fishmethods: Fishery Science Methods and Models in R
Version 1.10-2

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

AuthorGary A. Nelson <gary.nelson@state.ma.us>
Date of publication2017-05-19 18:37:51 UTC
MaintainerGary A. Nelson <gary.nelson@state.ma.us>
LicenseGPL (>= 2)
Version1.10-2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("fishmethods")

Popular man pages

bt.log: Back-transformation of log-transformed mean and variance
clus.mean: Estimation of Population Attributes and Effective Sample Size...
growth: Fitting Growth Curves to Length- or Weight-at-Age Data
vbfr: Francis' re-parameterization of the von Bertalanffy growth...
vblrt: Likelihood Ratio Tests for Comparing Multiple von Bertalanffy...
vbmultifit: Fit a Multi-Group von Bertalanffy Growth Model
ypr: Yield-Per-Recruit Analysis
See all...

All man pages Function index File listing

Man pages

agesurv: Age-based Survival Estimators
agesurvcl: Age-Based Survival and Mortality Estimators for Cluster...
alk: Create An Age-Length Key
alkD: Sample Size Determination for Age Subsampling Using the D...
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
bheq: Length-based Beverton-Holt Equilibrium Total Instantaneous...
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
catch: Number of cod captured in 10 standardized bottom trawl hauls...
catchmsy: Estimating MSY from catch and resilience
catch.select: Selectivity Ogive from a Catch Curve
catchsurvey: Catch-Survey Analysis
clus.lf: Statistical Comparison of Length Frequencies from Simple...
clus.mean: Estimation of Population Attributes and Effective Sample Size...
clus.rho: Intracluster Correlation Coefficients for Clustered Data
clus.rho.g: Calculate A Common Intracluster Correlation Coefficient Among...
clus.str.lf: Statistical Comparison of Length Frequencies from Stratified...
clus.t.test: Correcting a Two-Sample Test for Clustering
clus.vb.fit: Fit a Von Bertalanffy growth equation to clustered data via...
codcluslen: Lengths of Atlantic cod caught during Massachusetts Division...
codstrcluslen: Lengths of Atlantic cod caught during Massachusetts Division...
combinevar: Combining Mean and Variances from Multiple Samples
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...
cpuekapp: Trawl survey based abundance estimation using data sets with...
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...
epr: Eggs-Per-Recruit Analysis
fm_checkdesign: Check parameter structure of Hightower et al. (2001) models
fm_model_avg: Model Averaging for the Telemetry Method of Hightower et al....
fm_telemetry: Estimation of Fishing and Natural Mortality from Telemetry...
gap: Tukey's Gapping
Gerking: Mark-Recapture Data for Sunfish in an Indiana Lake
goosefish: Mean Length and Numbers of Lengths for Northern Goosefish,...
grotag: Maximum likelihood estimation of growth and growth...
growhamp: von Bertalanffy Growth Models for Tagging Data Incorporating...
growth: Fitting Growth Curves to Length- or Weight-at-Age Data
growthResid: Plot residuals of growth model fitted to tag data
growthTraject: Plot growth trajectories obtained from tagging data
growtrans: Growth Transition Matrix for a Size-Structured Population...
haddock: Biological data for haddock (Melanogrammus aeglefinus)
Hightower: Original data used in Hightower et al. (2001)
Hoenig: Tag Data from Hoenig et al. (1998)
irm_cr: Age-Independent Instantaneous Rates Model of Jiang et al....
irm_h: Age-Independent Instantaneous Rates Tag Return Model of...
Jensen: Age Frequency Data for Lake Whitefish By Individual Haul
Jiang: Tag Data from Jiang (2005)
kappenman: Pacific cod catch per effort from Table 1 in Kappenman (1999)
Kimura: Length and Age Data For Male and Female Pacific Hake
lifetable: Life Table Construction
lingcod: Catch data (metric tons) for lingcod 1889 to 2001
maki: Data from Maki et al. 2001
mature: Estimation of proportion mature at age when immature fish are...
M.empirical: Estimation of Natural Mortality Rates from Life History...
menhaden: Biological data for menhaden (Brevoortia tyrannus)
mort.al: Estimation of Mortality using Times-At-Large Data from...
mrN.single: Estimate of Population Size from a Single Mark-Recapture...
nshrimp: Data for Gulf of Maine northern shrimp
opt_slot: Optimum Slot and Trophy Size Limits for Recreational...
opt_trophy: Optimum Trophy Size Limits for Recreational Fisheries
pgen: Probability of a Management Parameter Exceeding a Reference...
pinfish: Length, age and sex data for pinfish (Lagodon rhomboides)...
powertrend: Power Analysis For Detecting Trends
pwpop: Estimate Net Reproductive Rates Over Multiple Periods Of An...
remp: Random Number Generation from an Empirical Distribution
rockbass: Age Frequency Data for Rock Bass
sblen: Total length (inches) of striped bass collected by...
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...
Shepherd: Seasonal Length Frequencies for Raja clavata
slca: A Weakly Parametric Method for the Analysis of Length...
surveyfit: Estimating the Relative Abundance of Fish From a Trawl Survey
surveyref: Quantitative reference points from stock abundance indices...
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
vbfr: Francis' re-parameterization of the von Bertalanffy growth...
vblrt: Likelihood Ratio Tests for Comparing Multiple von Bertalanffy...
vbmultifit: Fit a Multi-Group von Bertalanffy Growth Model
wolffish: Spring untransformed mean catch per tow for wolffish...
yellowtail: Fall average catch per tow for southern New England...
ypr: Yield-Per-Recruit Analysis
zt: Z-transform or center a time series

Functions

Gerking Man page
Hightower Man page
Hoenig Man page
Jensen Man page
Jiang Man page
Kimura Man page
M.empirical Man page Source code
Shepherd Man page
agesurv Man page Source code
agesurvcl Man page Source code
alk Man page Source code
alkD Man page Source code
alkdata Man page
alkprop Man page Source code
alkss Man page Source code
astrocalc4r Man page Source code
bheq Man page Source code
bhnoneq Man page Source code
bonito Man page
bt.log Man page Source code
buffalo Man page
catch Man page
catch.select Man page Source code
catchmsy Man page Source code
catchsurvey Man page Source code
clus.lf Man page Source code
clus.mean Man page Source code
clus.rho Man page Source code
clus.rho.g Man page Source code
clus.str.lf Man page Source code
clus.t.test Man page Source code
clus.vb.fit Man page Source code
codcluslen Man page
codstrcluslen Man page
combinevar Man page Source code
compare2 Man page Source code
convmort Man page Source code
counts Man page
cowcod Man page
cpuekapp Man page Source code
darter Man page
dbsra Man page Source code
deltadist Man page Source code
deplet Man page Source code
dlproj Man page Source code
epr Man page Source code
fm_checkdesign Man page Source code
fm_model_avg Man page Source code
fm_telemetry Man page Source code
gap Man page Source code
goosefish Man page
grotag Man page Source code
growhamp Man page Source code
growth Man page Source code
growthResid Man page Source code
growthTraject Man page Source code
growtrans Man page Source code
haddock Man page
irm_cr Man page Source code
irm_h Man page Source code
kappenman Man page
lifetable Man page Source code
lingcod Man page
maki Man page
mature Man page Source code
menhaden Man page
mort.al Man page Source code
mrN.single Man page Source code
nshrimp Man page Man page
opt_slot Man page Source code
opt_trophy Man page Source code
pgen Man page Source code
pinfish Man page
powertrend Man page Source code
pwpop Man page Source code
remp Man page Source code
rockbass Man page
sblen Man page
sbotos Man page
sbpr Man page Source code
schnabel Man page Source code
slca Man page Source code
surveyfit Man page Source code
surveyref Man page Source code
tag_model_avg Man page Source code
tanaka Man page
trout Man page
vbfr Man page Source code
vblrt Man page Source code
vbmultifit Man page Source code
wolffish Man page
yellowtail Man page
ypr Man page Source code
zt Man page Source code

Files

NAMESPACE
data
data/sblen.rda
data/kappenman.rda
data/buffalo.rda
data/catch.rda
data/Jensen.rda
data/bonito.rda
data/codcluslen.rda
data/Hightower.rda
data/cowcod.rda
data/trout.rda
data/nshrimp.rda
data/rockbass.rda
data/tanaka.rda
data/Shepherd.rda
data/codstrcluslen.rda
data/haddock.rda
data/Hoenig.rda
data/darter.rda
data/sbotos.rda
data/yellowtail.rda
data/pinfish.rda
data/counts.rda
data/lingcod.rda
data/Gerking.rda
data/wolffish.rda
data/menhaden.rda
data/Jiang.rda
data/goosefish.rda
data/alkdata.rda
data/Kimura.rda
data/maki.rda
R
R/catchmsy.R
R/remp.R
R/catchsurvey.R
R/fm_telemetry.R
R/growthTraject.R
R/alkss.R
R/combinevar.R
R/clus.t.test.R
R/growhamp.R
R/alkprop.R
R/lifetable.R
R/M.empirical.R
R/surveyfit.R
R/deltadist.R
R/surveyref.R
R/dbsra.R
R/powertrend.R
R/growthResid.R
R/astrocalc4r.R
R/bt.log.R
R/agesurvcl.R
R/deplet.R
R/schnabel.R
R/slca.R
R/clus.rho.R
R/clus.mean.R
R/zt.R
R/pgen.R
R/grotag.R
R/sbpr.R
R/catch.select.R
R/vblrt.R
R/irm_cr.R
R/fm_model_avg.R
R/bheq.R
R/clus.vb.fit.R
R/compare2.R
R/vbfr.R
R/mort.al.R
R/pwpop.R
R/growtrans.R
R/opt_trophy.R
R/clus.str.lf.R
R/growth.R
R/gap.R
R/bhnoneq.R
R/opt_slot.R
R/alk.R
R/vbmultifit.R
R/alkD.R
R/clus.rho.g.R
R/mature.R
R/dlproj.R
R/epr.R
R/irm_h.R
R/cpuekapp.R
R/convmort.R
R/fm_checkdesign.R
R/mrN.single.R
R/agesurv.R
R/ypr.R
R/clus.lf.R
R/tag_model_avg.R
MD5
DESCRIPTION
man
man/agesurv.Rd
man/catchmsy.Rd
man/haddock.Rd
man/alkprop.Rd
man/astrocalc4r.Rd
man/irm_cr.Rd
man/fm_checkdesign.Rd
man/lingcod.Rd
man/buffalo.Rd
man/goosefish.Rd
man/ypr.Rd
man/pinfish.Rd
man/darter.Rd
man/maki.Rd
man/mort.al.Rd
man/clus.vb.fit.Rd
man/dlproj.Rd
man/surveyfit.Rd
man/Jensen.Rd
man/slca.Rd
man/mature.Rd
man/wolffish.Rd
man/vbfr.Rd
man/clus.str.lf.Rd
man/zt.Rd
man/cpuekapp.Rd
man/alkss.Rd
man/cowcod.Rd
man/nshrimp.Rd
man/epr.Rd
man/bt.log.Rd
man/compare2.Rd
man/counts.Rd
man/tanaka.Rd
man/clus.rho.Rd
man/deltadist.Rd
man/codstrcluslen.Rd
man/Gerking.Rd
man/Kimura.Rd
man/powertrend.Rd
man/growhamp.Rd
man/convmort.Rd
man/Hoenig.Rd
man/alkdata.Rd
man/agesurvcl.Rd
man/trout.Rd
man/pgen.Rd
man/yellowtail.Rd
man/sblen.Rd
man/catch.Rd
man/Jiang.Rd
man/alk.Rd
man/growthResid.Rd
man/irm_h.Rd
man/gap.Rd
man/vblrt.Rd
man/growth.Rd
man/bhnoneq.Rd
man/growthTraject.Rd
man/grotag.Rd
man/M.empirical.Rd
man/Shepherd.Rd
man/clus.rho.g.Rd
man/rockbass.Rd
man/Hightower.Rd
man/fm_model_avg.Rd
man/pwpop.Rd
man/alkD.Rd
man/opt_trophy.Rd
man/surveyref.Rd
man/remp.Rd
man/menhaden.Rd
man/tag_model_avg.Rd
man/catch.select.Rd
man/mrN.single.Rd
man/lifetable.Rd
man/sbotos.Rd
man/opt_slot.Rd
man/schnabel.Rd
man/fm_telemetry.Rd
man/vbmultifit.Rd
man/clus.mean.Rd
man/dbsra.Rd
man/catchsurvey.Rd
man/clus.t.test.Rd
man/combinevar.Rd
man/sbpr.Rd
man/bheq.Rd
man/clus.lf.Rd
man/deplet.Rd
man/kappenman.Rd
man/codcluslen.Rd
man/growtrans.Rd
man/bonito.Rd
fishmethods documentation built on May 23, 2017, 9:12 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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