Tools to analyze and visualize time-uncertain geoscientific data

alignTimeseriesBin | Align and bin two timeseries into comparable bins |

ar1 | Estimate Auto-Regressive coefficient at 1-timesetep |

ar1Surrogates | Create a synthetic timeseries that emulates the... |

assignColors | Assign colors for map color scale |

axisLabel | Label axes |

bamCorrect | Corrects a Banded Age Model (BAM) |

baseMap | Make a base map |

bin | Bin Data |

bin2d | Two dimensional binning |

binEns | Bin ensemble data |

binTs | Bin every entry in a Timeseries object |

clearAll | Clear all variables and functions from global environment |

convertAD2BP | Convert years Calendar year (AD/BC or CE) to BP (1950) |

convertBP2AD | Convert years BP to Calendar year (AD/BC or CE) |

corEns | Ensemble correlation |

corMatrix | Matrix correlation |

corrIsopersist | Correlations and their significance according to AR(1)... |

createSyntheticTimeseries | Create a synthetic timeseries that emulates the... |

detachAll | Detach all packages |

effectiveN | Estimate effective sample size accounting for autocorrelation |

estimateUncertaintyFromRange | Estimate uncertainty estimates from high/low range |

fdr | False Discovery Testing of p-values from multiple testing |

fdrBasic | FDR Basic |

fdr.master | FDR Master |

flipCoords | Flip Coordinates |

gaussianize | Gaussianize |

geoChronRPlotTheme | Define a plot theme for GeoChronR |

getBaconDir | Get the name of bacon core directory |

getLegend | get a ggplot legend object |

getOs | What OS is this? |

getPlotRanges | Get ggplot x and y ranges |

getVariableIndex | Get the index of variable list |

kde_2d | Two dimensional kernel density estimation |

loadBaconOutput | Load the ensemble, summary and distribution data from a Bacon... |

mapAgeEnsembleToPaleoData | Map an ageEnsemble variable from a chron model to a... |

mapLipd | Map a LiPD object |

mapLipds | Map a list of LiPD objects |

meltDistributionTable | Melt distribution |

neotoma2Lipd | Create a LiPD object from Neotoma |

pcaEns | Perform principle components analysis (PCA) across an... |

plotChron | High-level chron plotting |

plotChronEns | Plot chron ensemble |

plotChronEnsDiff | Compare chron ensemble with paleoData age-model |

plotCorEns | Plot the results of an ensemble correlation |

plotHistEns | Plot an ensemble dataset as a histogram |

plotLine | Plot or add a line to plot |

plotModelDistributions | Plot probability distributions |

plotPcaEns | Map ensemble pca loadings and plot PC timeseries |

plotPvalsEnsFdr | Plot the the p-values of an ensemble correlation analysis in... |

plotRegressEns | Plot ensemble regression results |

plotScatterEns | Plot an ensemble of data as a scatterplot |

plotSpectraEns | Plot ensemble spectra output |

plotSummary | Plot a summary figure |

plotTimeseriesEnsLines | Plot an ensemble timeseries as a set of lines |

plotTimeseriesEnsRibbons | Plot an ensemble timeseries as ribbons of probabilities |

plotTimeseriesStack | Plot a bunch of timeseries in a vertical stack |

plotTrendLinesEns | Plot an ensemble of trendlines |

powerSpectrumEns | Calculate ensemble power spectra |

propAlt | Proportion of alternate hypotheses |

pullTsVariable | pull variable out of TS object |

pushTsVariable | push variable into of TS object |

pvalPearsonSerialCorrected | Calculate correlation p-value given sample size. |

quantile2d | Find quantiles across an ensemble |

regress | Simple ordinary least squeares regression |

regressEns | Ensemble regression |

runBacon | Generate a Bayesian Reconstruction Age Model (Bacon) and add... |

runBam | Generate a Banded Age Model (BAM) and add it into a LiPD... |

runBchron | Generate a Bayesian Reconstruction Age Model (Bacon) and add... |

runClam | Run a clam model |

sampleBaconAges | Sample ensemble ages from Bacon |

selectData | Select a LiPD "variable list" |

setupGeoChronR | Setup GeoChronR for first time use |

simulateBam | Simulate a Banded Age Model (BAM) |

storey | Storey estimator |

tidyTs | create tidy data.frame from TS |

writeBacon | Create the input file for a Bacon model from a LiPD object |

writeClam | write files for running a clam model |

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