Files in cbrown5/BenthicLatent
Bayesian latent variable model
.Rbuildignore
.gitignore
CITATION
DESCRIPTION
NAMESPACE
R/.Rapp.history
R/BenthicLatent.R
R/abundmod.R
R/abundmod_hyper.R
R/create_model_diagram.R
R/extract_params.R
R/fit_lvmod.R
R/fit_lvmod_ilr.R
R/hab_curve_plot.R
R/habitat_loadings_plot.R
R/list_to_df.R
R/mapabund.R
R/mapabund_hyper.R
R/plot_alpha_mnm.R
R/plot_beta_mnm.R
R/plot_effects.R
R/plot_latent_mnm.R
R/plot_latent_mnorm.R
data-raw/.Rapp.history
data-raw/1_data_prep_v2.R
data-raw/2_benthic_latent_mod_v3_multirun2.R
data-raw/2a_poissonmodel_matrix_latent_v3.txt
data-raw/2b_poissonmodel_matrix_latent_nofixed_v3.txt
data-raw/3_benthic_latent_mod_v3_multirun_view_results.R
data-raw/4_plot_results_best_model v2.R
data-raw/5_map-latent-variable.R
data-raw/8_benthic_latent_mod_method-comparison.R
data-raw/Appendix_S3_Benthic_Variables.csv
data-raw/BLM_numlv1_v3.RData
data-raw/BLM_numlv2_v3.RData
data-raw/BLM_numlv3_v3.RData
data-raw/BLM_numlv4_v3.RData
data-raw/BLM_numlv5_v3.RData
data-raw/BLM_numlv6_v3.RData
data-raw/BLM_numlv_2_cumdist_v3.RData
data-raw/BLM_numlv_2_ord_v3.RData
data-raw/BLM_numlv_2_ord_v3_boral.RData
data-raw/BenthicCoverSurveys.csv
data-raw/Benthic_Variables.csv
data-raw/GRID_sol_update/Solomon islands land uses.pdf
data-raw/GRID_sol_update/info/arc.dir
data-raw/GRID_sol_update/info/arc0000.dat
data-raw/GRID_sol_update/info/arc0000.nit
data-raw/GRID_sol_update/info/arc0001.dat
data-raw/GRID_sol_update/info/arc0001.nit
data-raw/GRID_sol_update/info/arc0002.dat
data-raw/GRID_sol_update/info/arc0002.nit
data-raw/GRID_sol_update/info/arc0002r.001
data-raw/GRID_sol_update/sol_update.aux
data-raw/GRID_sol_update/sol_update/dblbnd.adf
data-raw/GRID_sol_update/sol_update/hdr.adf
data-raw/GRID_sol_update/sol_update/metadata.xml
data-raw/GRID_sol_update/sol_update/prj.adf
data-raw/GRID_sol_update/sol_update/sta.adf
data-raw/GRID_sol_update/sol_update/vat.adf
data-raw/GRID_sol_update/sol_update/w001001.adf
data-raw/GRID_sol_update/sol_update/w001001x.adf
data-raw/JuvUVCSites_with_ReefTypes_16Jun2016.csv
data-raw/Kia reefs/Reef_Strata_Kia.dbf
data-raw/Kia reefs/Reef_Strata_Kia.prj
data-raw/Kia reefs/Reef_Strata_Kia.sbn
data-raw/Kia reefs/Reef_Strata_Kia.sbx
data-raw/Kia reefs/Reef_Strata_Kia.shp
data-raw/Kia reefs/Reef_Strata_Kia.shp.xml
data-raw/Kia reefs/Reef_Strata_Kia.shx
data-raw/Kia_Logging_Ponds/.Rapp.history
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.cpg
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.dbf
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.prj
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.sbn
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.sbx
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.shp
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.shp.xml
data-raw/Kia_Logging_Ponds/Kia_Logging_Ponds.shx
data-raw/LV mod estimtes of variance and bias.RData
data-raw/LandPoly.zip
data-raw/LandPoly/LandPoly.dbf
data-raw/LandPoly/LandPoly.prj
data-raw/LandPoly/LandPoly.shp
data-raw/LandPoly/LandPoly.shx
data-raw/Secchi_correlation.rda
data-raw/appendix-figures/algae-plots.jpeg
data-raw/appendix-figures/cca-habitats.jpeg
data-raw/appendix-figures/mds_habitats.jpeg
data-raw/area_reef_change.rda
data-raw/benthic_codes.csv
data-raw/benthic_latent_mod_v3_multirun_view_results.R
data-raw/distances_pondsrows_to_sitescols.csv
data-raw/north-arrow-2.png
data-raw/pregion/pregion.dbf
data-raw/pregion/pregion.prj
data-raw/pregion/pregion.shp
data-raw/pregion/pregion.shx
data-raw/results16sept2017.rda
data-raw/simulation-code-unused/2a_poissonmodel_matrix_latent_simtesting.txt
data-raw/simulation-code-unused/6_benthic_latent_mod_cross-validation.R
data-raw/simulation-code-unused/6_benthic_latent_mod_simulations.R
data-raw/simulation-code-unused/7_sims-graphs-cross-validation.R
data-raw/simulation-code-unused/7_sims-graphs.R
data-raw/waic.rda
man/BenthicLatent-package.Rd
ms/AppendixS5_model_evaluation.Rmd
ms/AppendixS6-comparison-to-vegan.Rmd
ms/Appendix_S1_BenthicCoverSurveys.csv
ms/Appendix_S2_Site_data.csv
ms/Appendix_S4_model_code.txt
ms/Baro logging.jpeg
ms/BenthicLatentLib.bib
ms/Brown_Hamilton_footprints-preprint.Rmd
ms/Brown_Hamilton_footprints-preprint.pdf
ms/Brown_Hamilton_inprep_footprint-of-pollution.pdf
ms/Brown_Hamilton_submitted.pdf
ms/benthic_latent_ms v5.Rmd
ms/conservation-biology.csl
ms/pollution_footprint_main_doc.Rmd
ms/pollution_footprint_tbls_figures.Rmd
ms/revision/Appendix_S1_Site_data.csv
ms/revision/Appendix_S2_BenthicCoverSurveys.csv
ms/revision/Appendix_S3_Benthic_Variables.csv
ms/revision/Appendix_S4_model_code.txt
ms/revision/Brown_Hamilton_resubmitted14Nov2017.pdf
ms/revision/Brown_Hamilton_submitted_fromCB.pdf
ms/revision/Fig1-revised.pdf
ms/revision/Fig2-revised.pdf
ms/revision/Fig3-revised.pdf
ms/revision/cross-validation.png
ms/revision/fig3.pdf
ms/revision/fig4.pdf
ms/revision/figure1.pdf
ms/revision/latentquantmap.png
ms/supplement.Rmd
ms/word-styles-reference-benthiclatent.Rmd
readme.md
