Files in brianstock/MixSIAR

Bayesian Mixing Models in R

.Rbuildignore

.gitignore

DESCRIPTION

Manual/alligator_comparison_table.png

Manual/alligator_eps_length.png

Manual/alligator_p_length.png

Manual/cladocera_diagnostic_plots.pdf

Manual/cladocera_diagnostics.txt

Manual/cladocera_diagnostics.txt~

Manual/cladocera_normal.RData

Manual/cladocera_normal_gelman.png

Manual/cladocera_normal_geweke.png

Manual/cladocera_posterior_density_diet_p_id 14.pdf Manual/cladocera_posterior_density_diet_p_id 7.pdf Manual/cladocera_prior_plot.pdf

Manual/cladocera_summary_statistics.txt

Manual/geese_isospace_plot_1_2.pdf Manual/geese_posterior_density_diet_p_Group 1.pdf

Manual/geese_short_diag.png

Manual/geese_short_diagnostics.txt

Manual/geese_short_diagnostics.txt~

Manual/geese_short_summary_statistics.txt

Manual/geese_sources.png

Manual/geese_test_diag.png

Manual/geese_test_diagnostics.txt

Manual/geese_test_diagnostics.txt~

Manual/geese_test_summary_statistics.txt

Manual/githubhome.png

Manual/githubissueex.png

Manual/githubissues.png

Manual/isopod_diagnostics.txt

Manual/isopod_diagnostics.txt~

Manual/isopod_normal.RData

Manual/isopod_normal_gelman.png

Manual/isopod_normal_geweke.png

Manual/isopod_posterior_density_diet_p_CP.pdf Manual/isopod_posterior_density_diet_p_global.pdf

Manual/isopod_summary_global.png

Manual/isopod_summary_statistics.txt

Manual/kw_inf_diagnostics.txt

Manual/kw_inf_posterior_density_diet_p_global.pdf

Manual/kw_inf_summary_statistics.txt

Manual/kw_isospace_plot_1_2.pdf Manual/kw_prior_plot.pdf

Manual/kw_summary.png

Manual/kw_uninf_diagnostics.txt

Manual/kw_uninf_posterior_density_diet_p_global.pdf

Manual/kw_uninf_summary_statistics.txt

Manual/kw_vlong.RData

Manual/lake_geweke.png

Manual/lake_isospace_plot_1_2.pdf

Manual/lake_normal.RData

Manual/lake_normal_diag.png

Manual/lake_normal_diagnostics.txt

Manual/lake_normal_diagnostics.txt~

Manual/lake_normal_summary_statistics.txt

Manual/lake_posterior_density_diet_max_Secchi.Mixed.pdf Manual/lake_posterior_density_diet_median_Secchi.Mixed.pdf Manual/lake_posterior_density_diet_min_Secchi.Mixed.pdf Manual/lake_posterior_density_diet_p_Secchi.Mixed.pdf

Manual/lake_sources1.png

Manual/lake_sources2.png

Manual/lake_sources3.png

Manual/mantis_CI_combined_coral.png

Manual/mantis_CI_combined_fac1.png

Manual/mantis_CI_combined_seagrass.png

Manual/mantis_CI_original_fac1.png

Manual/mantis_aggregated_prior.pdf Manual/mantis_isospace.pdf

Manual/mantis_normal.RData

Manual/mantis_prior_coral.pdf Manual/mantis_prior_seagrass.pdf Manual/mantis_prior_specialist.pdf Manual/mantis_prior_uninf.pdf

Manual/mantis_summary_combined.png

Manual/mantis_summary_original.png

Manual/mixsiar_error_datasets.bib

Manual/mixsiar_examples.bib

Manual/mixsiar_gui_shot.png

Manual/mixsiar_manual.bib

Manual/mixsiar_manual.lyx

Manual/mixsiar_manual.pdf Manual/mixsiar_manual_3.1.pdf Manual/mixsiar_manual_small.pdf

Manual/mixsiar_running.png

Manual/model_finished.png

Manual/model_finished2.png

Manual/palmyra_isospace_plot_1_2.pdf Manual/palmyra_posterior_density_diet_p_Blacktip shark.pdf Manual/palmyra_posterior_density_diet_p_Grey reef shark.pdf

Manual/palmyra_short.RData

Manual/palmyra_short_diagnostics.txt

Manual/palmyra_short_diagnostics.txt~

Manual/palmyra_short_gelman.png

Manual/palmyra_short_geweke.png

Manual/palmyra_short_summary.png

Manual/palmyra_short_summary_statistics.txt

Manual/processonly.png

Manual/regionpacksd.png

Manual/specifyprior.png

Manual/unconverged_posterior_density_diet_p_Group 5.pdf

Manual/wolf_model.png

Manual/wolves_consumer.png

Manual/wolves_isospace.pdf

Manual/wolves_normal.RData

Manual/wolves_normal_diag.png

Manual/wolves_normal_diagnostics.txt

Manual/wolves_normal_diagnostics.txt~

Manual/wolves_normal_geweke.png

Manual/wolves_normal_output.RData

Manual/wolves_pairs_plot.pdf Manual/wolves_posterior_density_SD.pdf Manual/wolves_posterior_density_diet_p_Pack 7.pdf Manual/wolves_posterior_density_diet_p_Region 1.pdf Manual/wolves_posterior_density_diet_p_global.pdf Manual/wolves_priors.pdf

Manual/wolves_sources.png

Manual/wolves_test_diag.png

Manual/wolves_test_diagnostics.txt

Manual/wolves_test_diagnostics.txt~

Manual/wolvesregion.png

MixSIAR.Rproj

NAMESPACE

NEWS.md R/calc_area.R R/combine_sources.R R/compare_models.R R/load_discr_data.R R/load_mix_data.R R/load_source_data.R R/mixsiar.R R/output_JAGS.R R/output_diagnostics.R R/output_pairs.R R/output_posteriors.R R/output_stats.R R/output_xy.R R/plot_continuous_var.R R/plot_data.R R/plot_data_one_iso.R R/plot_data_two_iso.R R/plot_intervals.R R/plot_prior.R R/run_model.R R/summary_stat.R R/write_JAGS_model.R README.md cran-comments.md

docs/404.html

docs/articles/cladocera_ex.html

docs/articles/geese_ex.html

docs/articles/index.html

docs/articles/isopod_ex.html

docs/articles/killerwhale_ex.html

docs/articles/lake_ex.html

docs/articles/modify_output.html

docs/articles/modify_output_files/figure-html/unnamed-chunk-16-1.png

docs/articles/modify_output_files/figure-html/unnamed-chunk-17-1.png

docs/articles/modify_output_files/figure-html/unnamed-chunk-19-1.png

docs/articles/modify_output_files/figure-html/unnamed-chunk-20-1.png

docs/articles/modify_output_files/figure-html/unnamed-chunk-21-1.png

docs/articles/modify_output_files/figure-html/unnamed-chunk-22-1.png

docs/articles/wolves_ex.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/extra.css

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/calc_area.html

docs/reference/combine_sources.html

docs/reference/compare_models.html

docs/reference/index.html

docs/reference/load_discr_data.html

docs/reference/load_mix_data.html

docs/reference/load_source_data.html

docs/reference/mixsiar_env.html

docs/reference/output_JAGS.html

docs/reference/output_diagnostics.html

docs/reference/output_pairs.html

docs/reference/output_posteriors.html

docs/reference/output_stats.html

docs/reference/output_xy.html

docs/reference/plot_continuous_var.html

docs/reference/plot_data.html

docs/reference/plot_data_one_iso.html

docs/reference/plot_data_two_iso.html

docs/reference/plot_intervals.html

docs/reference/plot_prior.html

docs/reference/run_model.html

docs/reference/summary_stat.html

docs/reference/write_JAGS_model.html

docs/sitemap.xml

inst/CITATION

inst/example_scripts/mixsiar_script_alligator.R inst/example_scripts/mixsiar_script_alligator_length_ind.R inst/example_scripts/mixsiar_script_cladocera.R inst/example_scripts/mixsiar_script_geese.R inst/example_scripts/mixsiar_script_isopod.R inst/example_scripts/mixsiar_script_killerwhale.R inst/example_scripts/mixsiar_script_lake.R inst/example_scripts/mixsiar_script_mantis.R inst/example_scripts/mixsiar_script_palmyra.R inst/example_scripts/mixsiar_script_snail.R inst/example_scripts/mixsiar_script_stormpetrel.R inst/example_scripts/mixsiar_script_wolves.R inst/example_scripts/mixsiar_script_wolves_normal.R inst/example_scripts/run_all_examples.R

inst/extdata/alligator_TEF.csv

inst/extdata/alligator_consumer.csv

inst/extdata/alligator_sources_simplemean.csv

inst/extdata/check.png

inst/extdata/cladocera_consumer.csv

inst/extdata/cladocera_discrimination.csv

inst/extdata/cladocera_sources.csv

inst/extdata/geese_consumer.csv

inst/extdata/geese_discrimination.csv

inst/extdata/geese_sources.csv

inst/extdata/isopod_consumer.csv

inst/extdata/isopod_discrimination.csv

inst/extdata/isopod_sources.csv

inst/extdata/killerwhale_consumer.csv

inst/extdata/killerwhale_discrimination.csv

inst/extdata/killerwhale_sources.csv

inst/extdata/lake_consumer.csv

inst/extdata/lake_discrimination.csv

inst/extdata/lake_sources.csv

inst/extdata/mantis_consumer.csv

inst/extdata/mantis_discrimination.csv

inst/extdata/mantis_source.csv

inst/extdata/palmyra_consumer.csv

inst/extdata/palmyra_discrimination.csv

inst/extdata/palmyra_sources.csv

inst/extdata/red_x.png

inst/extdata/snail_consumer.csv

inst/extdata/snail_discrimination.csv

inst/extdata/snail_sources.csv

inst/extdata/stormpetrel_consumer.csv

inst/extdata/stormpetrel_discrimination.csv

inst/extdata/stormpetrel_sources.csv

inst/extdata/wolves_consumer.csv

inst/extdata/wolves_discrimination.csv

inst/extdata/wolves_sources.csv

inst/mixsiar_manual_small.pdf man/calc_area.Rd man/combine_sources.Rd man/compare_models.Rd man/load_discr_data.Rd man/load_mix_data.Rd man/load_source_data.Rd man/mixsiar_env.Rd man/output_JAGS.Rd man/output_diagnostics.Rd man/output_pairs.Rd man/output_posteriors.Rd man/output_stats.Rd man/output_xy.Rd man/plot_continuous_var.Rd man/plot_data.Rd man/plot_data_one_iso.Rd man/plot_data_two_iso.Rd man/plot_intervals.Rd man/plot_prior.Rd man/run_model.Rd man/summary_stat.Rd man/write_JAGS_model.Rd

pkgdown/_pkgdown.yml

pkgdown/extra.css

tests/testthat.R tests/testthat/test_calc_area.R tests/testthat/test_ex1_wolves.R tests/testthat/test_ex2_geese.R tests/testthat/test_ex3_lake.R tests/testthat/test_ex4_palmyra.R tests/testthat/test_ex6_snail.R tests/testthat/test_ex7_stormpetrel.R tests/testthat/test_ex8_cladocera.R tests/testthat/test_ex9_isopod.R tests/testthat/test_load_discr_data.R tests/testthat/test_load_mix_data.R tests/testthat/test_load_source_data.R tests/testthat/test_run_model.R vignettes/cladocera_ex.Rmd vignettes/geese_ex.Rmd vignettes/isopod_ex.Rmd vignettes/killerwhale_ex.Rmd vignettes/lake_ex.Rmd vignettes/modify_output.Rmd vignettes/wolves_ex.Rmd

brianstock/MixSIAR documentation built on Oct. 23, 2020, 4:48 a.m.