Fishery Science Methods and Models

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Documentation for package ‘fishmethods’ version 1.12-1

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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_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)

-- I --

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 --

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