MixSIAR: Bayesian Mixing Models in R
Version 3.1.7

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.

AuthorBrian 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 publication2016-08-23 20:00:15
MaintainerBrian Stock <b1stock@ucsd.edu>
LicenseGPL-3
Version3.1.7
URL https://github.com/brianstock/MixSIAR
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MixSIAR")

Getting started

README.md
MixSIAR Script Example (Cladocera)
MixSIAR Script Example (Geese)
MixSIAR Script Example (Isopod)
MixSIAR Script Example (Killer Whale)
MixSIAR Script Example (Lake)
MixSIAR Script Example (Wolves)

Popular man pages

calc_area: Calculate the normalized surface area of the source convex...
load_discr_data: Load trophic discrimination factor (TDF) data
mixsiar: mixsiar
plot_continuous_var: Plot proportions by a continuous covariate
plot_data_two_iso: Plot biotracer data (2-D)
plot_prior: Plot prior
write_JAGS_model: Write the JAGS model file
See all...

All man pages Function index File listing

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

Functions

build_mix_win Man page Source code
build_source_win Man page Source code
calc_area Man page Source code
load_discr_data Man page Source code
load_mix_data Man page Source code
load_source_data Man page Source code
mixsiar Man page
mixsiar_gui Man page Source code
output_JAGS Man page Source code
plot_continuous_var Man page Source code
plot_data Man page Source code
plot_data_one_iso Man page Source code
plot_data_two_iso Man page Source code
plot_prior Man page Source code
run_model Man page Source code
write_JAGS_model Man page Source code

Files

inst
inst/CITATION
inst/mixsiar_manual_3.1_small.pdf
inst/example_scripts
inst/example_scripts/mixsiar_script_stormpetrel.R
inst/example_scripts/mixsiar_script_snail.R
inst/example_scripts/mixsiar_script_geese.R
inst/example_scripts/run_all_examples.R
inst/example_scripts/mixsiar_script_palmyra.R
inst/example_scripts/mixsiar_script_cladocera.R
inst/example_scripts/mixsiar_script_lake.R
inst/example_scripts/mixsiar_script_isopod.R
inst/example_scripts/mixsiar_script_killerwhale.R
inst/example_scripts/mixsiar_script_wolves.R
inst/extdata
inst/extdata/lake_consumer.csv
inst/extdata/cladocera_sources.csv
inst/extdata/isopod_sources.csv
inst/extdata/cladocera_discrimination.csv
inst/extdata/killerwhale_sources.csv
inst/extdata/check.png
inst/extdata/wolves_consumer.csv
inst/extdata/wolves_sources.csv
inst/extdata/palmyra_sources.csv
inst/extdata/geese_consumer.csv
inst/extdata/killerwhale_discrimination.csv
inst/extdata/stormpetrel_sources.csv
inst/extdata/isopod_discrimination.csv
inst/extdata/snail_sources.csv
inst/extdata/stormpetrel_consumer.csv
inst/extdata/palmyra_discrimination.csv
inst/extdata/stormpetrel_discrimination.csv
inst/extdata/snail_discrimination.csv
inst/extdata/isopod_consumer.csv
inst/extdata/palmyra_consumer.csv
inst/extdata/lake_discrimination.csv
inst/extdata/cladocera_consumer.csv
inst/extdata/red_x.png
inst/extdata/snail_consumer.csv
inst/extdata/lake_sources.csv
inst/extdata/geese_sources.csv
inst/extdata/killerwhale_consumer.csv
inst/extdata/wolves_discrimination.csv
inst/extdata/geese_discrimination.csv
inst/doc
inst/doc/wolves_ex.html
inst/doc/wolves_ex.Rmd
inst/doc/geese_ex.Rmd
inst/doc/killerwhale_ex.R
inst/doc/isopod_ex.Rmd
inst/doc/lake_ex.Rmd
inst/doc/killerwhale_ex.html
inst/doc/lake_ex.html
inst/doc/cladocera_ex.R
inst/doc/cladocera_ex.Rmd
inst/doc/cladocera_ex.html
inst/doc/isopod_ex.R
inst/doc/geese_ex.html
inst/doc/isopod_ex.html
inst/doc/lake_ex.R
inst/doc/geese_ex.R
inst/doc/wolves_ex.R
inst/doc/killerwhale_ex.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_run_model.R
tests/testthat/test_load_source_data.R
tests/testthat/test_calc_area.R
tests/testthat/test_ex5_killerwhale.R
tests/testthat/test_ex1_wolves.R
tests/testthat/test_ex7_stormpetrel.R
tests/testthat/test_ex3_lake.R
tests/testthat/test_ex8_cladocera.R
tests/testthat/test_ex2_geese.R
tests/testthat/test_ex6_snail.R
tests/testthat/test_ex4_palmyra.R
tests/testthat/test_ex9_isopod.R
tests/testthat/test_load_discr_data.R
tests/testthat/test_load_mix_data.R
NAMESPACE
NEWS.md
R
R/plot_data_one_iso.R
R/build_source_win.R
R/create_mixsiar_envir.R
R/calc_area.R
R/plot_continuous_var.R
R/load_mix_data.R
R/run_model.R
R/load_source_data.R
R/plot_data_two_iso.R
R/plot_prior.R
R/load_discr_data.R
R/build_mix_win.R
R/mixsiar_gui.R
R/plot_data.R
R/output_JAGS.R
R/write_JAGS_model.R
vignettes
vignettes/wolves_ex.Rmd
vignettes/geese_ex.Rmd
vignettes/isopod_ex.Rmd
vignettes/lake_ex.Rmd
vignettes/cladocera_ex.Rmd
vignettes/killerwhale_ex.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/output_JAGS.Rd
man/plot_prior.Rd
man/load_source_data.Rd
man/run_model.Rd
man/plot_data_one_iso.Rd
man/plot_continuous_var.Rd
man/mixsiar.Rd
man/plot_data.Rd
man/write_JAGS_model.Rd
man/build_source_win.Rd
man/calc_area.Rd
man/mixsiar_gui.Rd
man/plot_data_two_iso.Rd
man/load_mix_data.Rd
man/build_mix_win.Rd
man/load_discr_data.Rd
MixSIAR documentation built on May 19, 2017, 1:29 p.m.

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