Package: isotracer 1.1.7
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:
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isotracer.pdf |isotracer.html✨
isotracer/json (API)
NEWS
# Install 'isotracer' in R: |
install.packages('isotracer', repos = c('https://matthieu-bruneaux.r-universe.dev', '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 19 days agofrom:3101d112c1. Checks:OK: 1 WARNING: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 05 2024 |
R-4.5-win-x86_64 | WARNING | Nov 05 2024 |
R-4.5-linux-x86_64 | WARNING | Nov 05 2024 |
R-4.4-win-x86_64 | WARNING | Nov 05 2024 |
R-4.4-mac-x86_64 | WARNING | Nov 05 2024 |
R-4.4-mac-aarch64 | WARNING | Nov 05 2024 |
R-4.3-win-x86_64 | WARNING | Nov 05 2024 |
R-4.3-mac-x86_64 | WARNING | Nov 05 2024 |
R-4.3-mac-aarch64 | WARNING | Nov 05 2024 |
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
Rendered fromtutorial-110-derived-parameters.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Case study: Trinidadian streams (Collins et al. 2016)
Rendered fromcase-study-collins-2016.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-03-14
Defining pulse or drip events
Rendered fromtutorial-040-pulse-drip-events.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2019-12-12
Handling replication
Rendered fromtutorial-020-replication.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2019-12-12
How to simulate experiments
Rendered fromtutorial-120-howto-simulations.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Including fixed effects of covariates
Rendered fromtutorial-050-fixed-effects.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-03-14
MCMC output format
Rendered fromtutorial-080-mcmc-output-format.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Post-run diagnostics and analyses
Rendered fromtutorial-090-post-run-analyses.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Posterior predictive checks
Rendered fromtutorial-100-posterior-predictive-checks.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Prior predictive checks
Rendered fromtutorial-070-prior-predictive-checks.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Quick start
Rendered fromtutorial-010-quick-start.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2018-06-21
Setting steady-state compartments
Rendered fromtutorial-030-steady-state-comps.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2019-12-12
Testing parameter identifiability
Rendered fromtutorial-130-parameter-identifiability.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-21
Units and priors
Rendered fromtutorial-060-units-priors.Rmd
usingknitr::rmarkdown
on Nov 05 2024.Last update: 2024-11-05
Started: 2020-05-07