R: Fishery Science Methods and Models

# Fishery Science Methods and Models

## Documentation for package ‘fishmethods’ version 1.13-1

- DESCRIPTION file

## Help Pages

A B C D E F G H I J K L M N O P R S T V W Y Z

## -- A --

agesurv | Age-based Survival Estimators
agesurvcl | Age-Based Survival and Mortality Estimators for Cluster Sampling
alk | Create An Age-Length Key
alkD | Sample Size Determination for Age Subsampling Using the D statistic
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
AtkaMack | Length and Age Data For Male and Female Atka Mackerel

## -- B --

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.
bt.log | Back-transformation of log-transformed mean and variance
buffalo | Life Table Data for African Buffalo

## -- C --

catch | Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985
catch.select | Selectivity Ogive from a Catch Curve
catchmsy | Estimating MSY from catch and resilience
catchsurvey | Catch-Survey Analysis
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.rho | Intracluster Correlation Coefficients for Clustered Data
clus.rho.g | Calculate A Common Intracluster Correlation Coefficient Among Groups
clus.str.lf | Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
clus.t.test | Correcting a Two-Sample Test for Clustering
clus.vb.fit | Fit a Von Bertalanffy growth equation to clustered data via bootstrapping
codcluslen | Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985.
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
compare.lrt.plus | Comparison of growthlrt.plus model objects
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 2008
cpuekapp | Trawl survey based abundance estimation using data sets with unusually large catches

## -- D --

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 objects

## -- E --

ep.data | A sub-sample of data from a simulated population collected via length-stratified age sampling
epr | Eggs-Per-Recruit Analysis
ep_growth | Fitting the von Bertalanffy growth model to length-stratified age samples

## -- F --

fm_checkdesign | Check parameter structure of Hightower et al. (2001) models
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
fpc | Fishing Power Correction Factor from Experimental Fishing

## -- G --

gap | Tukey's Gapping
Gerking | Mark-Recapture Data for Sunfish in an Indiana Lake
goosefish | Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002
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.
growhamp | von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation
growth | Fitting Growth Curves to Length- or Weight-at-Age Data
growthlrt | Likelihood Ratio Tests for Comparing Multiple Growth Curves
growthlrt.plus | Likelihood Methods for Comparing Multiple Growth Curves
growthmultifit | Fit a Multi-Group Growth Model
growthResid | Plot residuals of growth model fitted to tag data
growthTraject | Plot growth trajectories obtained from tagging data
growth_LEP | A flexible maximum likelihood approach for fitting growth curves to tag-recapture data
growth_sel | Fitting a von Bertalanffy curve to length and age data biased by gear selectivity
growtrans | Growth Transition Matrix for a Size-Structured Population Dynamics Model

## -- H --

haddock | Biological data for haddock (Melanogrammus aeglefinus)
Hightower | Original data used in Hightower et al. (2001)
Hoenig | Tag Data from Hoenig et al. (1998)
hohe | age-length key and length frequency data from Hoenig and Heisey (1987)

## -- I --

inverse_alk | Inverse Age-Length Key Method of Hoenig and Heisey (1987)
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)

## -- J --

Jensen | Age Frequency Data for Lake Whitefish By Individual Haul
Jiang | Tag Data from Jiang (2005)

## -- K --

kappenman | Pacific cod catch per effort from Table 1 in Kappenman (1999)
Kimura | Length and Age Data For Male and Female Pacific Hake

## -- L --

lepdata | Simulated data based on parameters estimated from corrected 1980s bluefin tuna data used in Laslett et al.(2002)
lifetable | Life Table Construction
lingcod | Catch data (metric tons) for lingcod 1889 to 2001

## -- M --

M.empirical | Estimation of Natural Mortality Rates from Life History Parameters
maki | Data from Maki et al. 2001
mature | Estimation of proportion mature at age when immature fish are unavailable
menhaden | Biological data for menhaden (Brevoortia tyrannus)
mort.al | Estimation of Mortality using Times-At-Large Data from Tagging
mrN.single | Estimate of Population Size from a Single Mark-Recapture Experiment

## -- N --

nshrimp | Data for Gulf of Maine northern shrimp

## -- O --

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

## -- P --

P.donacina | Data from a growth study of New Zealand intertidal clams.
pgen | Probability of a Management Parameter Exceeding a Reference Point
pinfish | Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida
plot.grotagplus | Plotting Tagging-Growth Objects
powertrend | Power Analysis For Detecting Trends
print.grotagplus | Printing Tagging-Growth Objects
pwpop | Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression

## -- R --

remp | Random Number Generation from an Empirical Distribution
rig | Tagging data from a growth study of rig
rockbass | Age Frequency Data for Rock Bass

## -- S --

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
Shepherd | Seasonal Length Frequencies for Raja clavata
simulus | Age and size data for the growth_sel function
slca | A Weakly Parametric Method for the Analysis of Length Composition Data
sole | Flathead sole CPUEs
sr | Estimation and Model Comparison of Stock-Recruitment Relationships
striper | Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
surveyfit | Estimating the Relative Abundance of Fish From a Trawl Survey
surveyref | Quantitative reference points from stock abundance indices based on research surveys

## -- T --

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

## -- V --

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

## -- W --

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

## -- Y --

yellowtail | Fall average catch per tow for southern New England yellowtail flounder
ypr | Yield-Per-Recruit Analysis

## -- Z --

zt | Z-transform or center a time series