# fishmethods v1.10-4

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## Fishery Science Methods and Models in R

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

## Functions in fishmethods

Name | Description | |

Jiang | Tag Data from Jiang (2005) | |

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

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

Jensen | Age Frequency Data for Lake Whitefish By Individual Haul | |

M.empirical | Estimation of Natural Mortality Rates from Life History Parameters | |

P.donacina | Data from a growth study of New Zealand intertidal clams. | |

Shepherd | Seasonal Length Frequencies for Raja clavata | |

agesurv | Age-based Survival Estimators | |

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

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

agesurvcl | Age-Based Survival and Mortality Estimators for Cluster Sampling | |

alk | Create An Age-Length Key | |

astrocalc4r | Solar zenith angles for biological research | |

clus.rho | Intracluster Correlation Coefficients for Clustered Data | |

clus.rho.g | Calculate A Common Intracluster Correlation Coefficient Among Groups | |

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

buffalo | Life Table Data for African Buffalo | |

clus.str.lf | Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling | |

bheq | Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator | |

bhnoneq | Length-based Beverton-Holt Nonequilibrium Z Estimator | |

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

catchmsy | Estimating MSY from catch and resilience | |

catchsurvey | Catch-Survey Analysis | |

counts | Run size data for alewife (Alosa pseudoharengus) | |

cowcod | Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008 | |

fm_model_avg | Model Averaging for the Telemetry Method of Hightower et al. (2001) | |

fm_telemetry | Estimation of Fishing and Natural Mortality from Telemetry Data | |

growthResid | Plot residuals of growth model fitted to tag data | |

growthTraject | Plot growth trajectories obtained from tagging data | |

mature | Estimation of proportion mature at age when immature fish are unavailable | |

menhaden | Biological data for menhaden (Brevoortia tyrannus) | |

nshrimp | Data for Gulf of Maine northern shrimp | |

clus.t.test | Correcting a Two-Sample Test for Clustering | |

epr | Eggs-Per-Recruit Analysis | |

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

opt_slot | Optimum Slot and Trophy Size Limits for Recreational Fisheries | |

slca | A Weakly Parametric Method for the Analysis of Length Composition Data | |

sr | Estimation and Model Comparison of Stock-Recruitment Relationships | |

vbfr | Francis' re-parameterization of the von Bertalanffy growth equation for length-age data | |

growtrans | Growth Transition Matrix for a Size-Structured Population Dynamics Model | |

haddock | Biological data for haddock (Melanogrammus aeglefinus) | |

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

alkprop | Age-Length Key Proportions-At-Age | |

alkss | Sample Size Determination for Age Subsampling | |

clus.lf | Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling | |

clus.mean | Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Sampling | |

clus.vb.fit | Fit a Von Bertalanffy growth equation to clustered data via bootstrapping | |

vblrt | Likelihood Ratio Tests for Comparing Multiple von Bertalanffy Growth Curves | |

maki | Data from Maki et al. 2001 | |

pinfish | Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida | |

plot.grotagplus | Plotting Tagging-Growth Objects | |

rig | Tagging data from a growth study of rig | |

rockbass | Age Frequency Data for Rock Bass | |

surveyref | Quantitative reference points from stock abundance indices based on research surveys | |

alkD | Sample Size Determination for Age Subsampling Using the D statistic | |

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

catch | Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985 | |

codcluslen | Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985. | |

cpuekapp | Trawl survey based abundance estimation using data sets with unusually large catches | |

darter | Catch Removal Data For Fantail Darter | |

growhamp | von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation | |

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

tag_model_avg | Model Averaging for Instantaneous Rates Tag Return Models | |

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

lifetable | Life Table Construction | |

pwpop | Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression | |

remp | Random Number Generation from an Empirical Distribution | |

codstrcluslen | Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985. | |

combinevar | Combining Mean and Variances from Multiple Samples | |

dbsra | Depletion-Based Stock Reduction Analysis | |

deltadist | Delta Distribution Mean and Variance Estimators | |

gap | Tukey's Gapping | |

goosefish | Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002 | |

irm_cr | Age-Independent Instantaneous Rates Model of Jiang et al. (2007) Incorporating Catch and Release Tag Returns | |

irm_h | Age-Independent Instantaneous Rates Tag Return Model of Hoenig et al. (1998) | |

catch.select | Selectivity Ogive from a Catch Curve | |

compare2 | Comparisons of two age readers or two aging methods | |

convmort | Conversion of Mortality Rates | |

deplet | Catch-Effort Depletion Methods For a Closed Population | |

dlproj | This function performs projections for dbsra and catchmsy objects | |

powertrend | Power Analysis For Detecting Trends | |

print.grotagplus | Printing Tagging-Growth Objects | |

striper | Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass | |

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

yellowtail | Fall average catch per tow for southern New England yellowtail flounder | |

grotag | Maximum likelihood estimation of growth and growth variability from tagging data - Francis (1988) | |

grotagplus | Flexible maximum likelihood estimation of growth from multiple tagging datasets. | |

mort.al | Estimation of Mortality using Times-At-Large Data from Tagging | |

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

opt_trophy | Optimum Trophy Size Limits for Recreational Fisheries | |

pgen | Probability of a Management Parameter Exceeding a Reference Point | |

sblen | Total length (inches) of striped bass collected by Massachusetts volunteer anglers in 2014 | |

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 Experiments | |

vbmultifit | Fit a Multi-Group von Bertalanffy Growth Model | |

ypr | Yield-Per-Recruit Analysis | |

tanaka | Simulated alfonsino data for Tanaka (2006 | |

trout | Mark-recapture data for Kenai River trout trout | |

zt | Z-transform or center a time series | |

wolffish | Spring untransformed mean catch per tow for wolffish (Anarhichas lupus) | |

No Results! |

## Last month downloads

## Details

Date | 2017-10-16 |

License | GPL (>= 2) |

RoxygenNote | 6.0.1 |

NeedsCompilation | no |

Packaged | 2017-10-16 17:46:20 UTC; gnelson |

Repository | CRAN |

Date/Publication | 2017-10-16 18:00:09 UTC |

depends | boot , bootstrap , lme4 , MASS , numDeriv , R (>= 2.7.0) |

Contributors | Gary A Nelson |

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