Package index • geoChronR

Creating age ensembles
High-level age modelling functions Primary functions used to create and store age models into LiPD objects
`runBacon()`	Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object
`runBam()`	Generate a Banded Age Model (BAM) and add it into a LiPD object
`runBchron()`	Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object
`runOxcal()`	Generate an oxcal Age Model and add it into a LiPD object
`runOxcalModel()`	Generate an oxcal Age Model from Oxcal model code, then add it into a LiPD object
Bacon-related functions
`getBaconDir()`	Get the name of bacon core directory
`loadBaconOutput()`	Load the ensemble, summary and distribution data from a Bacon simulation
`runBacon()`	Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object
`sampleBaconAges()`	Sample ensemble ages from Bacon
`setBaconDir()`	Set the name of bacon core directory
`writeBacon()`	Create the input file for a Bacon model from a LiPD object
BChron-related functions
`runBchron()`	Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object
OxCal-related functions
`createOxcalModel()`	Create the oxcal model script
`getModelParametersFromOxcalText()`	Pull model parameters from OxCal Code
`loadOxcalOutput()`	Load oxcal output
`oxCalDateExpression()`	write oxcal expression for each date.
`runOxcal()`	Generate an oxcal Age Model and add it into a LiPD object
BAM-related functions
`bamCorrect()`	Corrects a Banded Age Model (BAM)
`runBam()`	Generate a Banded Age Model (BAM) and add it into a LiPD object
`simulateBam()`	Simulate a Banded Age Model (BAM)
Ensemble Analysis
Primary ensemble analysis functions Primary functions used to run ensemble analysis in geoChronR
`corEns()`	Ensemble correlation
`regressEns()`	Ensemble regression
`computeSpectraEns()`	Calculate ensemble power spectra
`pcaEns()`	Perform principle components analysis (PCA) across an ensemble
Correlation-related functions
`ar1()`	Estimate Auto-Regressive coefficient at 1-timesetep
`ar1Surrogates()`	Create a synthetic timeseries that emulates the characteristics of a variable
`corMatrix()`	Matrix correlation
`effectiveN()`	Estimate effective sample size accounting for autocorrelation
`plotCorEns()`	Plot the results of an ensemble correlation
`pvalMonteCarlo()`	Correlations and their significance according to AR(1) benchmarks
`pvalPearsonSerialCorrected()`	Calculate correlation p-value given sample size.
`fdr()`	False Discovery Testing of p-values from multiple testing
`fdr.master()`	FDR Master
`fdrBasic()`	FDR Basic
`propAlt()`	Proportion of alternate hypotheses
`storey()`	Storey estimator
Regression-related functions
`plotRegressEns()`	Plot ensemble regression results
`plotScatterEns()`	Plot an ensemble of data as a scatterplot
`plotTrendLinesEns()`	Plot an ensemble of trendlines
`regress()`	Simple ordinary least squeares regression
`regressEns()`	Ensemble regression
Spectral-analyis-related functions
`ar1Surrogates()`	Create a synthetic timeseries that emulates the characteristics of a variable
`computeSpectraEns()`	Calculate ensemble power spectra
`createSyntheticTimeseries()`	Create a synthetic timeseries that emulates the characteristics of a timeseries
`periodAnnotate()`	Annotate plot of spectra with given periodicities
`plotSpectrum()`	Plot spectrum with confidence limits
`reverselog10_trans()`	Reverse axis in log10 scale
PCA-related functions
`ar1Surrogates()`	Create a synthetic timeseries that emulates the characteristics of a variable
`createSyntheticTimeseries()`	Create a synthetic timeseries that emulates the characteristics of a timeseries
`pcaEns()`	Perform principle components analysis (PCA) across an ensemble
`plotPcaEns()`	Map ensemble pca loadings and plot PC timeseries
`plotScreeEns()`	create a scree plot for PCA analysis
Visualization
Plotting functions Primary functions to visualize data in geoChronR
`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 a rank-pvalue plot
`plotRegressEns()`	Plot ensemble regression results
`plotScatterEns()`	Plot an ensemble of data as a scatterplot
`plotScreeEns()`	create a scree plot for PCA analysis
`plotSpectraEns()`	Plot ensemble spectra output
`plotSpectrum()`	Plot spectrum with confidence limits
`plotSummary()`	Plot a summary figure
`plotSummaryTs()`	TS overview plot
`plotTimeAvailabilityTs()`	Create a Time availability plot
`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
Mapping functions
`baseMap()`	Make a base map
`mapLipd()`	Map a list of LiPD objects
`mapTs()`	Map a TS object
Plotting helper functions
`AD2BP_trans()`	convert an AD age scale to BP
`BP2AD_trans()`	convert a BP age scale to AD
`axisLabel()`	Label axes
`bin2d()`	Two dimensional binning
`geoChronRPlotTheme()`	Define a plot theme for GeoChronR
`getLegend()`	get a ggplot legend object
`getPlotRanges()`	Get ggplot x and y ranges
`kde2d()`	Two dimensional kernel density estimation
`meltDistributionTable()`	Melt distribution
`modeSelektor()`	ModeSelektor
`periodAnnotate()`	Annotate plot of spectra with given periodicities
`quantile2d()`	Find quantiles across an ensemble
`reverselog10_trans()`	Reverse axis in log10 scale
Other functions
Binning Functions used to bin data into regular intervals
`alignTimeseriesBin()`	Align and bin two timeseries into comparable bins
`bin()`	Bin Data
`bin2d()`	Two dimensional binning
`binEns()`	Bin ensemble data
`binTs()`	Bin every entry in a Timeseries object
LiPD manipulations Functions useful for manupulating LiPD objects
`createConcatenatedEnsembleMeasurementTable()`	Create a measurementTable from concatenated ensembles
`createModel()`	Create a chron or paleo model including adding ensemble data
`createMultiModelEnsemble()`	Create a multi-model ensemble
`createSummaryTableFromEnsembleTable()`	Create a summary table from an ensemble table
`createTSid()`	Create a random TSid
`estimateUncertaintyFromRange()`	Estimate uncertainty estimates from high/low range
`getVariableIndex()`	Get the index of variable list
`mapAgeEnsembleToPaleoData()`	Map an ageEnsemble variable from a chron model to a paleoMeasurement Table
`pullTsVariable()`	pull variable out of TS object
`selectData()`	Select a LiPD "variable list"
Utility functions Functions useful for a variety of internal, and potentially external, applications
`askUser()`	askUser
`concatEnsembleTimeseries()`	Concatenate two independent ensemble timeseries
`convertAD2BP()`	Convert years Calendar year (AD/BC or CE) to BP (1950)
`convertBP2AD()`	Convert years BP to Calendar year (AD/BC or CE)
`createChronMeasInputDf()`	Create a data frame for chron measurement data
`gaussianize()`	Gaussianize
`getLastVarString()`	Get the last set of parameters you used in createChronMeasInputDf()
`getOs()`	What OS is this?
`heuristicUnits()`	Makes a guess about the units of a time vector based on the values
`loadRemote()`	Load a remote RData file
`pullInstance()`	Pull one instance from an ensemble
`stringifyVariables()`	Convert var.names to strings
`surrogateDataFun()`	Use the write function from rEDM depending on the version

Reference

Creating age ensembles

High-level age modelling functions

Bacon-related functions

BChron-related functions

OxCal-related functions

BAM-related functions

Ensemble Analysis

Primary ensemble analysis functions

Correlation-related functions

Regression-related functions

Spectral-analyis-related functions

PCA-related functions

Visualization

Plotting functions

Mapping functions

Plotting helper functions

Other functions

Binning

LiPD manipulations

Utility functions