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fishmethods (version 1.9-0)

Fishery Science Methods and Models in R

Description

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

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Version

Install

install.packages('fishmethods')

Monthly Downloads

1,326

Version

1.9-0

License

GPL (>= 2)

Maintainer

Gary A Nelson

Last Published

October 9th, 2015

Functions in fishmethods (1.9-0)

Kimura

Length and Age Data For Male and Female Pacific Hake
M.empirical

Estimation of Natural Mortality Rates from Life History Parameters
bheq1

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

Length-based Beverton-Holt Nonequilibrium Z Estimator
astrocalc4r

Solar zenith angles for biological research
combinevar

Combining Mean and Variances from Multiple Samples
epr

Eggs-Per-Recruit Analysis
bheq2

Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator with Bias-Correction
clus.t.test

Correcting a Two-Sample Test for Clustering
alkprop

Age-Length Key Proportions-At-Age
darter

Catch Removal Data For Fantail Darter
alkdata

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

Tag Data from Jiang (2005)
agesurv

Age-based Survival Estimators
alk

Create An Age-Length Key
agesurvcl

Age-Based Survival and Mortality Estimators for Cluster Sampling
gap

Tukey's Gapping
cowcod

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

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

Estimating the Relative Abundance of Fish From a Trawl Survey
catchsurvey

Catch-Survey Analysis
growthTraject

Plot growth trajectories obtained from tagging data
clus.rho

Intracluster Correlation Coefficients for Clustered Data
tanaka

Simulated alfonsino data for Tanaka (2006
sbotos

Otolith ages of striped bass made by two age readers
schnabel

Population Size Estimates from Repeated Mark-Recapture Experiments
vbfr

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

Seasonal Length Frequencies for Raja clavata
alkD

Sample Size Determination for Age Subsampling Using the D statistic
Jensen

Age Frequency Data for Lake Whitefish By Individual Haul
pgen

Probability of a Management Parameter Exceeding a Reference Point
catch

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

Run size data for alewife (Alosa pseudoharengus)
kappenman

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

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

Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
clus.rho.g

Calculate A Common Intracluster Correlation Coefficient Among Groups
sbpr

Spawning Stock Biomass-Per-Recruit Analysis
zt

Z-transform or center a time series
dbsra

Depletion-Based Stock Reduction Analysis
catchmsy

Estimating MSY from catch and resilience
compare2

Comparisons of two age readers or two aging methods
cpuekapp

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

Catch-Effort Depletion Methods For a Closed Population
alkss

Sample Size Determination for Age Subsampling
convmort

Conversion of Mortality Rates
lifetable

Life Table Construction
bt.log

Back-transformation of log-transformed mean and variance
Gerking

Mark-Recapture Data for Sunfish in an Indiana Lake
nshrimp

Data for Gulf of Maine northern shrimp
clus.mean

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

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

Yield-Per-Recruit Analysis
clus.lf

Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling
powertrend

Power Analysis For Detecting Trends
dlproj

This function performs projections for dbsra and catchmsy objects
buffalo

Life Table Data for African Buffalo
rockbass

Age Frequency Data for Rock Bass
mort.al

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

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

Delta Distribution Mean and Variance Estimators
goosefish

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

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

Plot residuals of growth model fitted to tag data
Hoenig

Tag Data from Hoenig et al. (1998)
haddock

Biological data for haddock (Melanogrammus aeglefinus)
growtrans

Growth Transition Matrix for a Size-Structured Population Dynamics Model
opt_trophy

Optimum Trophy Size Limits for Recreational Fisheries
yellowtail

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

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

Random Number Generation from an Empirical Distribution
codcluslen

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

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

Model Averaging for Instantaneous Rates Tag Return Models
pwpop

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

Estimate of Population Size from a Single Mark-Recapture Experiment
irm_cr

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

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

Fit a Von Bertalanffy growth equation to clustered data via bootstrapping
surveyref

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

Optimum Slot and Trophy Size Limits for Recreational Fisheries
vblrt

Likelihood Ratio Tests for Comparing Two von Bertalanffy Growth Curves
menhaden

Biological data for menhaden (Brevoortia tyrannus)
slca

A Weakly Parametric Method for the Analysis of Length Composition Data