Package: TropFishR 1.6.5

TropFishR: Tropical Fisheries Analysis

A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>), as well as other more recent methods.

Authors:Tobias K. Mildenberger, Marc H. Taylor, Matthias Wolff

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

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

Peer review:

Bug tracker:https://github.com/tokami/tropfishr/issues

Datasets:
  • alba - Length-frequency data of the clam Abra alba
  • bream - Bream data
  • emperor - Emperor data
  • gillnet - Gillnet data
  • goatfish - Yellowstriped goatfish data
  • haddock - Haddock data
  • hake - Hake data
  • shrimps - Shrimp data
  • synCAA1 - Synthetic Catch-at-age data I
  • synCAA2 - Synthetic Catch-at-age data II
  • synCPUE - Synthetical catch per unit of effort (CPUE) dataset
  • synLFQ1 - Synthetic length-frequency data I
  • synLFQ2 - Synthetic length frequency data II
  • synLFQ3 - Synthetic length frequency data III
  • synLFQ4 - Synthetic length-frequency data IV
  • synLFQ5 - Synthetic length-frequency data V
  • synLFQ6 - Synthetic length-frequency data VI
  • synLFQ7 - Synthetic length-frequency data VII with seasonal oscillation
  • synLFQ8 - Synthetic length-frequency data VIII with variable harvest rate
  • tilapia - Tilapia data
  • trammelnet - Trammel net data
  • trawl_fishery_Java - Data from the trawl fishery off the North coast of Java
  • whiting - Whiting data

On CRAN:

assessmentfao-manualfishfish-stocks

8.09 score 25 stars 149 scripts 1.2k downloads 3 mentions 29 exports 40 dependencies

Last updated 1 months agofrom:8dfb37a34f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winNOTENov 20 2024
R-4.4-macNOTENov 20 2024
R-4.3-winNOTENov 20 2024
R-4.3-macNOTENov 20 2024

Exports:BhattacharyacatchCurvedate2yeardecELEFANELEFAN_GAELEFAN_SAgillnetfitgrowth_length_agegrowth_tagginglfqCreatelfqFitCurveslfqModifylfqRestructureM_empiricalpowell_wetherallpredict_modprod_modprod_mod_tsrecruitmentselectselect_Millarselect_ogivestartingPoint2tanchorstock_simVBGFVPAyeardec2dateZ_BevertonHoltZ_CPUE

Dependencies:bitclicodetoolscrayondoParallelexpmfansiffforeachGAgenericsGenSAgluegmmiteratorslatticelifecyclemagrittrMASSMatrixminpack.lmmsmmvtnormpillarpkgconfigplyrpropagateRcppRcppArmadilloreshape2rlangsandwichstringistringrsurvivaltibbletmvtnormutf8vctrszoo

Using the TropFishR ELEFAN functions

Marc H. Taylor

Rendered fromUsing_TropFishR_ELEFAN_functions.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2021-08-30
Started: 2017-12-18

Length-frequency data for TropFishR

Tobias K. Mildenberger

Rendered fromlfqData.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2021-10-03
Started: 2017-09-21

Single-species fish stock assessment with TropFishR

Tobias K. Mildenberger

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2021-08-30
Started: 2017-02-05

Readme and manuals

Help Manual

Help pageTopics
Length-frequency data of the clam Abra albaalba
Bhattacharya's methodBhattacharya
bream databream
Catch curvecatchCurve
Date - Year conversiondate2yeardec
ELEFANELEFAN
ELEFAN_GAELEFAN_GA
ELEFAN_SAELEFAN_SA
Emperor dataemperor
Gillnet datagillnet
Millar's original gillnet selectivity fitting functiongillnetfit
Yellowstriped goatfish datagoatfish
Estimation of growth parameter using length-at-age datagrowth_length_age
Growth from tagging datagrowth_tagging
Haddock datahaddock
Hake datahake
Create lfq data from length measurementslfqCreate
Fitting VBGF growth curves through lfq datalfqFitCurves
Modify lfq data for further analysislfqModify
Restructuring of length frequency datalfqRestructure
Empirical formulas for the estimation of natural mortalityM_empirical
Bhattacharya plotplot.Bhattacharya
Plotting catch curveplot.catchCurve
Plotting of length frequency data (with VBGF curves)plot.lfq
Plotting prediction models yield per recruit and Thompson & Bellplot.predict_mod
Plotting production modelsplot.prod_mod
Plotting time series production modelsplot.prod_mod_ts
Plot of recruitment patternsplot.recruitment
Selectivity plotplot.select
Millar's selectivity plotplot.select_Millar
VPA plotplot.VPA
Powell-Wetherall methodpowell_wetherall
Prediction modelspredict_mod
Production modelsprod_mod
Production models with time series fittingprod_mod_ts
Predict gillnet selectivity (old Millar method)rcurves_Millar
Recruitment patternsrecruitment
Millar's selectivity typesrtypes_Millar
Selectivity modelselect
Millar's selectivity modelselect_Millar
Selectivity patternsselect_ogive
Shrimp datashrimps
Convert FiSAT's starting point to t_anchor valuestartingPoint2tanchor
Stock simulationstock_sim
Synthetic Catch-at-age data IsynCAA1
Synthetic Catch-at-age data IIsynCAA2
Synthetical catch per unit of effort (CPUE) datasetsynCPUE
Synthetic length-frequency data IsynLFQ1
Synthetic length frequency data IIsynLFQ2
Synthetic length frequency data IIIsynLFQ3
Synthetic length-frequency data IV (with seasonal oscillation)synLFQ4
Synthetic length-frequency data V (without seasonal oscillation)synLFQ5
Synthetic length-frequency data VI (without seasonal oscillation)synLFQ6
Synthetic length-frequency data VII with seasonal oscillationsynLFQ7
Synthetic length-frequency data VIII with variable harvest ratesynLFQ8
Tilapia datatilapia
Trammel net datatrammelnet
Data from the trawl fishery off the North coast of Javatrawl_fishery_Java
Von Bertalanffy Growth function (VBGF)VBGF
Virtual Population Analysis (VPA)VPA
Whiting datawhiting
Year - Date conversionyeardec2date
Yield per recruitypr
Yield per recruit with selection ogiveypr_sel
Beverton & Holt's Z-EquationsZ_BevertonHolt
Estimate Z from CPUE dataZ_CPUE