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

Author | Gary A. Nelson <gary.nelson@state.ma.us> |

Date of publication | 2016-09-20 02:54:05 |

Maintainer | Gary A. Nelson <gary.nelson@state.ma.us> |

License | GPL (>= 2) |

Version | 1.10-0 |

**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

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

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