Creating age ensembles 


Highlevel age modelling functionsPrimary functions used to create and store age models into LiPD objects 

Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object 

Generate a Banded Age Model (BAM) and add it into a LiPD object 

Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object 

Generate an oxcal Age Model and add it into a LiPD object 

Generate an oxcal Age Model from Oxcal model code, then add it into a LiPD object 

Baconrelated functions 

Get the name of bacon core directory 

Load the ensemble, summary and distribution data from a Bacon simulation 

Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object 

Sample ensemble ages from Bacon 

Set the name of bacon core directory 

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

BChronrelated functions 

Generate a Bayesian Reconstruction Age Model (Bacon) and add it into a LiPD object 

OxCalrelated functions 

Create the oxcal model script 

Pull model parameters from OxCal Code 

Load oxcal output 

write oxcal expression for each date. 

Generate an oxcal Age Model and add it into a LiPD object 

BAMrelated functions 

Corrects a Banded Age Model (BAM) 

Generate a Banded Age Model (BAM) and add it into a LiPD object 

Simulate a Banded Age Model (BAM) 

Ensemble Analysis 

Primary ensemble analysis functionsPrimary functions used to run ensemble analysis in geoChronR 

Ensemble correlation 

Ensemble regression 

Calculate ensemble power spectra 

Perform principle components analysis (PCA) across an ensemble 

Correlationrelated functions 

Estimate AutoRegressive coefficient at 1timesetep 

Create a synthetic timeseries that emulates the characteristics of a variable 

Matrix correlation 

Estimate effective sample size accounting for autocorrelation 

Plot the results of an ensemble correlation 

Correlations and their significance according to AR(1) benchmarks 

Calculate correlation pvalue given sample size. 

False Discovery Testing of pvalues from multiple testing 

FDR Master 

FDR Basic 

Proportion of alternate hypotheses 

Storey estimator 

Regressionrelated functions 

Plot ensemble regression results 

Plot an ensemble of data as a scatterplot 

Plot an ensemble of trendlines 

Simple ordinary least squeares regression 

Ensemble regression 

Spectralanalyisrelated functions 

Create a synthetic timeseries that emulates the characteristics of a variable 

Calculate ensemble power spectra 

Create a synthetic timeseries that emulates the characteristics of a timeseries 

Annotate plot of spectra with given periodicities 

Plot spectrum with confidence limits 

Reverse axis in log10 scale 

PCArelated functions 

Create a synthetic timeseries that emulates the characteristics of a variable 

Create a synthetic timeseries that emulates the characteristics of a timeseries 

Perform principle components analysis (PCA) across an ensemble 

Map ensemble pca loadings and plot PC timeseries 

create a scree plot for PCA analysis 

Visualization 

Plotting functionsPrimary functions to visualize data in geoChronR 

Highlevel chron plotting 

Plot chron ensemble 

Compare chron ensemble with paleoData agemodel 

Plot the results of an ensemble correlation 

Plot an ensemble dataset as a histogram 

Plot or add a line to plot 

Plot probability distributions 

Map ensemble pca loadings and plot PC timeseries 

Plot the the pvalues of an ensemble correlation analysis in a rankpvalue plot 

Plot ensemble regression results 

Plot an ensemble of data as a scatterplot 

create a scree plot for PCA analysis 

Plot ensemble spectra output 

Plot spectrum with confidence limits 

Plot a summary figure 

TS overview plot 

Create a Time availability plot 

Plot an ensemble timeseries as a set of lines 

Plot an ensemble timeseries as ribbons of probabilities 

Plot a bunch of timeseries in a vertical stack 

Plot an ensemble of trendlines 

Mapping functions 

Make a base map 

Map a list of LiPD objects 

Map a TS object 

Plotting helper functions 

convert an AD age scale to BP 

convert a BP age scale to AD 

Label axes 

Two dimensional binning 

Define a plot theme for GeoChronR 

get a ggplot legend object 

Get ggplot x and y ranges 

Two dimensional kernel density estimation 

Melt distribution 

ModeSelektor 

Annotate plot of spectra with given periodicities 

Find quantiles across an ensemble 

Reverse axis in log10 scale 

Other functions 

BinningFunctions used to bin data into regular intervals 

Align and bin two timeseries into comparable bins 

Bin Data 

Two dimensional binning 

Bin ensemble data 

Bin every entry in a Timeseries object 

LiPD manipulationsFunctions useful for manupulating LiPD objects 

Create a measurementTable from concatenated ensembles 

Create a chron or paleo model including adding ensemble data 

Create a multimodel ensemble 

Create a summary table from an ensemble table 

Create a random TSid 

Estimate uncertainty estimates from high/low range 

Get the index of variable list 

Map an ageEnsemble variable from a chron model to a paleoMeasurement Table 

pull variable out of TS object 

Select a LiPD "variable list" 

Utility functionsFunctions useful for a variety of internal, and potentially external, applications 

askUser 

Concatenate two independent ensemble timeseries 

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

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

Create a data frame for chron measurement data 

Gaussianize 

Get the last set of parameters you used in createChronMeasInputDf() 

What OS is this? 

Makes a guess about the units of a time vector based on the values 

Load a remote RData file 

Pull one instance from an ensemble 

Convert var.names to strings 

Use the write function from rEDM depending on the version 