Package: icesFO 1.0.0.9005

Adriana Villamor

icesFO: Functions to support the creation of ICES Fisheries Overviews

Functions to support the creation of ICES Fisheries Overviews.

Authors:Adriana Villamor [aut, cre], Colin Millar [aut], Colm Lordan [aut], Youen Vermard [aut], Scott Large [aut], Sarah Millar [ctb]

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icesFO.pdf |icesFO.html✨
icesFO/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ices-tools-prod/icesfo/issues

On CRAN:

3.42 score 2 stars 264 scripts 38 exports 103 dependencies

Last updated 7 months agofrom:bd5a1ba677. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-winNOTEDec 09 2024
R-4.5-linuxNOTEDec 09 2024
R-4.4-winNOTEDec 09 2024
R-4.4-macNOTEDec 09 2024
R-4.3-winNOTEDec 09 2024
R-4.3-macNOTEDec 09 2024

Exports:CLD_trendscompute_technical_interactionsformat_annex_tableformat_catchesformat_sagformat_sag_statusformat_sidformat_stecf_effortformat_stecf_landingsguild_trendsload_areasload_asfis_speciesload_ecoregionload_historical_catchesload_official_catchesload_preliminary_catchesload_sag_refptsload_sag_statusload_sag_summaryload_sidload_statrec2ecoregionsplot_catch_trendsplot_CLD_barplot_discard_currentplot_discard_trendsplot_ecoregion_mapplot_effort_mapplot_GES_piesplot_guild_trendsplot_kobeplot_sar_mapplot_status_prop_piesplot_stecfplot_stock_trendsplot_technical_interactionsplot_vmsstock_trendsstockstatus_CLD_current

Dependencies:askpassbase64encbslibcachemclassclassIntclicolorspacecountrycodecpp11curldata.tableDBIdigestdotCall64dplyre1071evaluatefansifarverfastmapfieldsflextablefontawesomefontBitstreamVerafontLiberationfontquiverforcatsfsgdtoolsgenericsgetPassggplot2ggrepelggthemesgluegtablehighrhtmltoolshttricesConnecticesSAGicesVocabisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrmapsMASSMatrixmemoisemgcvmimemunsellnlmeofficeropensslpillarpkgconfigplyrproxypurrrR6raggrappdirsRColorBrewerRcpprlangrmarkdownrnaturalearthrstudioapis2sassscalessfspamstringistringrsyssystemfontsterratextshapingtibbletidyrtidyselecttinytexunitsutf8uuidvctrsviridisLitewhoamiwithrwkxfunxml2yamlzip

Readme and manuals

Help Manual

Help pageTopics
Functions to support the creation of ICES Fisheries OverviewsicesFO-package icesFO
Catch, discards, and landings by stockCLD_trends
Compute a matrix of technical interactions.compute_technical_interactions
Format the SAG status data for its use as an annex table.format_annex_table
Format the data from the time-series of ICES historical, official and preliminary catches.format_catches
Format the data from the ICES Stock Assessment Database.format_sag
Format the stock status data as is in the ICES Stock Assessment Database.format_sag_status
Format the data from the ICES Stock Information Database.format_sid
Format the data from STECF effort and landingsformat_stecf format_stecf_effort format_stecf_landings
Wrangling of format_sag outputguild_trends
Download ICES areas polygonsload_areas
Download ASFIS Species list from FAO.load_asfis_species
Download catch data from ICES web services.load_catches load_historical_catches load_official_catches load_preliminary_catches
Download ecoregion polygonsload_ecoregion
Download data from the ICES Stock Assessment database.load_sag load_sag_refpts load_sag_status load_sag_summary
Download data from the ICES Stock Information Database.load_sid
Download a statistical rectangles mapped to ecoregionload_statrec2ecoregions
Returns an ordered plot of catch bars colored according to F/F<sub>MSY</sub> and SSB/MSY B<sub>trigger</sub> by fish category and ecoregionplot_catch_trends
Returns an ordered plot of catch bars colored according to F/F<sub>MSY</sub> and SSB/MSY B<sub>trigger</sub> by fish category and ecoregionplot_CLD_bar
Returns a plot of discard rate by fish category for an ecoregion in the last assessment year.plot_discard_current
Returns a plot of discard rate trends by fish category for an ecoregion.plot_discard_trends
Returns an map of the ecoregion and the divisions included in itplot_ecoregion_map
Returns an map of the ecoregion and the divisions included in itplot_effort_map
Returns an ordered plot of catch bars colored according to F/F<sub>MSY</sub> and SSB/MSY B<sub>trigger</sub> by fish category and ecoregionplot_GES_pies
Plotting time series of F/Fmsy and SSB/MSY B trigger by guilds. This plots are used int the Ecosystem Overviews.plot_guild_trends
Returns a scatterplot of F/F<sub>MSY</sub> and SSB/MSY B<sub>trigger</sub> by fish category and ecoregionplot_kobe
Returns an map of the ecoregion and the divisions included in itplot_sar_map
Returns an ordered plot of catch bars colored according to F/F<sub>MSY</sub> and SSB/MSY B<sub>trigger</sub> by fish category and ecoregionplot_status_prop_pies
STECF Landings over time by country, guild, or speciesplot_stecf
Plotting time series of F/Fmsy and SSB/MSY B trigger for all stocks with data available by guild.plot_stock_trends
Visualise a matrix of technical interactions.plot_technical_interactions
VMS Effort and landings over time by country or gearplot_vms
Wrangling of format_sag outputstock_trends
Stock status relative to reference pointsstockstatus_CLD_current