TropFishR: Tropical Fisheries Analysis with R

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.

AuthorTobias K. Mildenberger, Marc H. Taylor, Matthias Wolff
Date of publication2017-02-26 16:38:27
MaintainerTobias K. Mildenberger <t.k.mildenberger@gmail.com>
LicenseGPL-3
Version1.1
https://github.com/tokami/TropFishR

View on CRAN

Man pages

alba: Length-frequency data of the clam Abra alba

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

lfqCreate: Create lfq data from length measurements

lfqFitCurves: Fitting VBGF growth curves through lfq data

lfqModify: Modify lfq data for further analysis

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

startingPoint2tanchor: Convert FiSAT's starting point to t_anchor value

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...

synLFQ6: Synthetic length-frequency data VI (without seasonal...

synLFQ7: Synthetic length-frequency data VII with seasonal oscillation

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

Functions

alba Man page
Bhattacharya Man page
bream Man page
catchCurve Man page
date2yeardec Man page
ELEFAN Man page
ELEFAN_GA Man page
ELEFAN_SA Man page
emperor Man page
gillnet Man page
gillnetfit Man page
goatfish Man page
growth_length_age Man page
growth_tagging Man page
haddock Man page
hake Man page
lfqCreate Man page
lfqFitCurves Man page
lfqModify Man page
lfqRestructure Man page
M_empirical Man page
plot.Bhattacharya Man page
plot.catchCurve Man page
plot.lfq Man page
plot.predict_mod Man page
plot.prod_mod Man page
plot.prod_mod_ts Man page
plot.recruitment Man page
plot.select Man page
plot.select_Millar Man page
plot.VPA Man page
powell_wetherall Man page
predict_mod Man page
prod_mod Man page
prod_mod_ts Man page
rcurves_Millar Man page
recruitment Man page
rtypes_Millar Man page
select Man page
select_Millar Man page
select_ogive Man page
shrimps Man page
startingPoint2tanchor Man page
stock_sim Man page
synCAA1 Man page
synCAA2 Man page
synCPUE Man page
synLFQ1 Man page
synLFQ2 Man page
synLFQ3 Man page
synLFQ4 Man page
synLFQ5 Man page
synLFQ6 Man page
synLFQ7 Man page
tilapia Man page
trammelnet Man page
trawl_fishery_Java Man page
VBGF Man page
VPA Man page
whiting Man page
yeardec2date Man page
ypr Man page
ypr_sel Man page
Z_BevertonHolt Man page
Z_CPUE Man page

Files

TropFishR
TropFishR/inst
TropFishR/inst/doc
TropFishR/inst/doc/tutorial.R
TropFishR/inst/doc/tutorial.html
TropFishR/inst/doc/tutorial.Rmd
TropFishR/NAMESPACE
TropFishR/data
TropFishR/data/trawl_fishery_Java.rda
TropFishR/data/synLFQ4.rda
TropFishR/data/bream.rda
TropFishR/data/alba.rda
TropFishR/data/hake.rda
TropFishR/data/synLFQ3.rda
TropFishR/data/synLFQ6.rda
TropFishR/data/goatfish.rda
TropFishR/data/synLFQ2.rda
TropFishR/data/synCPUE.rda
TropFishR/data/synLFQ5.rda
TropFishR/data/synLFQ7.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/alba.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/lfqCreate.R TropFishR/R/growth_tagging.R TropFishR/R/predict_mod.R TropFishR/R/synLFQ6.R TropFishR/R/startingPoint2tanchor.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/synLFQ7.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/R/lfqModify.R
TropFishR/vignettes
TropFishR/vignettes/tutorial.Rmd
TropFishR/vignettes/TropFishR.bib
TropFishR/README.md
TropFishR/MD5
TropFishR/build
TropFishR/build/vignette.rds
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/lfqModify.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/lfqCreate.Rd TropFishR/man/VBGF.Rd TropFishR/man/gillnet.Rd TropFishR/man/lfqRestructure.Rd TropFishR/man/startingPoint2tanchor.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/synLFQ7.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/synLFQ6.Rd TropFishR/man/M_empirical.Rd TropFishR/man/recruitment.Rd TropFishR/man/plot.VPA.Rd TropFishR/man/synLFQ1.Rd TropFishR/man/alba.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

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