Files in alketh/atlantistools
Process and Visualise Output from Atlantis Models
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yml
.github/workflows/secretScan.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/agg-data.R
R/calculate-biomass-spatial.R
R/calculate-consumed-biomass.R
R/calculate-spatial-overlap.R
R/catch.R
R/change-avail.R
R/change-prm-cohort.R
R/change-prm.R
R/check-df-names.R
R/check-growth.R
R/combine-ages.R
R/combine-groups.R
R/combine-runs.R
R/convert-bgm.R
R/convert-factor.R
R/convert-relative-initial.R
R/convert-time.R
R/data-preprocess.R
R/data.R
R/extract-prm.R
R/flip-layers.R
R/get-boundary.R
R/get-colpal.R
R/get-conv-mgnbiot.R
R/get-diet-fishbase.R
R/get-groups.R
R/get-growth-fishbase.R
R/get-ids-fishbase.R
R/get-maturity-fishbase.R
R/get-ref-biotoc.R
R/get-ref-fishbase.R
R/load-box.R
R/load-bps.R
R/load-dietcheck.R
R/load-dietmatrix.R
R/load-fgs.R
R/load-init-age.R
R/load-init.R
R/load-mort.R
R/load-nc-physics.R
R/load-nc.R
R/load-rec.R
R/load-spec-mort.R
R/load-spec-pred-mort.R
R/load-txt.R
R/pipe.R
R/plot-add-box.R
R/plot-add-polygon-overview.R
R/plot-add-range.R
R/plot-bar.R
R/plot-boxes.R
R/plot-consumed-biomass.R
R/plot-diet-bec-dev.R
R/plot-diet.R
R/plot-line.R
R/plot-rec.R
R/plot-spatial-box.R
R/plot-spatial-overlap.R
R/plot-spatial-ts.R
R/plot-species.R
R/preprocess-txt.R
R/prm-to-df.R
R/ref_to_bibkey.R
R/sc-init.R
R/scan-prm.R
R/scan-reference-fishbase.R
R/str-split-twice.R
R/theme-atlantis.R
R/utils-plot.R
R/utils.R
README.Rmd
README.md
atlantistools.Rproj
cran-comments.md
data-raw/data-create-reference-dfs.R
data-raw/data-fishbase.R
data-raw/data-reference.R
data-raw/data-vignette-model-preprocess.R
data-raw/shrink-output-trunk.R
data/fishbase_data.rda
data/preprocess.rda
data/ref_agemat.rda
data/ref_bio_cons.rda
data/ref_bio_sp.rda
data/ref_dietmatrix.rda
data/ref_dm.rda
data/ref_eat.rda
data/ref_grazing.rda
data/ref_growth.rda
data/ref_lit.rda
data/ref_n.rda
data/ref_nums.rda
data/ref_physics.rda
data/ref_resn.rda
data/ref_structn.rda
data/ref_vol.rda
data/ref_vol_dz.rda
inst/extdata/biotic-cancer-pagurus.html
inst/extdata/ref_bib.bib
inst/extdata/setas-model-new-becdev/README.txt
inst/extdata/setas-model-new-becdev/SETasFisheries.csv
inst/extdata/setas-model-new-becdev/SETasGroups.csv
inst/extdata/setas-model-new-becdev/VMPA_setas.bgm
inst/extdata/setas-model-new-becdev/VMPA_setas_biol_fishing_New.prm
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/VMPA_setas_run_fishing_F_New.prm
inst/extdata/setas-model-new-becdev/init_vmpa_setas_25032013.nc
inst/extdata/setas-model-new-becdev/outputSETAS.nc
inst/extdata/setas-model-new-becdev/outputSETASDietCheck.txt
inst/extdata/setas-model-new-becdev/outputSETASMort.txt
inst/extdata/setas-model-new-becdev/outputSETASPROD.nc
inst/extdata/setas-model-new-becdev/outputSETASSSB.txt
inst/extdata/setas-model-new-becdev/outputSETASSpecificMort.txt
inst/extdata/setas-model-new-becdev/outputSETASSpecificPredMort.txt
inst/extdata/setas-model-new-becdev/outputSETASYOY.txt
inst/extdata/setas-model-new-becdev/setas-bench.csv
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-trunk/INIT_VMPA_Jan2015.nc
inst/extdata/setas-model-new-trunk/README.txt
inst/extdata/setas-model-new-trunk/SETasFisheries.csv
inst/extdata/setas-model-new-trunk/SETasGroupsDem_NoCep.csv
inst/extdata/setas-model-new-trunk/VMPA_setas.bgm
inst/extdata/setas-model-new-trunk/VMPA_setas_biol_fishing_Trunk.prm
inst/extdata/setas-model-new-trunk/VMPA_setas_force_fish_Trunk.prm
inst/extdata/setas-model-new-trunk/VMPA_setas_physics.prm
inst/extdata/setas-model-new-trunk/VMPA_setas_run_fishing_F_Trunk.prm
inst/extdata/setas-model-new-trunk/outputSETAS.nc
inst/extdata/setas-model-new-trunk/outputSETASDietCheck.txt
inst/extdata/setas-model-new-trunk/outputSETASMort.txt
inst/extdata/setas-model-new-trunk/outputSETASPROD.nc
inst/extdata/setas-model-new-trunk/outputSETASSSB.txt
inst/extdata/setas-model-new-trunk/outputSETASSpecificMort.txt
inst/extdata/setas-model-new-trunk/outputSETASSpecificPredMort.txt
inst/extdata/setas-model-new-trunk/outputSETASYOY.txt
inst/extdata/setas-model-new-trunk/setas-bench.csv
inst/extdata/setas-model-new-trunk/setas-ssb-rec.csv
man/agg_data.Rd
man/calculate_biomass_spatial.Rd
man/calculate_consumed_biomass.Rd
man/calculate_spatial_overlap.Rd
man/change_avail.Rd
man/change_prm.Rd
man/change_prm_cohort.Rd
man/check_df_names.Rd
man/check_growth.Rd
man/combine_ages.Rd
man/combine_groups.Rd
man/combine_runs.Rd
man/convert_bgm.Rd
man/convert_factor.Rd
man/convert_relative_initial.Rd
man/convert_time.Rd
man/custom_grid.Rd
man/extract_prm.Rd
man/fishbase_data.Rd
man/flip_layers.Rd
man/get_boundary.Rd
man/get_colpal.Rd
man/get_conv_mgnbiot.Rd
man/get_diet_fishbase.Rd
man/get_groups.Rd
man/get_growth_fishbase.Rd
man/get_ids_fishbase.Rd
man/get_maturity_fishbase.Rd
man/get_ref_biotic.Rd
man/get_ref_fishbase.Rd
man/load_box.Rd
man/load_bps.Rd
man/load_dietcheck.Rd
man/load_dietmatrix.Rd
man/load_fgs.Rd
man/load_init.Rd
man/load_init_age.Rd
man/load_mort.Rd
man/load_nc.Rd
man/load_nc_physics.Rd
man/load_rec.Rd
man/load_spec_mort.Rd
man/load_spec_pred_mort.Rd
man/load_txt.Rd
man/pipe.Rd
man/plot_add_box.Rd
man/plot_add_polygon_overview.Rd
man/plot_add_range.Rd
man/plot_bar.Rd
man/plot_boxes.Rd
man/plot_consumed_biomass.Rd
man/plot_diet.Rd
man/plot_diet_bec_dev.Rd
man/plot_line.Rd
man/plot_rec.Rd
man/plot_spatial_box.Rd
man/plot_spatial_overlap.Rd
man/plot_spatial_ts.Rd
man/plot_species.Rd
man/preprocess.Rd
man/preprocess_txt.Rd
man/prm_to_df.Rd
man/ref_agemat.Rd
man/ref_bio_cons.Rd
man/ref_bio_sp.Rd
man/ref_dietmatrix.Rd
man/ref_dm.Rd
man/ref_eat.Rd
man/ref_grazing.Rd
man/ref_growth.Rd
man/ref_lit.Rd
man/ref_n.Rd
man/ref_nums.Rd
man/ref_physics.Rd
man/ref_resn.Rd
man/ref_structn.Rd
man/ref_to_bibkey.Rd
man/ref_vol.Rd
man/ref_vol_dz.Rd
man/sc_init.Rd
man/scan_prm.Rd
man/scan_reference_fishbase.Rd
man/str_split_twice.Rd
man/theme_atlantis.Rd
pkgdown/_pkgdown.yml
tests/figs/deps.txt
tests/figs/plots-visual/p01-plot-line-preprocess-biomass.svg
tests/figs/plots-visual/p02-plot-consumed-biomass-ref-bio-cons.svg
tests/figs/plots-visual/p06-plot-bar-preprocess-nums-age.svg
tests/figs/plots-visual/p07-plot-rec-preprocess-ssb-rec-ex-data.svg
tests/figs/plots-visual/p08-plot-spatial-overlap-sp-overlap-11.svg
tests/figs/plots-visual/p10-plot-sc-init-df-data1-mult-mum-mult-c.svg
tests/testthat.R
tests/testthat/helper-fontconfig.R
tests/testthat/test-agg-mean.R
tests/testthat/test-change-avail.R
tests/testthat/test-change-prm-cohort.R
tests/testthat/test-change-prm.R
tests/testthat/test-check-growth.R
tests/testthat/test-combine-groups.R
tests/testthat/test-combine-runs.R
tests/testthat/test-conv-mg-n-bio-t.R
tests/testthat/test-convert-factor.R
tests/testthat/test-convert-time.R
tests/testthat/test-diet-fishbase.R
tests/testthat/test-extract-prm.R
tests/testthat/test-flip-layers.R
tests/testthat/test-get-boundary.R
tests/testthat/test-get-ids-fishbase.R
tests/testthat/test-get-maturity-fishbase.R
tests/testthat/test-get-ref-biotic.R
tests/testthat/test-growth-fishbase.R
tests/testthat/test-load-dietcheck.R
tests/testthat/test-load-dietmatrix.R
tests/testthat/test-load-fgs.R
tests/testthat/test-load-init-age.R
tests/testthat/test-load-init.R
tests/testthat/test-load-nc.R
tests/testthat/test-load-rec.R
tests/testthat/test-load-spec-mort.R
tests/testthat/test-plot-spatial.R
tests/testthat/test-plots-visual.R
tests/testthat/test-preprocess-txt.R
tests/testthat/test-random.R
tests/testthat/test-ref-to-bibkey.R
tests/testthat/test-sc-init.R
tests/testthat/test-sc-overlap.R
tests/testthat/test-scan-reference-fishbase.R
tests/testthat/test-str-split-twice.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/Thumbs.db
vignettes/atlantistools.Rmd
vignettes/model-calibration-species.Rmd
vignettes/model-calibration.Rmd
vignettes/model-comparison.Rmd
vignettes/model-preprocess.Rmd
vignettes/package-demo.Rmd
