MixSIAR: Bayesian Mixing Models in R

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Creates and runs Bayesian mixing models to analyze biotracer 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', and includes both GUI (graphical user interface) and script versions.

Author
Brian Stock [cre, aut], Brice Semmens [aut], Eric Ward [ctb], Andrew Parnell [ctb], Andrew Jackson [ctb], Donald Phillips [ctb], Jon Moore [ctb], Stuart Bearhop [ctb], Richard Inger [ctb]
Date of publication
2016-08-23 20:00:15
Maintainer
Brian Stock <b1stock@ucsd.edu>
License
GPL-3
Version
3.1.7
URLs

View on CRAN

Man pages

build_mix_win
Build the window to read-in mixture data.
build_source_win
Build the window to read-in source data
calc_area
Calculate the normalized surface area of the source convex...
load_discr_data
Load trophic discrimination factor (TDF) data
load_mix_data
Load mixture data
load_source_data
Load source data
mixsiar
mixsiar
mixsiar_gui
Run the GUI version of MixSIAR
output_JAGS
Process mixing model output from JAGS
plot_continuous_var
Plot proportions by a continuous covariate
plot_data
Plot biotracer data
plot_data_one_iso
Plot biotracer data (1-D)
plot_data_two_iso
Plot biotracer data (2-D)
plot_prior
Plot prior
run_model
Run the JAGS model
write_JAGS_model
Write the JAGS model file

Files in this package

MixSIAR
MixSIAR/inst
MixSIAR/inst/CITATION
MixSIAR/inst/mixsiar_manual_3.1_small.pdf
MixSIAR/inst/example_scripts
MixSIAR/inst/example_scripts/mixsiar_script_stormpetrel.R
MixSIAR/inst/example_scripts/mixsiar_script_snail.R
MixSIAR/inst/example_scripts/mixsiar_script_geese.R
MixSIAR/inst/example_scripts/run_all_examples.R
MixSIAR/inst/example_scripts/mixsiar_script_palmyra.R
MixSIAR/inst/example_scripts/mixsiar_script_cladocera.R
MixSIAR/inst/example_scripts/mixsiar_script_lake.R
MixSIAR/inst/example_scripts/mixsiar_script_isopod.R
MixSIAR/inst/example_scripts/mixsiar_script_killerwhale.R
MixSIAR/inst/example_scripts/mixsiar_script_wolves.R
MixSIAR/inst/extdata
MixSIAR/inst/extdata/lake_consumer.csv
MixSIAR/inst/extdata/cladocera_sources.csv
MixSIAR/inst/extdata/isopod_sources.csv
MixSIAR/inst/extdata/cladocera_discrimination.csv
MixSIAR/inst/extdata/killerwhale_sources.csv
MixSIAR/inst/extdata/check.png
MixSIAR/inst/extdata/wolves_consumer.csv
MixSIAR/inst/extdata/wolves_sources.csv
MixSIAR/inst/extdata/palmyra_sources.csv
MixSIAR/inst/extdata/geese_consumer.csv
MixSIAR/inst/extdata/killerwhale_discrimination.csv
MixSIAR/inst/extdata/stormpetrel_sources.csv
MixSIAR/inst/extdata/isopod_discrimination.csv
MixSIAR/inst/extdata/snail_sources.csv
MixSIAR/inst/extdata/stormpetrel_consumer.csv
MixSIAR/inst/extdata/palmyra_discrimination.csv
MixSIAR/inst/extdata/stormpetrel_discrimination.csv
MixSIAR/inst/extdata/snail_discrimination.csv
MixSIAR/inst/extdata/isopod_consumer.csv
MixSIAR/inst/extdata/palmyra_consumer.csv
MixSIAR/inst/extdata/lake_discrimination.csv
MixSIAR/inst/extdata/cladocera_consumer.csv
MixSIAR/inst/extdata/red_x.png
MixSIAR/inst/extdata/snail_consumer.csv
MixSIAR/inst/extdata/lake_sources.csv
MixSIAR/inst/extdata/geese_sources.csv
MixSIAR/inst/extdata/killerwhale_consumer.csv
MixSIAR/inst/extdata/wolves_discrimination.csv
MixSIAR/inst/extdata/geese_discrimination.csv
MixSIAR/inst/doc
MixSIAR/inst/doc/wolves_ex.html
MixSIAR/inst/doc/wolves_ex.Rmd
MixSIAR/inst/doc/geese_ex.Rmd
MixSIAR/inst/doc/killerwhale_ex.R
MixSIAR/inst/doc/isopod_ex.Rmd
MixSIAR/inst/doc/lake_ex.Rmd
MixSIAR/inst/doc/killerwhale_ex.html
MixSIAR/inst/doc/lake_ex.html
MixSIAR/inst/doc/cladocera_ex.R
MixSIAR/inst/doc/cladocera_ex.Rmd
MixSIAR/inst/doc/cladocera_ex.html
MixSIAR/inst/doc/isopod_ex.R
MixSIAR/inst/doc/geese_ex.html
MixSIAR/inst/doc/isopod_ex.html
MixSIAR/inst/doc/lake_ex.R
MixSIAR/inst/doc/geese_ex.R
MixSIAR/inst/doc/wolves_ex.R
MixSIAR/inst/doc/killerwhale_ex.Rmd
MixSIAR/tests
MixSIAR/tests/testthat.R
MixSIAR/tests/testthat
MixSIAR/tests/testthat/test_run_model.R
MixSIAR/tests/testthat/test_load_source_data.R
MixSIAR/tests/testthat/test_calc_area.R
MixSIAR/tests/testthat/test_ex5_killerwhale.R
MixSIAR/tests/testthat/test_ex1_wolves.R
MixSIAR/tests/testthat/test_ex7_stormpetrel.R
MixSIAR/tests/testthat/test_ex3_lake.R
MixSIAR/tests/testthat/test_ex8_cladocera.R
MixSIAR/tests/testthat/test_ex2_geese.R
MixSIAR/tests/testthat/test_ex6_snail.R
MixSIAR/tests/testthat/test_ex4_palmyra.R
MixSIAR/tests/testthat/test_ex9_isopod.R
MixSIAR/tests/testthat/test_load_discr_data.R
MixSIAR/tests/testthat/test_load_mix_data.R
MixSIAR/NAMESPACE
MixSIAR/NEWS.md
MixSIAR/R
MixSIAR/R/plot_data_one_iso.R
MixSIAR/R/build_source_win.R
MixSIAR/R/create_mixsiar_envir.R
MixSIAR/R/calc_area.R
MixSIAR/R/plot_continuous_var.R
MixSIAR/R/load_mix_data.R
MixSIAR/R/run_model.R
MixSIAR/R/load_source_data.R
MixSIAR/R/plot_data_two_iso.R
MixSIAR/R/plot_prior.R
MixSIAR/R/load_discr_data.R
MixSIAR/R/build_mix_win.R
MixSIAR/R/mixsiar_gui.R
MixSIAR/R/plot_data.R
MixSIAR/R/output_JAGS.R
MixSIAR/R/write_JAGS_model.R
MixSIAR/vignettes
MixSIAR/vignettes/wolves_ex.Rmd
MixSIAR/vignettes/geese_ex.Rmd
MixSIAR/vignettes/isopod_ex.Rmd
MixSIAR/vignettes/lake_ex.Rmd
MixSIAR/vignettes/cladocera_ex.Rmd
MixSIAR/vignettes/killerwhale_ex.Rmd
MixSIAR/README.md
MixSIAR/MD5
MixSIAR/build
MixSIAR/build/vignette.rds
MixSIAR/DESCRIPTION
MixSIAR/man
MixSIAR/man/output_JAGS.Rd
MixSIAR/man/plot_prior.Rd
MixSIAR/man/load_source_data.Rd
MixSIAR/man/run_model.Rd
MixSIAR/man/plot_data_one_iso.Rd
MixSIAR/man/plot_continuous_var.Rd
MixSIAR/man/mixsiar.Rd
MixSIAR/man/plot_data.Rd
MixSIAR/man/write_JAGS_model.Rd
MixSIAR/man/build_source_win.Rd
MixSIAR/man/calc_area.Rd
MixSIAR/man/mixsiar_gui.Rd
MixSIAR/man/plot_data_two_iso.Rd
MixSIAR/man/load_mix_data.Rd
MixSIAR/man/build_mix_win.Rd
MixSIAR/man/load_discr_data.Rd