Man pages for nickmckay/GeoChronR
Tools to Analyze and Visualize Time-Uncertain Data
| AD2BP_trans | convert an AD age scale to BP |
| 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... |
| askUser | askUser |
| 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 |
| BP2AD_trans | convert a BP age scale to AD |
| computeSpectraEns | Calculate ensemble power spectra |
| 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) |
| corEns | Ensemble correlation |
| corMatrix | Matrix correlation |
| createChronMeasInputDf | Create a data frame for chron measurement data |
| createConcatenatedEnsembleMeasurementTable | Create a measurementTable from concatenated ensembles |
| createModel | Create a chron or paleo model including adding ensemble data |
| createMultiModelEnsemble | Create a multi-model ensemble |
| createOxcalModel | Create the oxcal model script |
| createSummaryTableFromEnsembleTable | Create a summary table from an ensemble table |
| createSyntheticTimeseries | Create a synthetic timeseries that emulates the... |
| createTSid | Create a random TSid |
| 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 |
| gaussianize | Gaussianize |
| generateEnsembleFromUncertainty | Create an ensemble from an uncertainty and AR1 estimate |
| geoChronRPlotTheme | Define a plot theme for GeoChronR |
| getBaconDir | Get the name of bacon core directory |
| getLastVarString | Get the last set of parameters you used in... |
| getLegend | get a ggplot legend object |
| getModelParametersFromOxcalText | Pull model parameters from OxCal Code |
| getOs | What OS is this? |
| getPlotRanges | Get ggplot x and y ranges |
| getVariableIndex | Get the index of variable list |
| heuristicUnits | Makes a guess about the units of a time vector based on the... |
| kde2d | Two dimensional kernel density estimation |
| loadBaconOutput | Load the ensemble, summary and distribution data from a Bacon... |
| loadOxcalOutput | Load oxcal output |
| loadRemote | Load a remote RData file |
| mapAgeEnsembleToPaleoData | Map an ageEnsemble variable from a chron model to a... |
| mapLipd | Map a list of LiPD objects |
| mapTs | Map a TS object |
| meltDistributionTable | Melt distribution |
| modeSelektor | ModeSelektor |
| oxCalDateExpression | write oxcal expression for each date. |
| pcaEns | Perform principle components analysis (PCA) across an... |
| periodAnnotate | Annotate plot of spectra with given periodicities |
| 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 |
| 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 |
| propAlt | Proportion of alternate hypotheses |
| pullInstance | Pull one instance from an ensemble |
| pullTsVariable | pull variable out of TS object |
| pvalMonteCarlo | Correlations and their significance according to AR(1)... |
| pvalPearsonSerialCorrected | Calculate correlation p-value given sample size. |
| quantile2d | Find quantiles across an ensemble |
| regress | Simple ordinary least squeares regression |
| regressEns | Ensemble regression |
| reverselog10_trans | Reverse axis in log10 scale |
| 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... |
| 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... |
| sampleBaconAges | Sample ensemble ages from Bacon |
| selectData | Select a LiPD "variable list" |
| setBaconDir | Set the name of bacon core directory |
| simulateAutoCorrelatedUncertainty | Simulate uncertainty in a dataset |
| simulateBam | Simulate a Banded Age Model (BAM) |
| storey | Storey estimator |
| stringifyVariables | Convert var.names to strings |
| surrogateDataFun | Use the write function from rEDM depending on the version |
| writeBacon | Create the input file for a Bacon model from a LiPD object |
