Files in pbs-assess/gfplot
Data Extraction and Plotting for DFO PBS Groundfish Stocks

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
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/fit-inla.R R/get-dat.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/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 data-raw/areas-species.R data-raw/boxes.R data-raw/example-data.R data-raw/redstripe-samples.R data-raw/survey-boundaries.R data-raw/survey-domain.R
data/hbll_grid.rda
data/hbll_n_grid.rda
data/hbll_s_grid.rda
data/pbs_areas.rda
data/pbs_species.rda
data/pop_samples.rda
data/pop_surv.rda
data/survey_boundaries.rda
docs/CONDUCT.html
docs/CONTRIBUTING.html
docs/articles/commercial-cpue-index.html
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/assign_areas.html
docs/reference/bind_samples.html
docs/reference/boot_iphc.html
docs/reference/calc_iphc_full_res.html
docs/reference/calc_iphc_ser_AB.html
docs/reference/calc_iphc_ser_all.html
docs/reference/compare_iphc_ser_A_D.html
docs/reference/compare_iphc_ser_B_C.html
docs/reference/countData1995.html
docs/reference/countData1995rs.html
docs/reference/countData2013.html
docs/reference/cpue-index-1.png
docs/reference/cpue-index-2.png
docs/reference/cpue-index.html
docs/reference/cpue-tweedie-1.png
docs/reference/cpue-tweedie-2.png
docs/reference/cpue-tweedie-3.png
docs/reference/cpue-tweedie.html
docs/reference/data1996to2002.html
docs/reference/f.html
docs/reference/fit_cpue_index_glmmtmb.html
docs/reference/fit_inla.html
docs/reference/fit_length_weight.html
docs/reference/fit_vb-1.png
docs/reference/fit_vb-2.png
docs/reference/fit_vb-3.png
docs/reference/fit_vb-4.png
docs/reference/fit_vb.html
docs/reference/format_iphc_longest.html
docs/reference/get.html
docs/reference/get_all_iphc_set_counts.html
docs/reference/get_cpue_historical.html
docs/reference/get_data.html
docs/reference/get_early_iphc.html
docs/reference/gfplot.html
docs/reference/hbll_grid.html
docs/reference/hbll_n_grid.html
docs/reference/hbll_s_grid.html
docs/reference/index.html
docs/reference/inject_filter.html
docs/reference/iphc-spp-names.csv.html
docs/reference/iphc_get_calc_plot.html
docs/reference/pbs2dlmtool_data.html
docs/reference/pbs_areas.html
docs/reference/pbs_species.html
docs/reference/pipe.html
docs/reference/plot_age_precision.html
docs/reference/plot_ages.html
docs/reference/plot_catch.html
docs/reference/plot_cpue_spatial-1.png
docs/reference/plot_cpue_spatial.html
docs/reference/plot_growth-1.png
docs/reference/plot_growth-2.png
docs/reference/plot_growth.html
docs/reference/plot_iphc_index.html
docs/reference/plot_lengths.html
docs/reference/plot_mat_ogive-1.png
docs/reference/plot_mat_ogive-2.png
docs/reference/plot_mat_ogive.html
docs/reference/plot_maturity_months-1.png
docs/reference/plot_maturity_months.html
docs/reference/plot_predictor_bubbles-1.png
docs/reference/plot_predictor_bubbles.html
docs/reference/plot_sample_avail-1.png
docs/reference/plot_sample_avail.html
docs/reference/plot_survey_index.html
docs/reference/plot_survey_sets-1.png
docs/reference/plot_survey_sets-2.png
docs/reference/plot_survey_sets-3.png
docs/reference/plot_survey_sets.html
docs/reference/pop_samples.html
docs/reference/pop_surv.html
docs/reference/predict_inla.html
docs/reference/qres_tweedie-1.png
docs/reference/qres_tweedie-2.png
docs/reference/qres_tweedie.html
docs/reference/run_sql.html
docs/reference/sample_trip_ids.html
docs/reference/setData1995.html
docs/reference/setData1995rs.html
docs/reference/setData2013.html
docs/reference/sim_cpue.html
docs/reference/sql_server_accessible.html
docs/reference/strata_areas.html
docs/reference/survey-spatial-modelling-1.png
docs/reference/survey-spatial-modelling.html
docs/reference/survey_boundaries.html
docs/reference/theme_pbs-1.png
docs/reference/theme_pbs.html
docs/reference/tidy_age_precision.html
docs/reference/tidy_comps.html
docs/reference/tidy_cpue_historic.html
docs/reference/tidy_cpue_historical.html
docs/reference/tidy_cpue_index.html
docs/reference/tidy_iphc_survey.html
docs/reference/tidy_sample_avail.html
docs/reference/tidy_survey_sets.html
docs/reference/weight_comps.html
gfplot.Rproj
inst/2018-04-27-twg.md 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/HBLL-N-S/PHMA_N_GRID.cpg
inst/extdata/HBLL-N-S/PHMA_N_GRID.dbf
inst/extdata/HBLL-N-S/PHMA_N_GRID.prj
inst/extdata/HBLL-N-S/PHMA_N_GRID.sbn
inst/extdata/HBLL-N-S/PHMA_N_GRID.sbx
inst/extdata/HBLL-N-S/PHMA_N_GRID.shp
inst/extdata/HBLL-N-S/PHMA_N_GRID.shp.xml
inst/extdata/HBLL-N-S/PHMA_N_GRID.shx
inst/extdata/HBLL-N-S/PHMA_S_GRID.cpg
inst/extdata/HBLL-N-S/PHMA_S_GRID.dbf
inst/extdata/HBLL-N-S/PHMA_S_GRID.prj
inst/extdata/HBLL-N-S/PHMA_S_GRID.sbn
inst/extdata/HBLL-N-S/PHMA_S_GRID.sbx
inst/extdata/HBLL-N-S/PHMA_S_GRID.shp
inst/extdata/HBLL-N-S/PHMA_S_GRID.shp.xml
inst/extdata/HBLL-N-S/PHMA_S_GRID.shx
inst/extdata/HBLL-inside/HBLL_INS_active_2019.dbf
inst/extdata/HBLL-inside/HBLL_INS_active_2019.prj
inst/extdata/HBLL-inside/HBLL_INS_active_2019.shp
inst/extdata/HBLL-inside/HBLL_INS_active_2019.shx
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.dbf
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.prj
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.sbn
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.sbx
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.shp
inst/extdata/LLSurveyBoundaries/IPHC_Research_SitesII.shx
inst/extdata/LLSurveyBoundaries/PHMA_MASTER_GRID_copy.dbf
inst/extdata/LLSurveyBoundaries/PHMA_MASTER_GRID_copy.prj
inst/extdata/LLSurveyBoundaries/PHMA_MASTER_GRID_copy.sbn
inst/extdata/LLSurveyBoundaries/PHMA_MASTER_GRID_copy.sbx
inst/extdata/LLSurveyBoundaries/PHMA_MASTER_GRID_copy.shp
inst/extdata/LLSurveyBoundaries/PHMA_MASTER_GRID_copy.shx
inst/extdata/PHMA_MASTER_GRID_2018_UTM9/PHMA_MASTER_GRID_2018_UTM9.cpg
inst/extdata/PHMA_MASTER_GRID_2018_UTM9/PHMA_MASTER_GRID_2018_UTM9.dbf
inst/extdata/PHMA_MASTER_GRID_2018_UTM9/PHMA_MASTER_GRID_2018_UTM9.prj
inst/extdata/PHMA_MASTER_GRID_2018_UTM9/PHMA_MASTER_GRID_2018_UTM9.qpj
inst/extdata/PHMA_MASTER_GRID_2018_UTM9/PHMA_MASTER_GRID_2018_UTM9.shp
inst/extdata/PHMA_MASTER_GRID_2018_UTM9/PHMA_MASTER_GRID_2018_UTM9.shx
inst/extdata/SARA_listings.xlsx
inst/extdata/SynopticTrawlSurveyBoundaries/HS_BLOB.dbf
inst/extdata/SynopticTrawlSurveyBoundaries/HS_BLOB.prj
inst/extdata/SynopticTrawlSurveyBoundaries/HS_BLOB.shp
inst/extdata/SynopticTrawlSurveyBoundaries/HS_BLOB.shx
inst/extdata/SynopticTrawlSurveyBoundaries/QCS_BLOB.dbf
inst/extdata/SynopticTrawlSurveyBoundaries/QCS_BLOB.prj
inst/extdata/SynopticTrawlSurveyBoundaries/QCS_BLOB.sbn
inst/extdata/SynopticTrawlSurveyBoundaries/QCS_BLOB.sbx
inst/extdata/SynopticTrawlSurveyBoundaries/QCS_BLOB.shp
inst/extdata/SynopticTrawlSurveyBoundaries/QCS_BLOB.shx
inst/extdata/SynopticTrawlSurveyBoundaries/WCHG_BLOB.dbf
inst/extdata/SynopticTrawlSurveyBoundaries/WCHG_BLOB.prj
inst/extdata/SynopticTrawlSurveyBoundaries/WCHG_BLOB.shp
inst/extdata/SynopticTrawlSurveyBoundaries/WCHG_BLOB.shx
inst/extdata/SynopticTrawlSurveyBoundaries/WCVI_BLOB.dbf
inst/extdata/SynopticTrawlSurveyBoundaries/WCVI_BLOB.prj
inst/extdata/SynopticTrawlSurveyBoundaries/WCVI_BLOB.shp
inst/extdata/SynopticTrawlSurveyBoundaries/WCVI_BLOB.shx
inst/extdata/ageing_methods.csv
inst/extdata/iphc-spp-names.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/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/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/fit_cpue_index_glmmtmb.Rd man/fit_inla.Rd man/fit_length_weight.Rd man/fit_vb.Rd man/get_cpue_historical.Rd man/get_data.Rd man/gfplot.Rd man/hbll_grid.Rd man/hbll_n_grid.Rd man/hbll_s_grid.Rd man/inject_filter.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/run_sql.Rd man/survey-spatial-modelling.Rd man/survey_boundaries.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
pbs-assess/gfplot documentation built on April 10, 2019, 8:02 p.m.