NOAA-EDAB/Rpath
R implementation of Ecopath with Ecosim

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R implementation of Ecopath with Ecosim

..Rcheck/00check.log
.Rbuildignore
.Renviron
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/secretScan.yml
.github/workflows/tests.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/Adjustments.R R/Auxiliary_functions.R R/Extract.R R/RcppExports.R R/Rpath_methods.R R/Rpath_pkg.R R/Rpath_support.R R/data.R R/ecopath.R R/ecopath_plot.R R/ecosense.R R/ecosim.R R/ecosim_multistep.R R/ecosim_plot.R R/old_stanza_code.R R/param.R R/write_functions.R README.md
Rpath.Rproj
_pkgdown.yml
data-raw/Ecosense_EBS_base.csv
data-raw/Ecosense_EBS_diet.csv
data-raw/Ecosense_EBS_pedigree.csv
data-raw/Ecosense_ECS_base.csv
data-raw/Ecosense_ECS_diet.csv
data-raw/Ecosense_ECS_pedigree.csv
data-raw/Ecosense_GOA_base.csv
data-raw/Ecosense_GOA_diet.csv
data-raw/Ecosense_GOA_pedigree.csv
data-raw/REcosystem.R data-raw/Rpath_unbalanced_data.R
data/AB.params.rda
data/Ecosense.EBS.rda
data/Ecosense.ECS.rda
data/Ecosense.GOA.rda
data/REco.params.rda
data/sense_vignette.RData
inst/extdata/Ecosense_EBS_base.csv
inst/extdata/Ecosense_EBS_diet.csv
inst/extdata/Ecosense_EBS_pedigree.csv
inst/extdata/Ecosense_ECS_base.csv
inst/extdata/Ecosense_ECS_diet.csv
inst/extdata/Ecosense_ECS_pedigree.csv
inst/extdata/Ecosense_GOA_base.csv
inst/extdata/Ecosense_GOA_diet.csv
inst/extdata/Ecosense_GOA_pedigree.csv
man/AB.params.Rd man/Ecosense.EBS.Rd man/Ecosense.ECS.Rd man/Ecosense.GOA.Rd man/MTI.Rd man/REco.params.Rd man/Rpath-package.Rd man/adjust.fishing.Rd man/adjust.forcing.Rd man/adjust.scenario.Rd man/check.rpath.params.Rd man/create.rpath.params.Rd man/extract.node.Rd man/frate.table.Rd man/get.rsim.fishing.Rd man/get.rsim.forcing.Rd man/get.rsim.params.Rd man/get.rsim.stanzas.Rd man/get.rsim.start_state.Rd man/read.rpath.params.Rd man/rpath.Rd man/rpath.groups.Rd man/rpath.stanzas.Rd man/rsim.deriv.Rd man/rsim.diet.Rd man/rsim.fishing.Rd man/rsim.forcing.Rd man/rsim.mort.Rd man/rsim.params.Rd man/rsim.plot.Rd man/rsim.run.Rd man/rsim.scenario.Rd man/rsim.sense.Rd man/rsim.sense.path.Rd man/rsim.stanzas.Rd man/rsim.state.Rd man/rsim.step.Rd man/set.rsim.scene.Rd man/stanzaplot.Rd man/webplot.Rd man/write.Rpath.Rd man/write.Rsim.Rd man/write.rpath.params.Rd
src/RcppExports.cpp
src/ecosim.cpp
src/ecosim.h
tests/testthat.R
tests/testthat/data/input/.gitignore
tests/testthat/data/input/REcosystem_Baseline_AB.csv
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedCat_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedCat_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedCat_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedCat_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedCat_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedCat_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedEff_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedEff_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedEff_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedEff_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedEff_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedEff_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedFRa_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedFRa_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedFRa_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedFRa_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedFRa_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedFRa_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedMig_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedMig_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedMig_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedMig_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedMig_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_AB_ForcedMig_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_AB_OutBiomass.rds
tests/testthat/data/input/REcosystem_Baseline_AB_OutCatch.rds
tests/testthat/data/input/REcosystem_Baseline_AB_OutGearCatch.rds
tests/testthat/data/input/REcosystem_Baseline_RK4.csv
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedCat_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedCat_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedCat_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedCat_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedCat_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedCat_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedEff_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedEff_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedEff_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedEff_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedEff_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedEff_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedFRa_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedFRa_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedFRa_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedFRa_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedFRa_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedFRa_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedMig_OutBiomass_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedMig_OutBiomass_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedMig_OutCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedMig_OutCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedMig_OutGearCatch_Jitter.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedMig_OutGearCatch_Stepped.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_OutBiomass.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_OutCatch.rds
tests/testthat/data/input/REcosystem_Baseline_RK4_OutGearCatch.rds
tests/testthat/data/input/REcosystem_Baseline_RpathObj_Summary.rds
tests/testthat/data/input/REcosystem_Baseline_RpathObj_TopLevel.rds
tests/testthat/data/input/REcosystem_Current_AB_ForcedBio_OutBiomass_Jitter.rds
tests/testthat/test-constants.R tests/testthat/test-rpath.R tests/testthat/test-utils-jitter.R tests/testthat/test-utils-plot.R tests/testthat/test-utils-stepify.R tests/testthat/test-utils.R
testthat
vignettes/ModelSetup.R vignettes/ModelSetup.Rmd vignettes/Rpath.Rmd vignettes/RunRpath.R vignettes/RunRpath.Rmd vignettes/RunRsim.R vignettes/RunRsim.Rmd vignettes/UnitTests.Rmd vignettes/ecosense.R vignettes/ecosense.Rmd
vignettes/ices-journal-of-marine-science.csl
vignettes/img/output_plot_example.png
vignettes/img/plot_01_no_difference.png
vignettes/img/plot_02_superimposed_with_difference.png
vignettes/img/plot_03_current-baseline.png
vignettes/references.bib
NOAA-EDAB/Rpath documentation built on June 5, 2024, 9:03 p.m.

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