# Bayesian Trophic Position Calculation with Stable Isotopes

## Documentation for package ‘tRophicPosition’ version 0.7.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

Bilagay | Data frame containing stable isotope values of Bilagay.
compareTwoDistributions | Function to compare two distributions and test a hypothesis, in a Bayesian context
credibilityIntervals | Plot credibility intervals and central tendency descriptor from posterior distributions of trophic position and/or alpha parameter
extractIsotopeData | Extract stable isotope data from a data frame
extractPredictiveData | Function to extract raw data from posterior predictive model-checking distributions
Finnish_Lakes | Data frame of food webs in Inari and Kilpis Lakes (Finland)
fromParallelTP | Function to extract raw data from parallel calculations of trophic position
generateTPData | A function to generate random stable isotope data for trophic position calculation
getPosteriorMode | Function to get mode from a posterior distribution
jagsBayesianModel | Returns a JAGS-based Bayesian model to use within tRophicPosition.
jagsOneBaseline | Defines a jags Bayesian model to fit a single baseline trophic position model
jagsTwoBaselines | Defines a jags Bayesian model to fit a two baselines trophic position model (without fractionation for C)
jagsTwoBaselinesFull | Defines a jags Bayesian model to fit a two baselines trophic position full model (with fractionation for C)
loadIsotopeData | Extract and load stable isotope data for selected consumers from a data frame
multiModelTP | Multiple model calculation of trophic position
multiSpeciesTP | Multiple species calculation of trophic position
Orestias | Named list containing stable isotope values of Orestias chungarensis
pairwiseComparisons | Function to perform pairwise comparisons between two or more posterior distributions
parametricTP | Parametric trophic position
plot.isotopeData | Plot stable isotope data (2 elements) with one or two baselines
plotMCMC | Internal function that plot a mcmc.list object.
plotTP | Function to plot a trophic position distribution
posteriorTP | Function to generate posterior samples of a trophic position JAGS model
Roach | Data frame of Roach in Lough Neagh
screenFoodWeb | Function that creates a biplot of a food web with stable isotope values (d13C and d15N)
screenIsotopeData | Function to plot and screen stable isotope data with one or more baselines.
simulateTDF | Simulate trophic discrimination factors
simulateTEF | Simulate trophic enrichment factors
summariseIsotopeData | Function that summarises a data frame containing stable isotope values (d13C and d15N) grouping by Species and FG columns
summary.isotopeData | Summary for stable isotope data
TDF | Trophic discrimination factors from bibliography
TEF | Trophic enrichment factors from bibliography
TPmodel | Function to create a JAGS-based Bayesian model to calculate trophic position
trophicDensityPlot | Function to plot posterior samples of trophic position estimates
Trout | Named list containing stable isotope values of Oncorhynchus mykiss