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fishmethods (version 1.13-1)

Fishery Science Methods and Models

Description

Functions for applying a wide range of fisheries stock assessment methods.

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Version

Install

install.packages('fishmethods')

Monthly Downloads

1,159

Version

1.13-1

License

GPL (>= 2)

Maintainer

Gary Nelson

Last Published

February 5th, 2025

Functions in fishmethods (1.13-1)

AtkaMack

Length and Age Data For Male and Female Atka Mackerel
alk

Create An Age-Length Key
bhnoneq

Length-based Beverton-Holt Nonequilibrium Z Estimator
alkD

Sample Size Determination for Age Subsampling Using the D statistic
bheq

Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator
agesurvcl

Age-Based Survival and Mortality Estimators for Cluster Sampling
catchsurvey

Catch-Survey Analysis
catch

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

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

Selectivity Ogive from a Catch Curve
bt.log

Back-transformation of log-transformed mean and variance
clus.mean

Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Sampling
buffalo

Life Table Data for African Buffalo
catchmsy

Estimating MSY from catch and resilience
clus.rho

Intracluster Correlation Coefficients for Clustered Data
clus.lf

Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling
clus.t.test

Correcting a Two-Sample Test for Clustering
codcluslen

Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985.
clus.rho.g

Calculate A Common Intracluster Correlation Coefficient Among Groups
clus.vb.fit

Fit a Von Bertalanffy growth equation to clustered data via bootstrapping
clus.str.lf

Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
compare.lrt.plus

Comparison of growthlrt.plus model objects
combinevar

Combining Mean and Variances from Multiple Samples
dbsra

Depletion-Based Stock Reduction Analysis
codstrcluslen

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

A sub-sample of data from a simulated population collected via length-stratified age sampling
dlproj

This function performs projections for dbsra and catchmsy objects
deltadist

Delta Distribution Mean and Variance Estimators
deplet

Catch-Effort Depletion Methods For a Closed Population
ep_growth

Fitting the von Bertalanffy growth model to length-stratified age samples
compare2

Comparisons of two age readers or two aging methods
convmort

Conversion of Mortality Rates
darter

Catch Removal Data For Fantail Darter
counts

Run size data for alewife (Alosa pseudoharengus)
cpuekapp

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

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

Estimation of Fishing and Natural Mortality from Telemetry Data
gap

Tukey's Gapping
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)
fm_model_avg

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

Eggs-Per-Recruit Analysis
fpc

Fishing Power Correction Factor from Experimental Fishing
fm_checkdesign

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

von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation
grotagplus

Flexible maximum likelihood estimation of growth from multiple tagging datasets.
growthResid

Plot residuals of growth model fitted to tag data
growth_LEP

A flexible maximum likelihood approach for fitting growth curves to tag-recapture data
haddock

Biological data for haddock (Melanogrammus aeglefinus)
growthTraject

Plot growth trajectories obtained from tagging data
growthmultifit

Fit a Multi-Group Growth Model
growtrans

Growth Transition Matrix for a Size-Structured Population Dynamics Model
growthlrt.plus

Likelihood Methods for Comparing Multiple Growth Curves
growth_sel

Fitting a von Bertalanffy curve to length and age data biased by gear selectivity
growth

Fitting Growth Curves to Length- or Weight-at-Age Data
growthlrt

Likelihood Ratio Tests for Comparing Multiple Growth Curves
kappenman

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

Life Table Construction
maki

Data from Maki et al. 2001
lepdata

Simulated data based on parameters estimated from corrected 1980s bluefin tuna data used in Laslett et al.(2002)
mature

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

age-length key and length frequency data from Hoenig and Heisey (1987)
lingcod

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

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

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

Optimum Trophy Size Limits for Recreational Fisheries
pgen

Probability of a Management Parameter Exceeding a Reference Point
nshrimp

Data for Gulf of Maine northern shrimp
powertrend

Power Analysis For Detecting Trends
plot.grotagplus

Plotting Tagging-Growth Objects
opt_slot

Optimum Slot and Trophy Size Limits for Recreational Fisheries
irm_h

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

Estimate of Population Size from a Single Mark-Recapture Experiment
mort.al

Estimation of Mortality using Times-At-Large Data from Tagging
menhaden

Biological data for menhaden (Brevoortia tyrannus)
pinfish

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

Age Frequency Data for Rock Bass
sblen

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

Random Number Generation from an Empirical Distribution
rig

Tagging data from a growth study of rig
simulus

Age and size data for the growth_sel function
schnabel

Population Size Estimates from Repeated Mark-Recapture Experiments
print.grotagplus

Printing Tagging-Growth Objects
striper

Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
sr

Estimation and Model Comparison of Stock-Recruitment Relationships
sbpr

Spawning Stock Biomass-Per-Recruit Analysis
sbotos

Otolith ages of striped bass made by two age readers
surveyfit

Estimating the Relative Abundance of Fish From a Trawl Survey
surveyref

Quantitative reference points from stock abundance indices based on research surveys
yellowtail

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

Flathead sole CPUEs
wolffish

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

Mark-recapture data for Kenai River trout trout
pwpop

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

Model Averaging for Instantaneous Rates Tag Return Models
vbfr

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

A Weakly Parametric Method for the Analysis of Length Composition Data
tanaka

Simulated alfonsino data for Tanaka (2006
zt

Z-transform or center a time series
ypr

Yield-Per-Recruit Analysis
Hightower

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

Seasonal Length Frequencies for Raja clavata
M.empirical

Estimation of Natural Mortality Rates from Life History Parameters
astrocalc4r

Solar zenith angles for biological research
P.donacina

Data from a growth study of New Zealand intertidal clams.
Kimura

Length and Age Data For Male and Female Pacific Hake
Jiang

Tag Data from Jiang (2005)
Hoenig

Tag Data from Hoenig et al. (1998)
Gerking

Mark-Recapture Data for Sunfish in an Indiana Lake
alkprop

Age-Length Key Proportions-At-Age
agesurv

Age-based Survival Estimators
alkdata

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

Age Frequency Data for Lake Whitefish By Individual Haul
alkss

Sample Size Determination for Age Subsampling