Package: mixfishtools 0.5.1

Marc Taylor

mixfishtools: WGMIXFISH tools for reproducibility

Contains plot templates used in WGMIXFISH-ADVICE and Fisheries Overviews.

Authors:Marc Taylor, Mikel Aristegui, Johnathan Ball, Harriet Cole, Paul Dolder

mixfishtools_0.5.1.tar.gz
mixfishtools_0.5.1.zip(r-4.7)mixfishtools_0.5.1.zip(r-4.6)mixfishtools_0.5.1.zip(r-4.5)
mixfishtools_0.5.1.tgz(r-4.6-any)mixfishtools_0.5.1.tgz(r-4.5-any)
mixfishtools_0.5.1.tar.gz(r-4.7-any)mixfishtools_0.5.1.tar.gz(r-4.6-any)
mixfishtools_0.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mixfishtools/json (API)

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

Bug tracker:https://github.com/ices-tools-dev/mixfishtools/issues

Datasets:
  • haddockWts - Short-term forecast individual weights for had.27.46a20
  • NSeffort - Data.frame Contains information on the total effort by year and gear categories
  • NSlandings - Data.frame Contains information on the total landings by year and gear categories
  • refTable - Look-up reference table for stocks and associated attributes
  • stfFltStkSum - Data.frame containing short-term forecast summary of catch-related variables per stock and fleet combination
  • stfFltSum - Data.frame containing short-term forecast summary of catch-related variables per fleet
  • stfMtStkSum - Data.frame containing short-term forecast summary of catch-related variables per stock, fleet, and metier combination
  • stock_props - Data.frame contains information on the stock, metiers and landings proportions
  • wgnsskStocks - FLStocks object with assessment estimated values

On CRAN:

Conda:

4.73 score 3 stars 8 scripts 14 exports 33 dependencies

Last updated from:d3cfef90c1. Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING236
source / vignettesOK285
linux-release-x86_64WARNING207
macos-release-arm64WARNING115
macos-oldrel-arm64WARNING113
windows-develWARNING178
windows-releaseWARNING152
windows-oldrelWARNING146
wasm-releaseOK122

Exports:gm_meanplot_alluvialplot_catch_changeplot_catchCompplot_catchCompSppplot_catchCompStkplot_catchScenStkplot_effortFltStkplot_FOgearTypeplot_landByMetStockplot_landByStockplot_overUnderFltStkplot_relEffortFltStkplot_stkMetProp

Dependencies:clicpp11dplyrfarvergenericsggalluvialggplot2ggrepelgluegtableisobandlabelinglazyevallifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerRcpprlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Guide to mixfishtools package
Introduction | Installation of mixfishtools | Mixed fisheries considerations | Headline plot of catch uptake by stock and scenario | Fleet effort restriction plot | Landing by stock plot | Landing by metier and stock plot | Other plotting functions | Catch composition | Plot catch composition for each fleet over time | Plot landings composition for each area by country-metier combinations | Plot landings composition for each metier by country for single year | Over-/under-quota plot | Catch alluvial plot
Rendered frommixfishtoolsGuide.Rmdusingknitr::rmarkdown

Last update: 2025-09-29
Started: 2024-06-20

Assessment WG guidance on providing FLR stock objects to WGMIXFISH
Introduction | General FLStock creation | Age-based stocks | Direct extraction from SAM using FLfse | Quality control checks | Biomass-based stocks with dynamics | Fixed stocks without dynamics (e.g. Nephops) | Direct setup through manual entry | Indirect setup through import | Other considerations for Nephrops FUs without survey estimates | Requested stocks | Stock specific requests | Software Versions
Rendered fromFLStock2WGMIXFISH.Rmdusingknitr::rmarkdown

Last update: 2025-04-19
Started: 2025-04-17

Reproducing the advice: WGMIXFISH quality control procedure
Introduction | The procedure | The FLStock with assessment summary | Extend FLStock for short-term forecast | Define forecast control | Run deterministic forecast with FLasher | Compare summary statistics | Typical problems | Special case: fixed dynamics and harvest rate advice (Nephrops) | Software Versions
Rendered fromreproduceAdvice.Rmdusingknitr::rmarkdown

Last update: 2025-04-17
Started: 2025-03-10

Readme and manuals

Help Manual

Help pageTopics
Geometric Meangm_mean
Short-term forecast individual weights for had.27.46a20haddockWts
Data.frame Contains information on the total effort by year and gear categoriesNSeffort
Data.frame Contains information on the total landings by year and gear categoriesNSlandings
Alluvial plotplot_alluvial
Plot fleet landings taken up relative to recent landings / quotaplot_catch_change
Plot landings or catch compositionsplot_catchComp
Plot landings (catch) composition by country and speciesplot_catchCompSpp
Plot landings or catch compositionsplot_catchCompStk
Headline advice plotplot_catchScenStk
Plot fleet effort to uptake stock quotasplot_effortFltStk
Plot total landings or effort by broad gear categoriesplot_FOgearType
Bar chart of landings by stock and metierplot_landByMetStock
Pie chart of landings by stockplot_landByStock
Plot over- and undershoot of stock quotas by fleetplot_overUnderFltStk
Relative fleet effort to uptake stock quotasplot_relEffortFltStk
Plot proportion of stock landings by metierplot_stkMetProp
Look-up reference table for stocks and associated attributesrefTable
Data.frame containing short-term forecast summary of catch-related variables per stock and fleet combinationstfFltStkSum
Data.frame containing short-term forecast summary of catch-related variables per fleetstfFltSum
Data.frame containing short-term forecast summary of catch-related variables per stock, fleet, and metier combinationstfMtStkSum
Data.frame contains information on the stock, metiers and landings proportionsstock_props
FLStocks object with assessment estimated valueswgnsskStocks