Files in mattjbayly/JoeModelCE
Joe Model for Cumulative Effects

.Rbuildignore

.github/.gitignore

.github/workflows/pkgdown.yaml

.gitignore

DESCRIPTION

JoeModelCE.Rproj

LICENSE

LICENSE.md

NAMESPACE

R/JoeModel_Run.R R/JoeModel_Run_Batch.R R/PopulationModel_Run.R R/Projection_DD.R R/StressorMagnitudeWorkbook.R R/StressorResponseWorkbook.R R/SystemCapacity.R R/Utility_CumulativeEffect.R R/Utility_JoeModel.R R/Utility_PopulationModel.R R/beta_param.R R/interaction_matrix_load.R R/interaction_matrix_sys_cap.R R/mean_Response.R R/pop_model_K_adj.R R/pop_model_bh_dd.R R/pop_model_ce_apply.R R/pop_model_matrix_elements.R R/pop_model_setup.R README.md

_pkgdown.yml

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/a01-joe-model.html

docs/articles/a01-joe-model_files/figure-html/dr_sample-1.png

docs/articles/a01-joe-model_files/figure-html/msc_plot-1.png

docs/articles/a01-joe-model_files/figure-html/tmsc_plot-1.png

docs/articles/a01-joe-model_files/kePrint-0.0.1/kePrint.js

docs/articles/a01-joe-model_files/lightable-0.0.1/lightable.css

docs/articles/a02-joe-model-batch-run.html

docs/articles/a02-joe-model-batch-run_files/figure-html/format_demo88-1.png

docs/articles/a02-joe-model-batch-run_files/figure-html/format_demo99-1.png

docs/articles/a03-population-model.html

docs/articles/a03-population-model_files/figure-html/m3-1.png

docs/articles/a03-population-model_files/figure-html/m3-2.png

docs/articles/a03-population-model_files/figure-html/m4b-1.png

docs/articles/a03-population-model_files/figure-html/m4b-2.png

docs/articles/a04-population-model-batch-run.html

docs/articles/a04-population-model-batch-run_files/figure-html/m3-1.png

docs/articles/a05-bc-cef.html

docs/articles/index.html

docs/authors.html

docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js

docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.1.3/bootstrap.min.css

docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/index.html

docs/link.svg

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/E_est.html

docs/reference/JoeModel_Run.html

docs/reference/JoeModel_Run_Batch.html

docs/reference/K_adj_old.html

docs/reference/Nb_est.html

docs/reference/PopulationModel_Run.html

docs/reference/Projection_DD.html

docs/reference/Rplot001.png

docs/reference/StressorMagnitudeWorkbook.html

docs/reference/StressorResponseWorkbook.html

docs/reference/SystemCapacity.html

docs/reference/beta_param.html

docs/reference/beta_stretch_val.html

docs/reference/bh_stage_f.html

docs/reference/ce.func.html

docs/reference/cor.AR1.html

docs/reference/cor.CompSym.html

docs/reference/d.vec.f.html

docs/reference/dd.N.bh.html

docs/reference/dd_calc.html

docs/reference/dd_stage.html

docs/reference/esub.html

docs/reference/f_rand.html

docs/reference/figures/JoeModelCE.png

docs/reference/figures/JoeModelCE_small.png

docs/reference/figures/scenarios_table.png

docs/reference/figures/shiny_app_cover.png

docs/reference/harm_k.html

docs/reference/index.html

docs/reference/init_pop.html

docs/reference/interaction_matrix_load.html

docs/reference/interaction_matrix_sys_cap.html

docs/reference/mean_Response.html

docs/reference/mn.sd.huc.html

docs/reference/pmx_eval.html

docs/reference/pop_model_K_adj.html

docs/reference/pop_model_ce_apply.html

docs/reference/pop_model_matrix_elements.html

docs/reference/pop_model_setup.html

docs/reference/proc.html

docs/reference/rbeta2.html

docs/reference/rtnorm_TruncatedDistributions.html

docs/reference/s0_optim.f.html

docs/reference/s_rand.html

docs/reference/stage_probs.html

docs/reference/tbeta_rnd.html

docs/search.json

docs/sitemap.xml

inst/extdata/habitat_dd_k.xlsx

inst/extdata/life_cycles.csv

inst/extdata/matrix_test/poly.cpg

inst/extdata/matrix_test/poly.dbf

inst/extdata/matrix_test/poly.prj

inst/extdata/matrix_test/poly.qmd

inst/extdata/matrix_test/poly.shp

inst/extdata/matrix_test/poly.shx

inst/extdata/matrix_test/stressor_magnitude_matrix.xlsx

inst/extdata/matrix_test/stressor_response_matrix.xlsx

inst/extdata/matrix_test/stressor_response_matrix_AB.xlsx

inst/extdata/matrix_test/~$stressor_magnitude_simple.xlsx

inst/extdata/matrix_test/~$stressor_response_simple.xlsx

inst/extdata/nicola/habitat_dd_k-nicola.xlsx

inst/extdata/nicola/life_cycles_chinook.csv

inst/extdata/nicola/nicola.gpkg

inst/extdata/nicola/stressor-magnitude-nicola.xlsx

inst/extdata/nicola/stressor-response-nicola.xlsx

inst/extdata/scenario_batch_joe.xlsx

inst/extdata/simple_test/nicola_test/stressor_magnitude.xlsx

inst/extdata/simple_test/nicola_test/stressor_response.xlsx

inst/extdata/simple_test/stressor_magnitude_simple.xlsx

inst/extdata/simple_test/stressor_response_simple.xlsx

inst/extdata/species_profiles/life_cycles_coho_Gibeau_Palen_2021.csv

inst/extdata/species_profiles/life_cycles_coho_nicola.csv

inst/extdata/species_profiles/life_cycles_no_stochasticity.csv

inst/extdata/species_profiles/life_cycles_sockeye_Spromberg_Meador_2006.csv

inst/extdata/species_profiles/life_cycles_socklow.csv

inst/extdata/species_profiles/life_cycles_steelhead_nicola.csv

inst/extdata/species_profiles/life_cycles_test_dd.csv

inst/extdata/species_profiles/life_cycles_test_dd2.csv

inst/extdata/stressor_magnitude_unc_ARTR.xlsx

inst/extdata/stressor_response_fixed_ARTR.xlsx

inst/figures/JoeModelCE.png

inst/figures/JoeModelCE_small.png

inst/figures/image12.png

inst/figures/shiny_app_cover.png

inst/misc/archive/Explore_Nicola_Coho.R inst/misc/archive/Explore_Nicola_Steelhead.R inst/misc/archive/Explore_Sockeye_Hatch.R inst/misc/archive/Joe_Model_Batch_Run.R inst/misc/archive/Projection_DD_Hatchery.R

inst/misc/archive/nicola/coho/coho_projection_matrix.csv

inst/misc/archive/nicola/coho/coho_symbolic_matrix.csv

inst/misc/archive/nicola/steelhead/steelhead_projection_matrix.csv

inst/misc/archive/nicola/steelhead/steelhead_symbolic_matrix.csv

man/E_est.Rd man/JoeModel_Run.Rd man/JoeModel_Run_Batch.Rd man/K_adj_old.Rd man/Nb_est.Rd man/PopulationModel_Run.Rd man/Projection_DD.Rd man/StressorMagnitudeWorkbook.Rd man/StressorResponseWorkbook.Rd man/SystemCapacity.Rd man/beta_param.Rd man/beta_stretch_val.Rd man/bh_stage_f.Rd man/ce.func.Rd man/cor.AR1.Rd man/cor.CompSym.Rd man/d.vec.f.Rd man/dd.N.bh.Rd man/dd_calc.Rd man/dd_stage.Rd man/esub.Rd man/f_rand.Rd

man/figures/JoeModelCE.png

man/figures/JoeModelCE_small.png

man/figures/scenarios_table.png

man/figures/shiny_app_cover.png

vignettes/.gitignore

vignettes/a01-joe-model.Rmd vignettes/a02-joe-model-batch-run.Rmd vignettes/a03-population-model.Rmd vignettes/a04-population-model-batch-run.Rmd vignettes/a05-bc-cef.Rmd

mattjbayly/JoeModelCE documentation built on Nov. 14, 2023, 5:34 p.m.

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mattjbayly/JoeModelCE
Joe Model for Cumulative Effects

Files in mattjbayly/JoeModelCE
Joe Model for Cumulative Effects

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mattjbayly/JoeModelCE Joe Model for Cumulative Effects

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mattjbayly/JoeModelCE
Joe Model for Cumulative Effects

Files in mattjbayly/JoeModelCE
Joe Model for Cumulative Effects