BDSKY Tools

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 |

plotOUProcessHPD | Functions for plotting OU processes |

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 |

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