Files in seananderson/pbs-synopsis
Data Extraction and Plotting for DFO PBS Groundfish Stocks

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.github/CONDUCT.md .github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/R-CMD-check.yaml
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CONDUCT.md CONTRIBUTING.md
DESCRIPTION
NAMESPACE
R/ageing-precision.R R/bind-samples.R R/catches.R R/cpue-index-tweedie.R R/cpue-map.R R/data.R R/extra.R R/gfplot.R R/growth.R R/localities.R R/mat-freq-month.R R/maturity.R R/plot-ages.R R/plot-lengths.R R/plot_predictor_bubbles.R R/prediction-grid.R R/quantile-residuals.R R/samples.R R/split-by-maturity.R R/split-by-sex-maturity.R R/survey-index.R R/surveys-spatial.R
R/sysdata.rda
R/theme-pbs.R R/tidy-comps.R R/tidy-cpue-historical.R R/tidy-cpue-index.R R/utils-pipe.R R/utils.R R/weight-props.R README.Rmd README.md
codecov.yml
data-raw/areas-species.R data-raw/boxes.R data-raw/example-data.R data-raw/maturity_assignment.R data-raw/redstripe-samples.R data-raw/survey-boundaries.R data-raw/survey-domain.R
data/dogfish_grid.rda
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data/pbs_areas.rda
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docs/reference/assign_areas.html
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gfplot.Rproj
inst/2018-04-27-twg.md inst/Adapting-tidy_cpue_index-for-hl.Rmd inst/archive/index2.R inst/archive/index_hg.R inst/archive/inla.R inst/archive/layout.R inst/archive/map.R inst/archive/plan.md inst/archive/playground.R inst/archive/plot_glmmfields_survey.R inst/archive/plot_glmmfields_survey_inla.R inst/archive/survey-functions-inla.R inst/delta-cpue-tmb-glmm.R inst/dlmtool-dat.Rmd
inst/extdata/.gitignore
inst/extdata/HBLL-N-S/PHMA_N_GRID.cpg
inst/extdata/HBLL-N-S/PHMA_N_GRID.dbf
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inst/extdata/HBLL_inside_survey/HBLL_Inside_North.CPG
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inst/extdata/HBLL_inside_survey/HBLL_Inside_South.CPG
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inst/extdata/HBLL_inside_survey/HBLL_Inside_South.prj
inst/extdata/HBLL_inside_survey/HBLL_Inside_South.sbn
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inst/extdata/HBLL_inside_survey/HBLL_Inside_South.shp.xml
inst/extdata/HBLL_inside_survey/HBLL_Inside_South.shx
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.dbf
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inst/extdata/SARA_listings.xlsx
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inst/extdata/ageing_methods.csv
inst/extdata/maturity_assignment.csv
inst/extdata/maturity_codes.xlsx
inst/extdata/maturity_short_names.csv
inst/extdata/other-surveys.csv
inst/extdata/spp-of-interest.csv
inst/flatfish-cpue.Rmd
inst/function-web.graffle
inst/function-web.pdf inst/pcod-cpue-vignette.Rmd inst/pcod-vb.Rmd inst/pcod-vignette.Rmd inst/sensor.R inst/shortraker-data.Rmd inst/splitting-by-mat.Rmd
inst/sql/get-age-precision.sql
inst/sql/get-catch.sql
inst/sql/get-comm-samples.sql
inst/sql/get-cpue-historic.sql
inst/sql/get-cpue-index.sql
inst/sql/get-cpue-spatial-ll.sql
inst/sql/get-cpue-spatial.sql
inst/sql/get-hake-catch.sql
inst/sql/get-management.sql
inst/sql/get-other-surveys.sql
inst/sql/get-sensor-data-fe-ctd.sql
inst/sql/get-sensor-data-fe-trawl.sql
inst/sql/get-sensor-data-fe.sql
inst/sql/get-sensor-data-ll-ctd.sql
inst/sql/get-sensor-data-ll-td.sql
inst/sql/get-sensor-data-trawl.sql
inst/sql/get-survey-index.sql
inst/sql/get-survey-samples.sql
inst/stan/aging-error.stan
inst/stan/logistic.stan
inst/stan/vb-nopriors.stan
inst/stan/vb.stan
inst/stan/vb_aging_error_gamma.stan
inst/stan/vb_gamma.stan
inst/test-weighting/awatea-wpa439(cat)-tt(145)-major(34567).csv
inst/test-weighting/awatea-wpa439(den)-ssid(1)-major(567).csv
inst/test-weighting/get-comm-samples-rowan.sql
inst/test-weighting/test-weighting.Rmd
inst/tex/synopsis-draft-body.tex
inst/tex/synopsis-plots.tex
inst/tidy-cpue-index-hl.R
inst/tmb/delta_gamma_cpue.cpp
inst/tmb/delta_gamma_cpue_1re.cpp
inst/tmb/delta_gamma_cpue_2re.cpp
inst/tmb/delta_lognormal_cpue.cpp
inst/tmb/deltalognormal.cpp
inst/tmb/deltalognormal_1re.cpp
inst/tmb/deltalognormal_2re.cpp
inst/tmb/deltalognormal_re.cpp
inst/tmb/lw.R
inst/tmb/lw.cpp
inst/tmb/tweedie_cpue.cpp
inst/tmb/tweedie_cpue_1re.cpp
inst/tmb/tweedie_cpue_2re.cpp
inst/tmb/vb.R
inst/tmb/vb.cpp
man-roxygen/ageing-precision-examples.R man/assign_areas.Rd man/bind_samples.Rd man/dogfish_grid.Rd man/fit_cpue_index_glmmtmb.Rd man/fit_length_weight.Rd man/fit_vb.Rd man/gfplot.Rd man/hbll_grid.Rd man/hbll_inside_n_grid.Rd man/hbll_inside_s_grid.Rd man/hbll_n_grid.Rd man/hbll_s_grid.Rd man/maturity_assignment.Rd man/maturity_short_names.Rd man/pbs_areas.Rd man/pbs_species.Rd man/pipe.Rd man/plot_age_precision.Rd man/plot_ages.Rd man/plot_catch.Rd man/plot_cpue_spatial.Rd man/plot_growth.Rd man/plot_lengths.Rd man/plot_mat_ogive.Rd man/plot_maturity_months.Rd man/plot_predictor_bubbles.Rd man/plot_sample_avail.Rd man/plot_survey_index.Rd man/plot_survey_sets.Rd man/pop_samples.Rd man/pop_surv.Rd man/qres_tweedie.Rd man/split_catch_by_sex.Rd man/split_catch_maturity.Rd man/survey-spatial-modelling.Rd man/survey_boundaries.Rd man/synoptic_grid.Rd man/theme_pbs.Rd man/tidy_age_precision.Rd man/tidy_comps.Rd man/tidy_cpue_historical.Rd man/tidy_cpue_index.Rd man/tidy_sample_avail.Rd man/tidy_survey_sets.Rd man/weight_comps.Rd tests/testthat.R
tests/testthat/cpue-index.txt
tests/testthat/test-cpue-standardization.R
tests/testthat/test-get-data.R
tests/testthat/test-plots.R tests/testthat/test-tidy-survey-sets.R tests/testthat/test-utils.R
seananderson/pbs-synopsis documentation built on April 4, 2024, 1:36 p.m.