fishmethods: Fishery Science Methods and Models in R

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

Author
Gary A. Nelson <gary.nelson@state.ma.us>
Date of publication
2016-09-20 02:54:05
Maintainer
Gary A. Nelson <gary.nelson@state.ma.us>
License
GPL (>= 2)
Version
1.10-0

View on CRAN

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
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 Two von Bertalanffy...
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

Files in this package

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