Files in r4atlantis/atlantisom

Generates Data Sets From Atlantis Scenarios

.Rbuildignore

.gitattributes

.github/workflows/install.yml

.github/workflows/pkgdown.yml

.gitignore

DESCRIPTION

NAMESPACE

R/.Rhistory

R/SS_write_EWAA.R R/SS_write_biol.R R/SS_write_comps.R R/SS_write_ts.R R/aggregateData.R R/aggregateDensityData.R R/aggregate_comps.R R/calc_Z.R R/calc_age2length.R R/calc_avgwtstage2age.R R/calc_biomass_age.R R/calc_biomass_pool.R R/calc_omdimensions.R R/calc_pred_cons.R R/calc_pred_diet.R R/calc_stage2age.R R/calc_timestep2time.R R/create_fishery_subset.R R/create_survey.R R/create_survey_diet.R R/create_survey_env.R R/get_boundary.R R/load_agebioind.R R/load_bioind.R R/load_biolprm.R R/load_box.R R/load_boxarea.R R/load_bps.R R/load_catch.R R/load_detailed_diet_comp.R R/load_diet_comp.R R/load_fgs.R R/load_fisheries.R R/load_meta.R R/load_nc.R R/load_nc_annage.R R/load_nc_catchtons.R R/load_nc_physics.R R/load_runprm.R R/load_yoy.R R/om_comps.R R/om_consindex.R R/om_diet.R R/om_index.R R/om_init.R R/om_species.R R/read_savedfisheries.R R/read_savedsurvs.R R/read_xml_atlantis.R R/reformat_compositions.R R/run_stocksynthesis.R R/run_truth.R R/sample_ages.R R/sample_diet.R R/sample_fish.R R/sample_fishery_totcatch.R R/sample_survey_biomass.R R/sample_survey_consumption.R R/sample_survey_numbers.R R/write_SS_ctl.R R/write_SS_dat.R R/write_meta.R README.md

atlantisOM.Rproj

config/CC3Config.R config/CCConfig.R config/Map_Polygons_Surveys.R config/NEMOWConfig.R config/NEUSConfig.R config/NOBAConfig.R config/census_spec.R config/fisherycensus.R config/omdimensions.R config/sardine_config.R config/sardine_nemow.R config/sardine_survey.R config/usersurvey.R

inst/extdata/SETAS_Example/Biology.prm

inst/extdata/SETAS_Example/Fisheries.csv

inst/extdata/SETAS_Example/Functional_groups.csv

inst/extdata/SETAS_Example/Geography.bgm

inst/extdata/SETAS_Example/Initial_condition.nc

inst/extdata/SETAS_Example/Run_settings.xml

inst/extdata/SETAS_Example/log.txt

inst/extdata/SETAS_Example/outputs.nc

inst/extdata/SETAS_Example/outputsBiomIndx.txt

inst/extdata/SETAS_Example/outputsCATCH.nc

inst/extdata/SETAS_Example/outputsCatch.txt

inst/extdata/SETAS_Example/outputsCatchPerFishery.txt

inst/extdata/SETAS_Example/outputsDietCheck.txt

inst/extdata/SETAS_Example/outputsPROD.nc

inst/extdata/SETAS_Example/outputsYOY.txt

inst/extdata/SETAS_Example/outputsrun_truth.RData

inst/extdata/Sardine_SS_files/forecast.ss

inst/extdata/Sardine_SS_files/gradient.dat

inst/extdata/Sardine_SS_files/sardEM_3_3.ctl

inst/extdata/Sardine_SS_files/sardEM_3_3.dat

inst/extdata/Sardine_SS_files/ss.par

inst/extdata/Sardine_SS_files/starter.ss

man-roxygen/area.R man-roxygen/bboxes.R man-roxygen/biolprm.R man-roxygen/bps.R man-roxygen/comp_data.R man-roxygen/dat.R man-roxygen/dir.R man-roxygen/fgs.R man-roxygen/file_agebioind.R man-roxygen/file_bgm.R man-roxygen/file_bioind.R man-roxygen/file_biolprm.R man-roxygen/file_catch.R man-roxygen/file_fgs.R man-roxygen/file_fish.R man-roxygen/file_init.R man-roxygen/file_nc.R man-roxygen/file_out.R man-roxygen/file_runprm.R man-roxygen/file_yoy.R man-roxygen/meta.R man-roxygen/nums.R man-roxygen/pooln.R man-roxygen/resn.R man-roxygen/save.R man-roxygen/scenario.R man-roxygen/select_groups.R man-roxygen/structn.R man-roxygen/toutinc.R man-roxygen/type.R man-roxygen/verbose.R man-roxygen/vol.R man-roxygen/yoy.R man/SS_write_EWAA.Rd man/SS_write_biol.Rd man/SS_write_comps.Rd man/SS_write_ts.Rd man/aggregateData.Rd man/aggregateDensityData.Rd man/aggregate_comps.Rd man/calc_Z.Rd man/calc_age2length.Rd man/calc_avgwtstage2age.Rd man/calc_biomass_age.Rd man/calc_biomass_pool.Rd man/calc_pred_cons.Rd man/calc_pred_diet.Rd man/calc_stage2age.Rd man/calc_timestep2time.Rd man/create_fishery_subset.Rd man/create_survey.Rd man/create_survey_diet.Rd man/create_survey_env.Rd man/get_boundary.Rd man/load_agebioind.Rd man/load_bioind.Rd man/load_biolprm.Rd man/load_box.Rd man/load_boxarea.Rd man/load_bps.Rd man/load_catch.Rd man/load_detailed_diet_comp.Rd man/load_diet_comp.Rd man/load_fgs.Rd man/load_fisheries.Rd man/load_meta.Rd man/load_nc.Rd man/load_nc_annage.Rd man/load_nc_catchtons.Rd man/load_nc_physics.Rd man/load_runprm.Rd man/load_yoy.Rd man/om_comps.Rd man/om_consindex.Rd man/om_diet.Rd man/om_index.Rd man/om_init.Rd man/om_species.Rd man/read_savedfisheries.Rd man/read_savedsurvs.Rd man/reformat_compositions.Rd man/run_stocksynthesis.Rd man/run_truth.Rd man/sample_ages.Rd man/sample_diet.Rd man/sample_fish.Rd man/sample_fishery_totcatch.Rd man/sample_survey_biomass.Rd man/sample_survey_consumption.Rd man/sample_survey_numbers.Rd man/write_SS_ctl.Rd man/write_SS_dat.Rd man/write_meta.Rd

nemow_demo/CC_2063_OA_OFF_22/CCV3catchN_census_sard_hake.rds

nemow_demo/CC_2063_OA_OFF_22/CCV3catchage_census_sard_hake.rds

nemow_demo/CC_2063_OA_OFF_22/CCV3catchlengthwt_census_sard_hake.rds

nemow_demo/CC_2063_OA_OFF_22/CCV3lengthwt_census_sard_hake.rds

nemow_demo/CC_2063_OA_OFF_22/CCV3natage_census_sard_hake.rds

nemow_demo/CC_2063_OA_OFF_22/CCV3surveyBcensus.rds

nemow_demo/CC_2063_OA_OFF_22/CCV3surveyNcensus.rds

nemow_demo/CC_2063_OA_OFF_22/CalCurrentV3Groups.csv

nemow_demo/CC_2063_OA_OFF_22/CalCurrentV3_Biol.prm

nemow_demo/CC_2063_OA_OFF_22/CalCurrentV3_run.xml

nemow_demo/CC_2063_OA_OFF_22/CalCurrentV3_utm.bgm

nemow_demo/CC_2063_OA_OFF_22/Sardine_truth.RData

nemow_demo/CC_2063_OA_OFF_22/outputCCV3BiomIndx.txt

nemow_demo/CC_2063_OA_OFF_22/outputCCV3Catch.txt

outputCCV3run_truth.RData

pkgdown/_pkgdown.yml

vignettes/.gitignore

vignettes/AtlantisToStockAssessment.Rmd vignettes/atlantisom.Rmd

vignettes/cjfas.csl

vignettes/refs.bib

r4atlantis/atlantisom documentation built on Nov. 12, 2023, 2:59 a.m.