fishmethods: Fishery Science Methods and Models in R

Fishery science methods and models from published literature and contributions from colleagues.

AuthorGary A. Nelson <>
Date of publication2017-03-07 16:55:06
MaintainerGary A. Nelson <>
LicenseGPL (>= 2)

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Man pages

agesurv: Age-based Survival Estimators

agesurvcl: Age-Based Survival and Mortality Estimators for Cluster...

alk: Create An Age-Length Key

alkD: Sample Size Determination for Age Subsampling Using the D...

alkdata: Age-Length Key for Gulf of Hauraki snapper, 1992-1993

alkprop: Age-Length Key Proportions-At-Age

alkss: Sample Size Determination for Age Subsampling

astrocalc4r: Solar zenith angles for biological research

bheq: Length-based Beverton-Holt Equilibrium Total Instantaneous...

bhnoneq: Length-based Beverton-Holt Nonequilibrium Z Estimator

bonito: Data from an age and growth study of the pacific bonito.

bt.log: Back-transformation of log-transformed mean and variance

buffalo: Life Table Data for African Buffalo

catch: Number of cod captured in 10 standardized bottom trawl hauls...

catchmsy: Estimating MSY from catch and resilience Selectivity Ogive from a Catch Curve

catchsurvey: Catch-Survey Analysis

clus.lf: Statistical Comparison of Length Frequencies from Simple...

clus.mean: Estimation of Population Attributes and Effective Sample Size...

clus.rho: Intracluster Correlation Coefficients for Clustered Data

clus.rho.g: Calculate A Common Intracluster Correlation Coefficient Among...

clus.str.lf: Statistical Comparison of Length Frequencies from Stratified...

clus.t.test: Correcting a Two-Sample Test for Clustering Fit a Von Bertalanffy growth equation to clustered data via...

codcluslen: Lengths of Atlantic cod caught during Massachusetts Division...

codstrcluslen: Lengths of Atlantic cod caught during Massachusetts Division...

combinevar: Combining Mean and Variances from Multiple Samples

compare2: Comparisons of two age readers or two aging methods

convmort: Conversion of Mortality Rates

counts: Run size data for alewife (_Alosa pseudoharengus_)

cowcod: Catch data (metric tons) for cowcod Sebastes levis 1900 to...

cpuekapp: Trawl survey based abundance estimation using data sets with...

darter: Catch Removal Data For Fantail Darter

dbsra: Depletion-Based Stock Reduction Analysis

deltadist: Delta Distribution Mean and Variance Estimators

deplet: Catch-Effort Depletion Methods For a Closed Population

dlproj: This function performs projections for dbsra and catchmsy...

epr: Eggs-Per-Recruit Analysis

fm_checkdesign: Check parameter structure of Hightower et al. (2001) models

fm_model_avg: Model Averaging for the Telemetry Method of Hightower et al....

fm_telemetry: Estimation of Fishing and Natural Mortality from Telemetry...

gap: Tukey's Gapping

Gerking: Mark-Recapture Data for Sunfish in an Indiana Lake

goosefish: Mean Length and Numbers of Lengths for Northern Goosefish,...

grotag: Maximum likelihood estimation of growth and growth...

growhamp: von Bertalanffy Growth Models for Tagging Data Incorporating...

growth: Fitting Growth Curves to Length- or Weight-at-Age Data

growthResid: Plot residuals of growth model fitted to tag data

growthTraject: Plot growth trajectories obtained from tagging data

growtrans: Growth Transition Matrix for a Size-Structured Population...

haddock: Biological data for haddock (Melanogrammus aeglefinus)

Hightower: Original data used in Hightower et al. (2001)

Hoenig: Tag Data from Hoenig et al. (1998)

irm_cr: Age-Independent Instantaneous Rates Model of Jiang et al....

irm_h: Age-Independent Instantaneous Rates Tag Return Model of...

Jensen: Age Frequency Data for Lake Whitefish By Individual Haul

Jiang: Tag Data from Jiang (2005)

kappenman: Pacific cod catch per effort from Table 1 in Kappenman (1999)

Kimura: Length and Age Data For Male and Female Pacific Hake

lifetable: Life Table Construction

lingcod: Catch data (metric tons) for lingcod 1889 to 2001

M.empirical: Estimation of Natural Mortality Rates from Life History...

menhaden: Biological data for menhaden (Brevoortia tyrannus) Estimation of Mortality using Times-At-Large Data from...

mrN.single: Estimate of Population Size from a Single Mark-Recapture...

nshrimp: Data for Gulf of Maine northern shrimp

opt_slot: Optimum Slot and Trophy Size Limits for Recreational...

opt_trophy: Optimum Trophy Size Limits for Recreational Fisheries

pgen: Probability of a Management Parameter Exceeding a Reference...

pinfish: Length, age and sex data for pinfish (Lagodon rhomboides)...

powertrend: Power Analysis For Detecting Trends

pwpop: Estimate Net Reproductive Rates Over Multiple Periods Of An...

remp: Random Number Generation from an Empirical Distribution

rockbass: Age Frequency Data for Rock Bass

sblen: Total length (inches) of striped bass collected by...

sbotos: Otolith ages of striped bass made by two age readers

sbpr: Spawning Stock Biomass-Per-Recruit Analysis

schnabel: Population Size Estimates from Repeated Mark-Recapture...

Shepherd: Seasonal Length Frequencies for Raja clavata

slca: A Weakly Parametric Method for the Analysis of Length...

surveyfit: Estimating the Relative Abundance of Fish From a Trawl Survey

surveyref: Quantitative reference points from stock abundance indices...

tag_model_avg: Model Averaging for Instantaneous Rates Tag Return Models

tanaka: Simulated alfonsino data for Tanaka (2006

trout: Mark-recapture data for Kenai River trout trout

vbfr: Francis' re-parameterization of the von Bertalanffy growth...

vblrt: Likelihood Ratio Tests for Comparing Multiple von Bertalanffy...

vbmultifit: Fit a Multi-Group von Bertalanffy Growth Model

wolffish: Spring untransformed mean catch per tow for wolffish...

yellowtail: Fall average catch per tow for southern New England...

ypr: Yield-Per-Recruit Analysis

zt: Z-transform or center a time series


agesurv Man page
agesurvcl Man page
alk Man page
alkD Man page
alkdata Man page
alkprop Man page
alkss Man page
astrocalc4r Man page
bheq Man page
bhnoneq Man page
bonito Man page
bt.log Man page
buffalo Man page
catch Man page
catchmsy Man page Man page
catchsurvey Man page
clus.lf Man page
clus.mean Man page
clus.rho Man page
clus.rho.g Man page
clus.str.lf Man page
clus.t.test Man page Man page
codcluslen Man page
codstrcluslen Man page
combinevar Man page
compare2 Man page
convmort Man page
counts Man page
cowcod Man page
cpuekapp Man page
darter Man page
dbsra Man page
deltadist Man page
deplet Man page
dlproj Man page
epr Man page
fm_checkdesign Man page
fm_model_avg Man page
fm_telemetry Man page
gap Man page
Gerking Man page
goosefish Man page
grotag Man page
growhamp Man page
growth Man page
growthResid Man page
growthTraject Man page
growtrans Man page
haddock Man page
Hightower Man page
Hoenig Man page
irm_cr Man page
irm_h Man page
Jensen Man page
Jiang Man page
kappenman Man page
Kimura Man page
lifetable Man page
lingcod Man page
M.empirical Man page
menhaden Man page Man page
mrN.single Man page
nshrimp Man page
nshrimp Man page
opt_slot Man page
opt_trophy Man page
pgen Man page
pinfish Man page
powertrend Man page
pwpop Man page
remp Man page
rockbass Man page
sblen Man page
sbotos Man page
sbpr Man page
schnabel Man page
Shepherd Man page
slca Man page
surveyfit Man page
surveyref Man page
tag_model_avg Man page
tanaka Man page
trout Man page
vbfr Man page
vblrt Man page
vbmultifit Man page
wolffish Man page
yellowtail Man page
ypr Man page
zt Man page


fishmethods/R/catchmsy.R fishmethods/R/remp.R fishmethods/R/catchsurvey.R fishmethods/R/fm_telemetry.R fishmethods/R/growthTraject.R fishmethods/R/alkss.R fishmethods/R/combinevar.R fishmethods/R/clus.t.test.R fishmethods/R/growhamp.R fishmethods/R/alkprop.R fishmethods/R/lifetable.R fishmethods/R/M.empirical.R fishmethods/R/surveyfit.R fishmethods/R/deltadist.R fishmethods/R/surveyref.R fishmethods/R/dbsra.R fishmethods/R/powertrend.R fishmethods/R/growthResid.R fishmethods/R/astrocalc4r.R fishmethods/R/bt.log.R fishmethods/R/agesurvcl.R fishmethods/R/deplet.R fishmethods/R/schnabel.R fishmethods/R/slca.R fishmethods/R/clus.rho.R fishmethods/R/clus.mean.R fishmethods/R/zt.R fishmethods/R/pgen.R fishmethods/R/grotag.R fishmethods/R/sbpr.R fishmethods/R/ fishmethods/R/vblrt.R fishmethods/R/irm_cr.R fishmethods/R/fm_model_avg.R fishmethods/R/bheq.R fishmethods/R/ fishmethods/R/compare2.R fishmethods/R/vbfr.R fishmethods/R/ fishmethods/R/pwpop.R fishmethods/R/growtrans.R fishmethods/R/opt_trophy.R fishmethods/R/clus.str.lf.R fishmethods/R/growth.R fishmethods/R/gap.R fishmethods/R/bhnoneq.R fishmethods/R/opt_slot.R fishmethods/R/alk.R fishmethods/R/vbmultifit.R fishmethods/R/alkD.R fishmethods/R/clus.rho.g.R fishmethods/R/dlproj.R fishmethods/R/epr.R fishmethods/R/irm_h.R fishmethods/R/cpuekapp.R fishmethods/R/convmort.R fishmethods/R/fm_checkdesign.R fishmethods/R/mrN.single.R fishmethods/R/agesurv.R fishmethods/R/ypr.R fishmethods/R/clus.lf.R fishmethods/R/tag_model_avg.R
fishmethods/man/agesurv.Rd fishmethods/man/catchmsy.Rd fishmethods/man/haddock.Rd fishmethods/man/alkprop.Rd fishmethods/man/astrocalc4r.Rd fishmethods/man/irm_cr.Rd fishmethods/man/fm_checkdesign.Rd fishmethods/man/lingcod.Rd fishmethods/man/buffalo.Rd fishmethods/man/goosefish.Rd fishmethods/man/ypr.Rd fishmethods/man/pinfish.Rd fishmethods/man/darter.Rd fishmethods/man/ fishmethods/man/ fishmethods/man/dlproj.Rd fishmethods/man/surveyfit.Rd fishmethods/man/Jensen.Rd fishmethods/man/slca.Rd fishmethods/man/wolffish.Rd fishmethods/man/vbfr.Rd fishmethods/man/clus.str.lf.Rd fishmethods/man/zt.Rd fishmethods/man/cpuekapp.Rd fishmethods/man/alkss.Rd fishmethods/man/cowcod.Rd fishmethods/man/nshrimp.Rd fishmethods/man/epr.Rd fishmethods/man/bt.log.Rd fishmethods/man/compare2.Rd fishmethods/man/counts.Rd fishmethods/man/tanaka.Rd fishmethods/man/clus.rho.Rd fishmethods/man/deltadist.Rd fishmethods/man/codstrcluslen.Rd fishmethods/man/Gerking.Rd fishmethods/man/Kimura.Rd fishmethods/man/powertrend.Rd fishmethods/man/growhamp.Rd fishmethods/man/convmort.Rd fishmethods/man/Hoenig.Rd fishmethods/man/alkdata.Rd fishmethods/man/agesurvcl.Rd fishmethods/man/trout.Rd fishmethods/man/pgen.Rd fishmethods/man/yellowtail.Rd fishmethods/man/sblen.Rd fishmethods/man/catch.Rd fishmethods/man/Jiang.Rd fishmethods/man/alk.Rd fishmethods/man/growthResid.Rd fishmethods/man/irm_h.Rd fishmethods/man/gap.Rd fishmethods/man/vblrt.Rd fishmethods/man/growth.Rd fishmethods/man/bhnoneq.Rd fishmethods/man/growthTraject.Rd fishmethods/man/grotag.Rd fishmethods/man/M.empirical.Rd fishmethods/man/Shepherd.Rd fishmethods/man/clus.rho.g.Rd fishmethods/man/rockbass.Rd fishmethods/man/Hightower.Rd fishmethods/man/fm_model_avg.Rd fishmethods/man/pwpop.Rd fishmethods/man/alkD.Rd fishmethods/man/opt_trophy.Rd fishmethods/man/surveyref.Rd fishmethods/man/remp.Rd fishmethods/man/menhaden.Rd fishmethods/man/tag_model_avg.Rd fishmethods/man/ fishmethods/man/mrN.single.Rd fishmethods/man/lifetable.Rd fishmethods/man/sbotos.Rd fishmethods/man/opt_slot.Rd fishmethods/man/schnabel.Rd fishmethods/man/fm_telemetry.Rd fishmethods/man/vbmultifit.Rd fishmethods/man/clus.mean.Rd fishmethods/man/dbsra.Rd fishmethods/man/catchsurvey.Rd fishmethods/man/clus.t.test.Rd fishmethods/man/combinevar.Rd fishmethods/man/sbpr.Rd fishmethods/man/bheq.Rd fishmethods/man/clus.lf.Rd fishmethods/man/deplet.Rd fishmethods/man/kappenman.Rd fishmethods/man/codcluslen.Rd fishmethods/man/growtrans.Rd fishmethods/man/bonito.Rd

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