TropFishR: Tropical Fisheries Analysis with R

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Fish stock assessment methods and fisheries models based on the FAO Manual "Introduction to tropical fish stock assessment" by P. Sparre and S.C. Venema <http://www.fao.org/docrep/W5449E/W5449E00.htm>. Focus is the analysis of length-frequency data and data poor fisheries.

Author
Tobias K. Mildenberger, Marc H. Taylor, Matthias Wolff
Date of publication
2016-09-09 10:22:16
Maintainer
Tobias K. Mildenberger <t.k.mildenberger@gmail.com>
License
GPL-3
Version
1.0.0
URLs

View on CRAN

Man pages

Bhattacharya
Bhattacharya's method
bream
bream data
catchCurve
Catch curve
date2yeardec
Date - Year conversion
ELEFAN
ELEFAN
ELEFAN_GA
ELEFAN_GA
ELEFAN_SA
ELEFAN_SA
emperor
Emperor data
gillnet
Gillnet data
gillnetfit
Millar's original gillnet selectivity fitting function
goatfish
Yellowstriped goatfish data
growth_length_age
Estimation of growth parameter using length-at-age data
growth_tagging
Growth from tagging data
haddock
Haddock data
hake
Hake data
lfqFitCurves
Fitting VBGF growth curves through lfq data
lfqRestructure
Restructuring of length frequency data
M_empirical
Empirical formulas for the estimation of natural mortality
plot.Bhattacharya
Bhattacharya plot
plot.catchCurve
Plotting catch curve
plot.lfq
Plotting of length frequency data (with VBGF curves)
plot.predict_mod
Plotting prediction models yield per recruit and Thompson &...
plot.prod_mod
Plotting production models
plot.prod_mod_ts
Plotting time series production models
plot.recruitment
Plot of recruitment patterns
plot.select
Selectivity plot
plot.select_Millar
Millar's selectivity plot
plot.VPA
VPA plot
powell_wetherall
Powell-Wetherall method
predict_mod
Prediction models
prod_mod
Production models
prod_mod_ts
Production models with time series fitting
rcurves_Millar
Predict gillnet selectivity (old Millar method)
recruitment
Recruitment patterns
rtypes_Millar
Millar's selectivity types
select
Selectivity model
select_Millar
Millar's selectivity model
select_ogive
Selectivity patterns
shrimps
Shrimp data
stock_sim
Stock simulation
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 (with seasonal...
synLFQ5
Synthetic length-frequency data V (without seasonal...
tilapia
Tilapia data
trammelnet
Trammel net data
trawl_fishery_Java
Data from the trawl fishery off the North coast of Java
VBGF
Von Bertalanffy Growth function (VBGF)
VPA
Virtual Population Analysis (VPA)
whiting
Whiting data
yeardec2date
Year - Date conversion
ypr
Yield per recruit
ypr_sel
Yield per recruit with selection ogive
Z_BevertonHolt
Beverton & Holt's Z-Equations
Z_CPUE
Estimate Z from CPUE data

Files in this package

TropFishR
TropFishR/NAMESPACE
TropFishR/data
TropFishR/data/trawl_fishery_Java.rda
TropFishR/data/synLFQ4.rda
TropFishR/data/bream.rda
TropFishR/data/hake.rda
TropFishR/data/synLFQ3.rda
TropFishR/data/goatfish.rda
TropFishR/data/synLFQ2.rda
TropFishR/data/synCPUE.rda
TropFishR/data/synLFQ5.rda
TropFishR/data/whiting.rda
TropFishR/data/haddock.rda
TropFishR/data/gillnet.rda
TropFishR/data/tilapia.rda
TropFishR/data/shrimps.rda
TropFishR/data/synCAA1.rda
TropFishR/data/synLFQ1.rda
TropFishR/data/synCAA2.rda
TropFishR/data/trammelnet.rda
TropFishR/data/emperor.rda
TropFishR/R
TropFishR/R/emperor.R
TropFishR/R/select.R
TropFishR/R/ELEFAN.R
TropFishR/R/synCAA1.R
TropFishR/R/shrimps.R
TropFishR/R/synLFQ1.R
TropFishR/R/stock_sim.R
TropFishR/R/plot.recruitment.R
TropFishR/R/yeardec2date.R
TropFishR/R/plot.select.R
TropFishR/R/Z_CPUE.R
TropFishR/R/plot.predict_mod.R
TropFishR/R/gillnetfit.R
TropFishR/R/bream.R
TropFishR/R/Bhattacharya.R
TropFishR/R/synCAA2.R
TropFishR/R/VBGF.R
TropFishR/R/rcurves_Millar.R
TropFishR/R/synCPUE.R
TropFishR/R/date2yeardec.R
TropFishR/R/synLFQ3.R
TropFishR/R/rtypes_Millar.R
TropFishR/R/goatfish.R
TropFishR/R/synLFQ4.R
TropFishR/R/growth_length_age.R
TropFishR/R/select_Millar.R
TropFishR/R/ELEFAN_SA.R
TropFishR/R/gillnet.R
TropFishR/R/Z_BevertonHolt.R
TropFishR/R/synLFQ2.R
TropFishR/R/growth_tagging.R
TropFishR/R/predict_mod.R
TropFishR/R/powell_wetherall.R
TropFishR/R/prod_mod_ts.R
TropFishR/R/hake.R
TropFishR/R/prod_mod.R
TropFishR/R/tilapia.R
TropFishR/R/whiting.R
TropFishR/R/synLFQ5.R
TropFishR/R/ELEFAN_GA.R
TropFishR/R/trawl_fishery_Java.R
TropFishR/R/plot.catchCurve.R
TropFishR/R/plot.lfq.R
TropFishR/R/lfqFitCurves.R
TropFishR/R/plot.Bhattacharya.R
TropFishR/R/plot.VPA.R
TropFishR/R/catchCurve.R
TropFishR/R/plot.select_Millar.R
TropFishR/R/VPA.R
TropFishR/R/select_ogive.R
TropFishR/R/trammelnet.R
TropFishR/R/plot.prod_mod_ts.R
TropFishR/R/lfqRestructure.R
TropFishR/R/plot.prod_mod.R
TropFishR/R/M_empirical.R
TropFishR/R/haddock.R
TropFishR/R/ypr_sel.R
TropFishR/R/ypr.R
TropFishR/R/recruitment.R
TropFishR/README.md
TropFishR/MD5
TropFishR/DESCRIPTION
TropFishR/man
TropFishR/man/trammelnet.Rd
TropFishR/man/plot.predict_mod.Rd
TropFishR/man/rtypes_Millar.Rd
TropFishR/man/plot.select.Rd
TropFishR/man/haddock.Rd
TropFishR/man/ELEFAN_SA.Rd
TropFishR/man/tilapia.Rd
TropFishR/man/synCAA2.Rd
TropFishR/man/ypr.Rd
TropFishR/man/whiting.Rd
TropFishR/man/synLFQ2.Rd
TropFishR/man/powell_wetherall.Rd
TropFishR/man/hake.Rd
TropFishR/man/synLFQ4.Rd
TropFishR/man/prod_mod_ts.Rd
TropFishR/man/goatfish.Rd
TropFishR/man/shrimps.Rd
TropFishR/man/emperor.Rd
TropFishR/man/bream.Rd
TropFishR/man/synCPUE.Rd
TropFishR/man/select_Millar.Rd
TropFishR/man/plot.Bhattacharya.Rd
TropFishR/man/plot.recruitment.Rd
TropFishR/man/Bhattacharya.Rd
TropFishR/man/prod_mod.Rd
TropFishR/man/yeardec2date.Rd
TropFishR/man/predict_mod.Rd
TropFishR/man/growth_tagging.Rd
TropFishR/man/synLFQ3.Rd
TropFishR/man/select_ogive.Rd
TropFishR/man/ypr_sel.Rd
TropFishR/man/Z_CPUE.Rd
TropFishR/man/VBGF.Rd
TropFishR/man/gillnet.Rd
TropFishR/man/lfqRestructure.Rd
TropFishR/man/rcurves_Millar.Rd
TropFishR/man/growth_length_age.Rd
TropFishR/man/catchCurve.Rd
TropFishR/man/synCAA1.Rd
TropFishR/man/stock_sim.Rd
TropFishR/man/trawl_fishery_Java.Rd
TropFishR/man/ELEFAN.Rd
TropFishR/man/plot.select_Millar.Rd
TropFishR/man/plot.lfq.Rd
TropFishR/man/date2yeardec.Rd
TropFishR/man/synLFQ5.Rd
TropFishR/man/M_empirical.Rd
TropFishR/man/recruitment.Rd
TropFishR/man/plot.VPA.Rd
TropFishR/man/synLFQ1.Rd
TropFishR/man/lfqFitCurves.Rd
TropFishR/man/Z_BevertonHolt.Rd
TropFishR/man/ELEFAN_GA.Rd
TropFishR/man/gillnetfit.Rd
TropFishR/man/plot.catchCurve.Rd
TropFishR/man/VPA.Rd
TropFishR/man/plot.prod_mod_ts.Rd
TropFishR/man/plot.prod_mod.Rd
TropFishR/man/select.Rd