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Package: mixfishtools 0.5.0

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_0.5.0.tar.gz
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mixfishtools.pdf |mixfishtools.html✨
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
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
wgnsskStocks - FLStocks object with assessment estimated values

On CRAN:

4.90 score 2 stars 3 scripts 10 exports 40 dependencies

Last updated 14 days agofrom:1dc33567d7. Checks:1 OK, 8 NOTE. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 12 2025
R-4.5-win	NOTE	Mar 12 2025
R-4.5-mac	NOTE	Mar 12 2025
R-4.5-linux	NOTE	Mar 12 2025
R-4.4-win	NOTE	Mar 12 2025
R-4.4-mac	NOTE	Mar 12 2025
R-4.4-linux	NOTE	Mar 12 2025
R-4.3-win	NOTE	Mar 12 2025
R-4.3-mac	NOTE	Mar 12 2025

Exports:gm_mean plot_catch_change plot_catchAlluvial plot_catchComp plot_catchScenStk plot_effortFltStk plot_landByMetStock plot_landByStock plot_overUnderFltStk plot_relEffortFltStk

Dependencies:cli colorspace cpp11 dplyr fansi farver generics ggalluvial ggplot2 ggrepel glue gtable isoband labeling lattice lazyeval lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Guide to mixfishtools package

Rendered frommixfishtoolsGuide.Rmdusingknitr::rmarkdownon Mar 12 2025.

Last update: 2025-03-12
Started: 2024-06-20

Reproducing the advice: WGMIXFISH quality control procedure

Rendered fromreproduceAdvice.Rmdusingknitr::rmarkdownon Mar 12 2025.

Last update: 2025-03-12
Started: 2025-03-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Geometric Mean	gm_mean
Short-term forecast individual weights for had.27.46a20	haddockWts
Plot fleet landings taken up relative to recent landings / quota	plot_catch_change
Alluvial plot of catch	plot_catchAlluvial
Plot landings or catch compositions	plot_catchComp
Headline advice plot	plot_catchScenStk
Plot fleet effort to uptake stock quotas	plot_effortFltStk
Bar chart of landings by stock and metier	plot_landByMetStock
Pie chart of landings by stock	plot_landByStock
Plot over- and undershoot of stock quotas by fleet	plot_overUnderFltStk
Relative fleet effort to uptake stock quotas	plot_relEffortFltStk
Look-up reference table for stocks and associated attributes	refTable
Data.frame containing short-term forecast summary of catch-related variables per stock and fleet combination	stfFltStkSum
Data.frame containing short-term forecast summary of catch-related variables per fleet	stfFltSum
Data.frame containing short-term forecast summary of catch-related variables per stock, fleet, and metier combination	stfMtStkSum
FLStocks object with assessment estimated values	wgnsskStocks