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 publication2016-12-30 10:12:17
MaintainerTobias K. Mildenberger <t.k.mildenberger@gmail.com>
LicenseGPL-3
Version1.0.2
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...

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/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/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/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/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/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/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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.