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fishmethods (version 1.11-0)

Fishery Science Methods and Models

Description

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

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Install

install.packages('fishmethods')

Monthly Downloads

1,159

Version

1.11-0

License

GPL (>= 2)

Maintainer

Gary Nelson

Last Published

November 20th, 2018

Functions in fishmethods (1.11-0)

M.empirical

Estimation of Natural Mortality Rates from Life History Parameters

Jiang

Tag Data from Jiang (2005)

clus.rho

Intracluster Correlation Coefficients for Clustered Data

clus.rho.g

Calculate A Common Intracluster Correlation Coefficient Among Groups

Kimura

Length and Age Data For Male and Female Pacific Hake

bhnoneq

Length-based Beverton-Holt Nonequilibrium Z Estimator

bonito

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

Hoenig

Tag Data from Hoenig et al. (1998)

clus.str.lf

Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling

clus.lf

Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling

agesurv

Age-based Survival Estimators

Shepherd

Seasonal Length Frequencies for Raja clavata

Jensen

Age Frequency Data for Lake Whitefish By Individual Haul

agesurvcl

Age-Based Survival and Mortality Estimators for Cluster Sampling

clus.t.test

Correcting a Two-Sample Test for Clustering

alk

Create An Age-Length Key

bt.log

Back-transformation of log-transformed mean and variance

alkD

Sample Size Determination for Age Subsampling Using the D statistic

buffalo

Life Table Data for African Buffalo

counts

Run size data for alewife (Alosa pseudoharengus)

alkdata

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

clus.mean

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

catch

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

catch.select

Selectivity Ogive from a Catch Curve

compare2

Comparisons of two age readers or two aging methods

convmort

Conversion of Mortality Rates

cowcod

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

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

fm_model_avg

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

epr

Eggs-Per-Recruit Analysis

fm_checkdesign

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

cpuekapp

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

deltadist

Delta Distribution Mean and Variance Estimators

dbsra

Depletion-Based Stock Reduction Analysis

fm_telemetry

Estimation of Fishing and Natural Mortality from Telemetry Data

darter

Catch Removal Data For Fantail Darter

Gerking

Mark-Recapture Data for Sunfish in an Indiana Lake

Hightower

Original data used in Hightower et al. (2001)

growth

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

alkprop

Age-Length Key Proportions-At-Age

alkss

Sample Size Determination for Age Subsampling

grotagplus

Flexible maximum likelihood estimation of growth from multiple tagging datasets.

goosefish

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

growhamp

von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation

grotag

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

irm_h

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

kappenman

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

haddock

Biological data for haddock (Melanogrammus aeglefinus)

growthResid

Plot residuals of growth model fitted to tag data

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)

growthTraject

Plot growth trajectories obtained from tagging data

pgen

Probability of a Management Parameter Exceeding a Reference Point

catchmsy

Estimating MSY from catch and resilience

growthlrt

Likelihood Ratio Tests for Comparing Multiple Growth Curves

irm_cr

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

mrN.single

Estimate of Population Size from a Single Mark-Recapture Experiment

catchsurvey

Catch-Survey Analysis

pinfish

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

lifetable

Life Table Construction

lingcod

Catch data (metric tons) for lingcod 1889 to 2001

nshrimp

Data for Gulf of Maine northern shrimp

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.

remp

Random Number Generation from an Empirical Distribution

rig

Tagging data from a growth study of rig

vbfr

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

wolffish

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

opt_slot

Optimum Slot and Trophy Size Limits for Recreational Fisheries

opt_trophy

Optimum Trophy Size Limits for Recreational Fisheries

rockbass

Age Frequency Data for Rock Bass

sbotos

Otolith ages of striped bass made by two age readers

sblen

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

sbpr

Spawning Stock Biomass-Per-Recruit Analysis

surveyref

Quantitative reference points from stock abundance indices based on research surveys

tanaka

Simulated alfonsino data for Tanaka (2006

mort.al

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

tag_model_avg

Model Averaging for Instantaneous Rates Tag Return Models

deplet

Catch-Effort Depletion Methods For a Closed Population

dlproj

This function performs projections for dbsra and catchmsy objects

trout

Mark-recapture data for Kenai River trout trout

yellowtail

Fall average catch per tow for southern New England yellowtail flounder

schnabel

Population Size Estimates from Repeated Mark-Recapture Experiments

slca

A Weakly Parametric Method for the Analysis of Length Composition Data

fpc

Fishing Power Correction Factor from Experimental Fishing

Estimation and Model Comparison of Stock-Recruitment Relationships

growthmultifit

Fit a Multi-Group Growth Model

plot.grotagplus

Plotting Tagging-Growth Objects

growtrans

Growth Transition Matrix for a Size-Structured Population Dynamics Model

ypr

Yield-Per-Recruit Analysis

powertrend

Power Analysis For Detecting Trends

pwpop

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

striper

Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass

surveyfit

Estimating the Relative Abundance of Fish From a Trawl Survey

Z-transform or center a time series

print.grotagplus

Printing Tagging-Growth Objects

astrocalc4r

Solar zenith angles for biological research

bheq

Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator

P.donacina

Data from a growth study of New Zealand intertidal clams.