Package: isotracer 1.1.8
Matthieu Bruneaux
isotracer: Isotopic Tracer Analysis Using MCMC
Implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.
Authors:
isotracer_1.1.8.tar.gz
isotracer_1.1.8.tar.gz(r-4.5-noble)isotracer_1.1.8.tar.gz(r-4.4-noble)
isotracer.pdf |isotracer.html✨
isotracer/json (API)
NEWS
| # Install 'isotracer' in R: |
| install.packages('isotracer', repos = 'https://cloud.r-project.org') |
Bug tracker:https://gitlab.com/matthieu-bruneaux/isotracer
- aquarium_mod - A simple aquarium network model, ready to run
- aquarium_run - An MCMC run from a simple aquarium network model
- eelgrass - Eelgrass phosphate incorporation data
- lalaja - Dataset for nitrogren fluxes in a Trinidadian mountain stream
- li2017 - Protein degradation in Arabidopsis plants
- li2017_counts - Protein degradation in Arabidopsis plants
- li2017_prots - Protein degradation in Arabidopsis plants
- trini_mod - Network model for nitrogen fluxes in Trinidadian streams
Last updated 26 days agofrom:5871e6324b. Checks:1 OK, 2 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 07 2025 |
| R-4.5-linux-x86_64 | NOTE | Mar 07 2025 |
| R-4.4-linux-x86_64 | NOTE | Mar 07 2025 |
Exports:%>%add_covariatesadd_pulse_eventas_tbl_graphas.mcmc.listavailable_priorscalculate_steady_statecompsconstant_pdelta2propdicexponential_pfilterfilter_by_groupgamma_pggflowsggtopogroupshcauchy_pmcmc_heatmapmissing_priorsnew_networkModelnormal_pparamsposterior_predictpriorsprojectprop_familyprop2deltaquick_sankeyrun_mcmcsample_fromsample_from_priorsample_paramssankeyscaled_beta_pselectset_half_lifeset_initset_obsset_paramsset_priorset_priorsset_prop_familyset_size_familyset_splitset_steadyset_toposize_familystanfit_to_named_mcmclisttidy_datatidy_dpptidy_flowstidy_mcmctidy_posterior_predicttidy_steady_statestidy_trajectoriestopotraceplotuniform_pvarnames
Dependencies:abindbackportsBHcallrcheckmateclicodacolorspacecpp11data.tabledescdistributionaldplyrfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatex2explatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr
Calculating derived parameters
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Case study: Trinidadian streams (Collins et al. 2016)
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Defining pulse or drip events
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Handling replication
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How to simulate experiments
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Including fixed effects of covariates
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MCMC output format
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Post-run diagnostics and analyses
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Posterior predictive checks
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Prior predictive checks
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Quick start
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Setting steady-state compartments
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Testing parameter identifiability
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Units and priors
Rendered fromtutorial-060-units-priors.Rmdusingknitr::rmarkdownon Mar 07 2025.Last update: 2025-03-07
Started: 2021-09-27
Citation
To cite 'isotracer' in publications, you can use the references below (the first one is the original methodological paper, the second one is the paper introducing the package implementation):
López-Sepulcre A, Bruneaux M, Collins SM, El-Sabaawi R, Flecker AS, Thomas SA (2020). “A new method to reconstruct quantitative food webs and nutrient flows from isotope tracer addition experiments.” The American Naturalist, 195(6), 964–985. doi:10.1086/708546.
Bruneaux M, López-Sepulcre A (2022). “isotracer: An R package for the analysis of tracer addition experiments.” Methods in Ecology and Evolution, 13(5), 1119–1134. doi:10.1111/2041-210X.13822.
Corresponding BibTeX entries:
@Article{,
title = {A new method to reconstruct quantitative food webs and
nutrient flows from isotope tracer addition experiments},
volume = {195},
doi = {10.1086/708546},
number = {6},
journal = {The American Naturalist},
author = {Andrés López-Sepulcre and Matthieu Bruneaux and Sarah M.
Collins and Rana El-Sabaawi and Alexander S. Flecker and Steven
A. Thomas},
year = {2020},
pages = {964--985},
}
@Article{,
title = {isotracer: An R package for the analysis of tracer
addition experiments},
volume = {13},
doi = {10.1111/2041-210X.13822},
number = {5},
journal = {Methods in Ecology and Evolution},
author = {Matthieu Bruneaux and Andrés López-Sepulcre},
year = {2022},
pages = {1119--1134},
}
Readme and manuals
isotracer: an R package for the analysis of tracer addition experiments
Isotope tracer addition experiments are used to answer a wide variety of biological, ecological and evolutionary questions. In these experiments, a labeled element is injected into a biological system and its fate is traced throughout the system to estimate the flux of matter across compartments. Tracer additions can be used across all levels of biological organization from cells and tissues, to organisms and ecosystems. The isotracer package provides tools to analyze data from such experiments.
Getting started
The recommended way to install the package is to get the latest version from CRAN:
install.packages("isotracer")
The documentation for the latest stable version is available online. Start with the Quick Start tutorial!
If you are feeling adventurous, you might want to install the latest development version from GitLab. It might have new features that the stable version on CRAN doesn’t have yet, but it might also be less stable:
devtools::install_gitlab("matthieu-bruneaux/isotracer")
How to cite the package
Running citation("isotracer") will return two references you can use
if you want to cite isotracer.
The first reference is the paper describing the original method:
- López-Sepulcre A, Bruneaux M, Collins SM, El-Sabaawi R, Flecker AS, Thomas SA (2020). “A new method to reconstruct quantitative food webs and nutrient flows from isotope tracer addition experiments.” The American Naturalist, 195(6), 964-985. doi: 10.1086/708546 (URL: https://doi.org/10.1086/708546).
The second reference is the paper introducing isotracer itself:
- Bruneaux M, López-Sepulcre A (2022). “isotracer: An R package for the analysis of tracer addition experiments.” Methods in Ecology and Evolution, 13(5), 1119-1134. doi: 10.1111/2041-210X.13822 (URL: https://doi.org/10.1111/2041-210X.13822).
