Function reference
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-packageOsteoBioR-packageOsteoBioR - The 'OsteoBioR' package.
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TemporalIso-classTemporalIso - S4 class for temporal estimation of isotopic values
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add_na_row() - Add NA Row
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adjustTimeColumn() - Adjust Time Column
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breakPointDetectionUI()breakPointDetectionServer() - Break Point Detection UI
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cleanAndSplitData() - Clean and Split Data
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cleanComb() - Clean the comb matrix
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combineDataAndModelOutputs() - Combine Data and Model Outputs
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compareWithHeuristic() - Compare models using heuristic
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compareWithLoo() - Compare models using loo
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compareWithWAIC() - Compare models using waic
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computeResult() - Function to compute resulting isotopic values out of historic ones
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config() - Config
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defaultInputsForUI() - Default Inputs for UI
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estimateIntervals() - Function to estimate temporal changes in isotopic values
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estimateTimePoint() - Function to estimate isotopic value for specific time point(s)
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export(<TemporalIso>) - Export of TemporalIso samples as csv
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exportCSV() - Export to csv
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exportFilename() - Filename of Export
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exportJSON() - Export to json
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exportXLSX() - Export to xlsx
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extendXAxis() - Extend X Axis
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extractIndividuals() - Extract Individuals
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extractModelOutputs() - Extract Model Outputs
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extractSavedModels() - Extract Saved Models
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getBreaks() - Get Breaks
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getCellChoices() - Get cell choices
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getComb() - Get the comb matrix
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getEntry() - Get Entry
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getExampleDataMatrix() - Get Example Matrix of Data
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getExampleIsotopeVals() - Get Example Matrix of Isotopic Values
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getHelp() - Get Text for Help Panel in Shiny App
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getLabel() - Get Label
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getPlotData() - Get Plot Data
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getSeed() - Get Seed
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getShiftTime() - Calculate time points of shifted isotopic values
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getSiteStayTimes() - Calculate estimated stay times for locations given isotopic values
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getTimeMax() - Get Time Maximum
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getTimeMin() - Get Time Minimum
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getUserDefinedEst() - Calculate estimates for user defined intervals
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getXAxisData() - Get X-Axis Data
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infoButtonUI()infoButtonServer() - Info Button UI
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joinTimeForDerivation() - Get Breaks for Derivation
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logDebug() - LogDebug
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logWarn() - LogWarn
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logging() - Logging
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matrixUI()matrixServer() - Matrix Module
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mcpCompareModelsUI()mcpCompareModelsServer() - MCP Compare Models UI
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mcpFormulasUI()mcpFormulasServer() - MCP Formulas UI
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mcpModelingUI()mcpModelingServer() - MCP Modeling UI
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mcpOutUI()mcpOutServer() - MCP Output UI
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mcpShowSingleModelUI()mcpShowSingleModelServer() - MCP Show Single Model UI
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messageNoModelsToPlot() - Message for no models to plot
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modelSpecificationsServer() - server funtion of modelSpecifications module
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modelSpecificationsUI() - ui function of modelSpecifications module
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pasteLabelForDerivation() - Paste Label for Derivation Plot
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plot(<TemporalIso>,<missing>) - Plots for TemporalIso objects
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plotTime() - Plot of credibility intervals for each time interval, plotted as timeseries
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readExampleMatrix() - Get Example Matrix
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removeModelOutputs() - Remove Model Outputs
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runMcp() - Run mcp model
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setFormulasAndPriors() - Set formulas and priors
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setVarsForUncMatrix() - Set Vars For Unc Matrix
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shinyModule - Server and UI Functions for Shiny Module
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splitComb() - Split the comb matrix into two matrices
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startApplication() - Start Application
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timePlotFormattingServer() - Server function of time plot formatting
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timePlotFormattingUI() - UI function of time plot formatting
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updateMatrixNamesInput() - Update only matrix row/colnames
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updateTime() - Extract Plot Data
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validateFormula() - Check formula syntax