Install MixSIAR from Github | Run wolves example | Set output options to return ggplot objects | Diagnostics | Summary statistics | Posterior density plots | Continuous effect
Package: MixSIAR 3.1.12
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.zip(r-4.7)MixSIAR_3.1.12.zip(r-4.6)MixSIAR_3.1.12.zip(r-4.5)
MixSIAR_3.1.12.tgz(r-4.6-any)MixSIAR_3.1.12.tgz(r-4.5-any)
MixSIAR_3.1.12.tar.gz(r-4.7-any)MixSIAR_3.1.12.tar.gz(r-4.6-any)
MixSIAR_3.1.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MixSIAR/json (API)
| # Install 'MixSIAR' in R: |
| install.packages('MixSIAR', repos = c('https://brianstock.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/brianstock/mixsiar/issues
Last updated from:037978f3de. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 150 | ||
| source / vignettes | OK | 209 | ||
| linux-release-x86_64 | OK | 215 | ||
| macos-release-arm64 | OK | 130 | ||
| macos-oldrel-arm64 | OK | 172 | ||
| windows-devel | OK | 105 | ||
| windows-release | OK | 108 | ||
| windows-oldrel | OK | 98 | ||
| wasm-release | OK | 170 |
Exports:calc_areacombine_sourcescompare_modelsload_discr_dataload_mix_dataload_source_dataoutput_diagnosticsoutput_JAGSoutput_pairsoutput_posteriorsoutput_statsoutput_xyplot_continuous_varplot_dataplot_data_one_isoplot_data_two_isoplot_intervalsplot_priorrun_modelsummary_statwrite_JAGS_model
Dependencies:abindbackportsbayesplotbootcheckmateclicodacpp11crayondistributionaldplyrfarverforcatsgenericsGGallyggmcmcggplot2ggridgesggstatsgluegtablehmsisobandlabelinglatticelifecycleloomagrittrMASSMatrixMatrixModelsmatrixStatsmcmcMCMCpacknumDerivpatchworkpillarpkgconfigplyrposteriorprettyunitsprogresspurrrquantregR2jagsR2WinBUGSR6RColorBrewerRcppreshapereshape2rjagsrlangS7scalesspSparseMsplancsstringistringrsurvivaltensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr
Modifying MixSIAR plots
Last update: 2020-10-20
Started: 2020-10-19
Ex 6: Cladocera
Cladocera Example | Load MixSIAR package | Load mixture data | Load source data | Load discrimination data | Plot data | Plot prior | Write JAGS model file | Run model | Analyze diagnostics and output
Last update: 2020-10-16
Started: 2016-03-11
Ex 1: Wolves
Wolves Example | Load MixSIAR package | Load mixture data | Load source data | Load discrimination data | Plot data | Calculate convex hull area | Plot prior | Write JAGS model file | Run model | Analyze diagnostics and output
Last update: 2020-10-16
Started: 2016-03-07
Ex 2: Geese
Geese Example | Load MixSIAR package | Load mixture data | Load source data | Load discrimination data | Plot data | Calculate convex hull area | Plot prior | Write JAGS model file | Run model | Analyze diagnostics and output
Last update: 2020-10-16
Started: 2016-03-11
Ex 3: Lake
Lake Example | Load MixSIAR package | Load mixture data | Load source data | Load discrimination data | Plot data | Calculate convex hull area | Plot prior | Write JAGS model file | Run model | Analyze diagnostics and output
Last update: 2020-10-16
Started: 2016-03-11
Ex 4: Killer Whale
Killer Whale Example | Load MixSIAR package | Load mixture data | Load source data | Load discrimination data | Plot data | Run the model with uninformative prior | Run the model with informative prior
Last update: 2020-10-16
Started: 2016-03-11
Ex 5: Isopod
Isopod Example | Load MixSIAR package | Load mixture data | Load source data | Load discrimination data | Plot data | Plot prior | Write JAGS model file | Run model | Analyze diagnostics and output
Last update: 2020-10-16
Started: 2016-03-11
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 |
| Output diagnostics | output_diagnostics |
| Process mixing model output from JAGS | output_JAGS |
| Output pairs plots | output_pairs |
| Output posterior density plots | output_posteriors |
| Output summary statistics | output_stats |
| Output XY/trace plots | output_xy |
| 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 |
