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fishmethods (version 1.10-4)

Fishery Science Methods and Models in R

Description

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

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Install

install.packages('fishmethods')

Monthly Downloads

1,166

Version

1.10-4

License

GPL (>= 2)

Maintainer

Gary A Nelson

Last Published

October 16th, 2017

Functions in fishmethods (1.10-4)

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)