights of a tree
getWeeksFrom the first week BEFORE start up to end (strict)
getYearDateConvert from date to decimal fraction of year
gridSkylineInterpolates skyline on a time grid (returns a matrix)
gridSkylineDatesGrid the skyline between two dates
gridSkylineVecVersion using apply, but it is slower for some enigmatic...
labelPlotLabel plot in top left corner
likOUCalculates the likelihood of observing a trajectory under a...
logLikOUCalculates the log-likelihood of observing a trajectory under...
NewFigNeed to follow with dev.off()
paddedrangeGet range and pad by some percentage of the range on either...
pal.darkPalette of diverging dark colours (Paired palette from...
pal.lightPalette of diverging light colours (Paired palette from...
plotBeanPlotPlot beans
plotBMProcessPriorsThis function does not really plot the true quantiles -...
plotCrossSectionPlot cross section of the likelihood surface of par1, for...
plotHPDsPlot distributions using beans
plotJellyBeanHPDsGet HPDs and plot jelly beans
plotJellyBeansPlot jelly beans
plotOUProcessHPDFunctions for plotting OU processes
plotOUProcessHPDEmpiricalPlot empirical 95 from simulating nTraj replicates, which can...
plotOUProcessPriorsThis function does not really plot the true quantiles -...
plotPriorPlot a parametric distribution where the distribution is...
plotQuantileGradientPlot the quantiles for OU or BM process as a gradient across...
plotRoundedBarsPlot a rounded bar (jelly bean)
plotSkylinePlot a Skyline.
plotSkylinePrettyPlot a pretty skyline. Contains default options for drawing...
quantilesBMCalculate quantiles of BM process at different timepoints
quantilesOUCalculate quantiles of OU process at different timepoints
readLogfileRead in BEAST2 logfile
removeInfiniteRemove all rows containing non-finite values
revMatrixReverses each column (margin=2) or row (margin=1) of a matrix
simulateBMSimulate BM trajectory
simulateDiscreteOUFunctions for simulating Ornstein-Uhlenbeck processes and...
simulateOUSimulate OU trajectory using the analytical solution obtained...
simulateOUslowSimulate OU trajectory using the analytical solution obtained...
standardDevOUStandard deviation of OU process at times t starting at x0 at...
timerWrapper for timing a function
laduplessis/bdskytools documentation built on July 18, 2018, 6:24 p.m.