Package: rcef 0.1.0

Damian Villagra

rcef: Discard Raising and Length/Age Catch Allocation over CEF (RDBES) Data

Implements the ICES discard-raising and length/age catch allocation workflows over CEF (RDBES) long-format data: discard-rate and sampling-coverage tables with the plots that draw them, plots of the numbers and mean weight at length and age, and plots of the raised and allocated catch, with one colour palette for all of them. Wraps the RDBESStockCoord engines catchRaising() and catchAllocationAoL(), and writes what they give in the format of the stock coordination (Catch Combined and Distributions Combined).

Authors:Damian Villagra [aut, cre], Yves Reecht [aut], RDBESStockCoord contributors [ctb]

rcef_0.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rcef/json (API)

# Install 'rcef' in R:
install.packages('rcef', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dvillagra26/rcef/issues

On CRAN:

Conda:

3.21 score 36 scripts 71 exports 113 dependencies

Last updated from:c3bccadd58. Checks:6 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develWARNING189
source / vignettesERROR593
linux-releaseWARNING179
macos-releaseWARNING152
macos-oldrelWARNING117
windows-develWARNING114
windows-oldrelWARNING116
wasm-releaseOK158

Exports:aol_classesaol_finishapp_themebiology_dist_prepbiology_keybuild_coverage_stratabuild_discard_clusterscatch_category_partscatch_domaincatchAllocationcatchAllocationAoLcatchAtAoLcatchAtAoLAggregationcatchCombinedcatchRaisingcategory_colscheck_group_conditionsclass_axis_scaleconvert_fieldconvert_unitscoverage_cellscoverage_thresholdscoverage_whatderive_fieldsderive_hintdistributionsCombinedfacet_layerfunICoutCEFfunIntercatchCEFfunMakeRelationgeom_col_hatchgrp_AoL_alloc_conditiongrp_AoL_alloc_Ngrp_AoL_alloc_WLgrp_catch_raisinggrp_catch_raising_conditionlink_checkmeanWoLatAoLmeanWoLatAoLAggregationmesh_var_levelsOUTLINEOUTLINE_LWplot_catchesplot_coloursplot_compare_raisedplot_coverage_barplot_coverage_gridplot_coverage_mapplot_discard_cluster_variablesplot_discard_clustersplot_DRplot_MWaLoAplot_NaLoAplot_recommended_groupsplot_riverprep_distributionsraised_overview_tablerecommend_groupssave_on_exitscenario_listscf_headerscf_inputscf_samplingscf_tablespread_AoLSTATUS_LEVELSstatus_marksstrata_familiesstrata_sentencesub_wrapunit2ratio

Dependencies:abindbackportsbase64encbootbroombslibcachemcarcarDatacliclustercolorspacecowplotcpp11crosstalkdata.tableDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluateFactoMineRfarverfastmapflashClustfontawesomeforecastFormulafracdifffsgenericsggalluvialggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetsirlbaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivotelpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS7sassscalesscatterplot3dshowtextshowtextdbSparseMstringistringrsurvivalsysfontstibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Sampling coverage and discard rate per stratumbuild_coverage_strata
Which strata share a discard rate, and which variables predict thatbuild_discard_clusters
Catch Allocation (CAR and CAS): how the discards were raised, in the format of the stock coordinationcatchAllocation
Allocate length or age distributions to the catchcatchAllocationAoL
Catch at length or age: the numbers of an allocation, added upcatchAtAoLAggregation
Catch Combined (CC): the catch of a stock, added up, in the format of the stock coordinationcatchCombined
Raise the discards of each group from its donor poolcatchRaising
Function to check groups consistencycheck_group_conditions
Coverage: which strata are sampled well enoughcoverage-plots plot_coverage_bar plot_coverage_grid
Derive the grouping columns from a CEF catch table - or from its distributionsderive_fields
Distributions Combined (DC): the numbers and mean weights at length or age, in the format of the stock coordinationdistributionsCombined
InterCatch output to CEF formatfunICoutCEF
InterCatch exchange format to CEF v17.1funIntercatchCEF
Function to create stock_relation from ICES databasesfunMakeRelation
Mean weight at length or age: the mean weights of an allocation, averagedmeanWoLatAoLAggregation
Catch weight per stratum, before or after the raisingplot_catches
Raised catch of several scenarios, side by sideplot_compare_raised
Coverage map: one pie per ICES areaplot_coverage_map
Which variable best predicts the discard-rate clusterplot_discard_cluster_variables
Discard-rate clusters, shown on the map of 'dims'plot_discard_clusters
Discard rate per stratum, before or after the raisingplot_DR
Mean weight at length or age, before or after the allocationplot_MWaLoA
Numbers at length or age, before or after the allocationplot_NaLoA
The level each stratum is raised fromplot_recommended_groups
River plot: which strata are raised from which groupplot_river
Imported against raised catch, by catch category: one raised catch or severalraised_overview_table
Groups for the raising and the allocation, from a hierarchy of variablesprint.rcef_groups recommend_groups
Saving a plot as it is drawnsaving-plots