Package: tRophicPosition 0.8.1

Claudio Quezada-Romegialli

tRophicPosition: Bayesian Trophic Position Estimation with Stable Isotopes

Estimates the trophic position of a consumer relative to a baseline species. It implements a Bayesian approach which combines an interface to the 'JAGS' MCMC library of 'rjags' and stable isotopes. Users are encouraged to test the package and send bugs and/or errors to [email protected].

Authors:Claudio Quezada-Romegialli, Andrew L Jackson, Chris Harrod

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tRophicPosition.pdf |tRophicPosition.html✨
tRophicPosition/json (API)
NEWS

# Install 'tRophicPosition' in R:
install.packages('tRophicPosition', repos = c('https://benjaminhlina.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/benjaminhlina/trophicposition/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • Bilagay - Data frame containing stable isotope values of Bilagay.
  • Finnish_Lakes - Data frame of food webs in Inari and Kilpis Lakes
  • Orestias - Named list containing stable isotope values of Orestias chungarensis
  • Roach - Data frame of Roach in Lough Neagh
  • Trout - Named list containing stable isotope values of Oncorhynchus mykiss

On CRAN:

5.53 score 21 scripts 97 downloads 6 mentions 27 exports 51 dependencies

Last updated 28 days agofrom:53238ff589 (on Hlina-update-docs-seeds). Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 09 2024
R-4.5-winOKOct 09 2024
R-4.5-linuxOKOct 09 2024
R-4.4-winOKOct 09 2024
R-4.4-macOKOct 09 2024
R-4.3-winOKOct 09 2024
R-4.3-macOKOct 09 2024

Exports:compareTwoDistributionscredibilityIntervalsextractIsotopeDataextractPredictiveDatafromParallelTPgenerateTPDatagetPosteriorModejagsBayesianModeljagsOneBaselinejagsTwoBaselinesjagsTwoBaselinesFullloadIsotopeDatamultiModelTPmultiSpeciesTPpairwiseComparisonsparametricTPplotTPposteriorTPscreenFoodWebscreenIsotopeDatasimulateTDFsimulateTEFsummariseIsotopeDataTDFTEFTPmodeltrophicDensityPlot

Dependencies:apeashclicodacolorspacecorpcorcubaturedata.tabledigestfansifarverFNNggplot2gluegridExtragtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustMCMCglmmmgcvmulticoolmunsellmvtnormnlmepillarpkgconfigplyrpracmaR6RColorBrewerRcpprjagsrlangscalestensorAtibbleutf8vctrsviridisLitewithr

tRophicPosition: calculating trophic position for multiple species

Claudio Quezada-Romegialli, Andrew L Jackson & Chris Harrod

Rendered fromMultiple_species_calculation_of_trophic_position_in_R_1.Rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2024-09-11
Started: 2022-12-11

Short guide to the use of tRophicPosition

Claudio Quezada-Romegialli, Andrew L Jackson & Chris Harrod

Rendered fromShort_guide_to_tRophicPosition.Rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2024-07-16
Started: 2017-05-29

Using tRophicPosition to estimate TP through the use of multiple models

Claudio Quezada-Romegialli, Andrew L Jackson & Chris Harrod

Rendered fromMultiple_model_calculation_of_trophic_position_in_R.Rmdusingknitr::rmarkdownon Oct 09 2024.

Last update: 2024-07-16
Started: 2017-05-29

Readme and manuals

Help Manual

Help pageTopics
Data frame containing stable isotope values of Bilagay.Bilagay
Function to compare two distributions and test a hypothesis, in a Bayesian contextcompareTwoDistributions
Plot credibility intervals and central tendency descriptor from posterior distributions of trophic position and/or alpha parametercredibilityIntervals
Extract stable isotope data from a data frameextractIsotopeData
Function to extract raw data from posterior predictive model-checking distributionsextractPredictiveData
Data frame of food webs in Inari and Kilpis Lakes (Finland)Finnish_Lakes
Function to extract raw data from parallel calculations of trophic positionfromParallelTP
A function to generate random stable isotope data for trophic position calculationgenerateTPData
Function to get mode from a posterior distributiongetPosteriorMode
Returns a JAGS-based Bayesian model to use within tRophicPosition.jagsBayesianModel
Defines a jags Bayesian model to fit a single baseline trophic position modeljagsOneBaseline
Defines a jags Bayesian model to fit a two baselines trophic position model (without fractionation for C)jagsTwoBaselines
Defines a jags Bayesian model to fit a two baselines trophic position full model (with fractionation for C)jagsTwoBaselinesFull
Extract and load stable isotope data for selected consumers from a data frameloadIsotopeData
Multiple model calculation of trophic positionmultiModelTP
Multiple species calculation of trophic positionmultiSpeciesTP
Named list containing stable isotope values of Orestias chungarensisOrestias
Function to perform pairwise comparisons between two or more posterior distributionspairwiseComparisons
Parametric trophic positionparametricTP
Plot stable isotope data (2 elements) with one or two baselinesplot.isotopeData
Internal function that plot a mcmc.list object.plotMCMC
Function to plot a trophic position distributionplotTP
Function to generate posterior samples of a trophic position JAGS modelposteriorTP
Data frame of Roach in Lough NeaghRoach
Function that creates a biplot of a food web with stable isotope values (d13C and d15N)screenFoodWeb
Function to plot and screen stable isotope data with one or more baselines.screenIsotopeData
Simulate trophic discrimination factorssimulateTDF
Simulate trophic enrichment factorssimulateTEF
Function that summarises a data frame containing stable isotope values (d13C and d15N) grouping by Species and FG columnssummariseIsotopeData
Summary for stable isotope datasummary.isotopeData
Trophic discrimination factors from bibliographyTDF
Trophic enrichment factors from bibliographyTEF
Function to create a JAGS-based Bayesian model to calculate trophic positionTPmodel
Function to plot posterior samples of trophic position estimatestrophicDensityPlot
Named list containing stable isotope values of Oncorhynchus mykissTrout