Files in atlantistools

Process and Visualise Output from Atlantis Models

NAMESPACE

MD5

DESCRIPTION

README.md vignettes/model-preprocess.Rmd vignettes/model-calibration.Rmd vignettes/model-calibration-species.Rmd vignettes/model-comparison.Rmd vignettes/package-demo.Rmd

vignettes/Thumbs.db

inst/extdata/setas-model-new-trunk/setas-bench.csv

inst/extdata/setas-model-new-trunk/outputSETASSpecificMort.txt

inst/extdata/setas-model-new-trunk/outputSETASSpecificPredMort.txt

inst/extdata/setas-model-new-trunk/INIT_VMPA_Jan2015.nc

inst/extdata/setas-model-new-trunk/VMPA_setas_physics.prm

inst/extdata/setas-model-new-trunk/outputSETAS.nc

inst/extdata/setas-model-new-trunk/README.txt

inst/extdata/setas-model-new-trunk/SETasFisheries.csv

inst/extdata/setas-model-new-trunk/outputSETASDietCheck.txt

inst/extdata/setas-model-new-trunk/outputSETASYOY.txt

inst/extdata/setas-model-new-trunk/outputSETASPROD.nc

inst/extdata/setas-model-new-trunk/SETasGroupsDem_NoCep.csv

inst/extdata/setas-model-new-trunk/VMPA_setas.bgm

inst/extdata/setas-model-new-trunk/setas-ssb-rec.csv

inst/extdata/setas-model-new-trunk/VMPA_setas_force_fish_Trunk.prm

inst/extdata/setas-model-new-trunk/outputSETASSSB.txt

inst/extdata/setas-model-new-trunk/VMPA_setas_biol_fishing_Trunk.prm

inst/extdata/setas-model-new-trunk/VMPA_setas_run_fishing_F_Trunk.prm

inst/extdata/setas-model-new-becdev/setas-bench.csv

inst/extdata/setas-model-new-becdev/README.txt

inst/extdata/setas-model-new-becdev/SETasGroups.csv

inst/extdata/setas-model-new-becdev/outputSETASSpecificPredMort.txt

inst/extdata/setas-model-new-becdev/SETasFisheries.csv

inst/extdata/setas-model-new-becdev/outputSETASPROD.nc

inst/extdata/setas-model-new-becdev/outputSETASYOY.txt

inst/extdata/setas-model-new-becdev/VMPA_setas_biol_fishing_New.prm

inst/extdata/setas-model-new-becdev/outputSETAS.nc

inst/extdata/setas-model-new-becdev/VMPA_setas_run_fishing_F_New.prm

inst/extdata/setas-model-new-becdev/outputSETASSSB.txt

inst/extdata/setas-model-new-becdev/VMPA_setas.bgm

inst/extdata/setas-model-new-becdev/VMPA_setas_force_fish.prm

inst/extdata/setas-model-new-becdev/VMPA_setas_physics.prm

inst/extdata/setas-model-new-becdev/setas-ssb-rec.csv

inst/extdata/setas-model-new-becdev/shrink-output-becdev.R

inst/extdata/setas-model-new-becdev/outputSETASSpecificMort.txt

inst/extdata/setas-model-new-becdev/outputSETASDietCheck.txt

inst/extdata/setas-model-new-becdev/init_vmpa_setas_25032013.nc

inst/doc/model-preprocess.Rmd inst/doc/model-calibration.R inst/doc/package-demo.Rmd inst/doc/model-comparison.R inst/doc/model-calibration.pdf

inst/doc/package-demo.html

inst/doc/model-comparison.pdf inst/doc/model-calibration-species.Rmd inst/doc/package-demo.R inst/doc/model-preprocess.R inst/doc/model-calibration-species.pdf inst/doc/model-calibration-species.R inst/doc/model-comparison.Rmd inst/doc/model-calibration.Rmd

inst/doc/model-preprocess.html

R/load-rec.R R/catch.R R/data.R R/convert-bgm.R R/combine-groups.R R/get-conv-mgnbiot.R R/calculate-consumed-biomass.R R/get-groups.R R/load-init.R R/load-nc-physics.R R/theme-atlantis.R R/load-nc.R R/get-ids-fishbase.R R/change-prm.R R/agg-data.R R/plot-bar.R R/utils-plot.R R/load-bps.R R/plot-rec.R R/load-dietcheck.R R/sc-init.R R/utils.R R/load-init-age.R R/ref_to_bibkey.R R/change-prm-cohort.R R/get-maturity-fishbase.R R/str-split-twice.R R/check-growth.R R/data-preprocess.R R/combine-runs.R R/load-box.R R/plot-line.R R/scan-reference-fishbase.R R/get-boundary.R R/plot-boxes.R R/plot-diet.R R/preprocess-txt.R R/prm-to-df.R R/check-df-names.R R/get-growth-fishbase.R R/pipe.R R/get-colpal.R R/load-spec-mort.R R/load-fgs.R R/get-ref-fishbase.R R/convert-time.R R/combine-ages.R R/plot-species.R R/plot-add-polygon-overview.R R/flip-layers.R R/load-dietmatrix.R R/calculate-biomass-spatial.R R/plot-spatial-ts.R R/convert-factor.R R/calculate-spatial-overlap.R R/get-diet-fishbase.R R/change-avail.R R/plot-add-box.R R/plot-diet-bec-dev.R R/scan-prm.R R/plot-consumed-biomass.R R/convert-relative-initial.R R/plot-spatial-overlap.R R/plot-add-range.R R/plot-spatial-box.R R/extract-prm.R R/load-txt.R

data/ref_dietmatrix.rda

data/ref_growth.rda

data/preprocess.rda

data/ref_dm.rda

data/ref_bio_cons.rda

data/ref_eat.rda

data/ref_bio_sp.rda

data/ref_resn.rda

data/ref_nums.rda

data/ref_n.rda

data/fishbase_data.rda

data/ref_vol.rda

data/ref_grazing.rda

data/ref_agemat.rda

data/ref_physics.rda

data/ref_vol_dz.rda

data/ref_structn.rda

tests/testthat.R tests/testthat/test-load-dietcheck.R tests/testthat/test-get-boundary.R tests/testthat/helper-fontconfig.R tests/testthat/test-load-dietmatrix.R tests/testthat/test-extract-prm.R tests/testthat/test-combine-runs.R tests/testthat/test-utils.R tests/testthat/test-sc-overlap.R tests/testthat/test-plot-spatial.R tests/testthat/test-convert-time.R tests/testthat/test-plot-species.R tests/testthat/test-load-rec.R tests/testthat/test-get-ids-fishbase.R tests/testthat/test-load-nc.R tests/testthat/test-flip-layers.R tests/testthat/test-change-avail.R tests/testthat/Rplots.pdf tests/testthat/test-agg-mean.R tests/testthat/test-growth-fishbase.R tests/testthat/test-sc-init.R tests/testthat/test-combine-groups.R tests/testthat/test-diet-fishbase.R tests/testthat/test-convert-factor.R tests/testthat/test-random.R tests/testthat/test-change-prm.R tests/testthat/test-conv-mg-n-bio-t.R tests/testthat/test-load-spec-mort.R tests/testthat/test-str-split-twice.R tests/testthat/test-change-prm-cohort.R tests/testthat/test-load-fgs.R tests/testthat/test-load-init-age.R tests/testthat/test-load-init.R tests/testthat/test-preprocess-txt.R tests/testthat/test-check-growth.R

tests/figs/deps.txt

tests/figs/plot-species/line-plot-preprocess-biomass.svg

build/vignette.rds

man/load_fgs.Rd man/ref_vol_dz.Rd man/change_prm.Rd man/convert_bgm.Rd man/load_nc_physics.Rd man/plot_consumed_biomass.Rd man/calculate_consumed_biomass.Rd man/combine_ages.Rd man/preprocess_txt.Rd man/plot_diet.Rd man/ref_physics.Rd man/sc_init.Rd man/plot_bar.Rd man/get_colpal.Rd man/fishbase_data.Rd man/load_txt.Rd man/plot_line.Rd man/check_df_names.Rd man/ref_dietmatrix.Rd man/plot_diet_bec_dev.Rd man/load_nc.Rd man/change_prm_cohort.Rd man/ref_bio_cons.Rd man/plot_add_box.Rd man/extract_prm.Rd man/flip_layers.Rd man/get_maturity_fishbase.Rd man/preprocess.Rd man/scan_reference_fishbase.Rd man/ref_resn.Rd man/calculate_biomass_spatial.Rd man/ref_to_bibkey.Rd man/ref_bio_sp.Rd man/pipe.Rd man/get_growth_fishbase.Rd man/plot_add_polygon_overview.Rd man/load_init.Rd man/get_groups.Rd man/load_box.Rd man/get_ids_fishbase.Rd man/get_conv_mgnbiot.Rd man/load_dietmatrix.Rd man/prm_to_df.Rd man/load_init_age.Rd man/check_growth.Rd man/calculate_spatial_overlap.Rd man/plot_add_range.Rd man/convert_time.Rd man/get_ref_fishbase.Rd man/load_spec_mort.Rd man/ref_eat.Rd man/ref_agemat.Rd man/load_rec.Rd man/ref_n.Rd man/load_bps.Rd man/combine_groups.Rd man/ref_nums.Rd man/convert_factor.Rd man/plot_spatial_ts.Rd man/ref_grazing.Rd man/plot_rec.Rd man/get_boundary.Rd man/plot_spatial_box.Rd man/change_avail.Rd man/agg_data.Rd man/scan_prm.Rd man/plot_species.Rd man/get_diet_fishbase.Rd man/ref_structn.Rd man/plot_boxes.Rd man/str_split_twice.Rd man/convert_relative_initial.Rd man/ref_dm.Rd man/plot_spatial_overlap.Rd man/ref_growth.Rd man/ref_vol.Rd man/theme_atlantis.Rd man/load_dietcheck.Rd man/combine_runs.Rd man/custom_grid.Rd

atlantistools documentation built on Aug. 16, 2017, 9:05 a.m.