Package: MixSIAR 3.1.12
Brian Stock
MixSIAR: Bayesian Mixing Models in R
Creates and runs Bayesian mixing models to analyze biological tracer data (i.e. stable isotopes, fatty acids), which estimate the proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR' is not one model, but a framework that allows a user to create a mixing model based on their data structure and research questions, via options for fixed/ random effects, source data types, priors, and error terms. 'MixSIAR' incorporates several years of advances since 'MixSIR' and 'SIAR'.
Authors:
MixSIAR_3.1.12.tar.gz
MixSIAR_3.1.12.tar.gz(r-4.5-noble)MixSIAR_3.1.12.tar.gz(r-4.4-noble)
MixSIAR_3.1.12.tgz(r-4.4-emscripten)MixSIAR_3.1.12.tgz(r-4.3-emscripten)
MixSIAR.pdf |MixSIAR.html✨
MixSIAR/json (API)
NEWS
| # Install 'MixSIAR' in R: |
| install.packages('MixSIAR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/brianstock/mixsiar/issues
Last updated 4 years agofrom:01ee546e42. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 02 2024 |
| R-4.5-linux | OK | Oct 02 2024 |
Exports:calc_areacombine_sourcescompare_modelsload_discr_dataload_mix_dataload_source_dataoutput_JAGSplot_continuous_varplot_dataplot_data_one_isoplot_data_two_isoplot_intervalsplot_priorrun_modelsummary_statwrite_JAGS_model
Dependencies:abindbackportsbayesplotbootcheckmateclicodacolorspacecpp11crayondistributionaldplyrfansifarverforcatsgenericsGGallyggmcmcggplot2ggridgesggstatsgluegtablehmsisobandlabelinglatticelifecycleloomagrittrMASSMatrixMatrixModelsmatrixStatsmcmcMCMCpackmgcvmunsellnlmenumDerivpatchworkpillarpkgconfigplyrposteriorprettyunitsprogresspurrrquantregR2jagsR2WinBUGSR6RColorBrewerRcppreshapereshape2rjagsrlangscalesspSparseMsplancsstringistringrsurvivaltensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr
Ex 1: Wolves
Rendered fromwolves_ex.Rmdusingknitr::rmarkdownon Oct 02 2024.Last update: 2020-10-20
Started: 2016-06-25
Ex 2: Geese
Rendered fromgeese_ex.Rmdusingknitr::rmarkdownon Oct 02 2024.Last update: 2020-10-20
Started: 2016-06-25
Ex 3: Lake
Rendered fromlake_ex.Rmdusingknitr::rmarkdownon Oct 02 2024.Last update: 2020-10-20
Started: 2016-06-25
Ex 4: Killer Whale
Rendered fromkillerwhale_ex.Rmdusingknitr::rmarkdownon Oct 02 2024.Last update: 2020-10-20
Started: 2016-06-25
Ex 5: Isopod
Rendered fromisopod_ex.Rmdusingknitr::rmarkdownon Oct 02 2024.Last update: 2020-10-20
Started: 2016-06-25
Ex 6: Cladocera
Rendered fromcladocera_ex.Rmdusingknitr::rmarkdownon Oct 02 2024.Last update: 2020-10-20
Started: 2016-06-25
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate the normalized surface area of the source convex hull | calc_area |
| Combine sources from a finished MixSIAR model (_a posteriori_) | combine_sources |
| Compare the predictive accuracy of 2 or more MixSIAR models | compare_models |
| Load trophic discrimination factor (TDF) data | load_discr_data |
| Load mixture data | load_mix_data |
| Load source data | load_source_data |
| mixsiar | mixsiar_env |
| Process mixing model output from JAGS | output_JAGS |
| Plot proportions by a continuous covariate | plot_continuous_var |
| Plot biotracer data | plot_data |
| Plot biotracer data (1-D) | plot_data_one_iso |
| Plot biotracer data (2-D) | plot_data_two_iso |
| Plot posterior uncertainty intervals from a MixSIAR model | plot_intervals |
| Plot prior | plot_prior |
| Run the JAGS model | run_model |
| Summary statistics from posterior of MixSIAR model | summary_stat |
| Write the JAGS model file | write_JAGS_model |
