fishmethods: Fishery Science Methods and Models in R

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

AuthorGary A. Nelson <gary.nelson@state.ma.us>
Date of publication2016-09-20 02:54:05
MaintainerGary A. Nelson <gary.nelson@state.ma.us>
LicenseGPL (>= 2)
Version1.10-0

View on CRAN

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

catch.select: 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

clus.vb.fit: 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)

mort.al: 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 Two von Bertalanffy...

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

Files in this package

fishmethods
fishmethods/NAMESPACE
fishmethods/data
fishmethods/data/sblen.rda
fishmethods/data/kappenman.rda
fishmethods/data/buffalo.rda
fishmethods/data/catch.rda
fishmethods/data/Jensen.rda
fishmethods/data/bonito.rda
fishmethods/data/codcluslen.rda
fishmethods/data/Hightower.rda
fishmethods/data/cowcod.rda
fishmethods/data/trout.rda
fishmethods/data/nshrimp.rda
fishmethods/data/rockbass.rda
fishmethods/data/tanaka.rda
fishmethods/data/Shepherd.rda
fishmethods/data/codstrcluslen.rda
fishmethods/data/haddock.rda
fishmethods/data/Hoenig.rda
fishmethods/data/darter.rda
fishmethods/data/sbotos.rda
fishmethods/data/yellowtail.rda
fishmethods/data/pinfish.rda
fishmethods/data/counts.rda
fishmethods/data/lingcod.rda
fishmethods/data/Gerking.rda
fishmethods/data/wolffish.rda
fishmethods/data/menhaden.rda
fishmethods/data/Jiang.rda
fishmethods/data/goosefish.rda
fishmethods/data/alkdata.rda
fishmethods/data/Kimura.rda
fishmethods/R
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/catch.select.R fishmethods/R/vblrt.R fishmethods/R/irm_cr.R fishmethods/R/fm_model_avg.R fishmethods/R/bheq.R fishmethods/R/clus.vb.fit.R fishmethods/R/compare2.R fishmethods/R/vbfr.R fishmethods/R/mort.al.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/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/MD5
fishmethods/DESCRIPTION
fishmethods/man
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/mort.al.Rd fishmethods/man/clus.vb.fit.Rd 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/catch.select.Rd 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/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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