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fishmethods (version 1.12-0)
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
1,012
Version
1.12-0
License
GPL (>= 2)
Maintainer
Gary Nelson
Last Published
January 25th, 2023
Functions in fishmethods (1.12-0)
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P.donacina
Data from a growth study of New Zealand intertidal clams.
Hightower
Original data used in Hightower et al. (2001)
Gerking
Mark-Recapture Data for Sunfish in an Indiana Lake
Shepherd
Seasonal Length Frequencies for Raja clavata
M.empirical
Estimation of Natural Mortality Rates from Life History Parameters
alk
Create An Age-Length Key
astrocalc4r
Solar zenith angles for biological research
bonito
Data from an age and growth study of the pacific bonito.
alkD
Sample Size Determination for Age Subsampling Using the D statistic
alkprop
Age-Length Key Proportions-At-Age
alkss
Sample Size Determination for Age Subsampling
agesurvcl
Age-Based Survival and Mortality Estimators for Cluster Sampling
bhnoneq
Length-based Beverton-Holt Nonequilibrium Z Estimator
alkdata
Age-Length Key for Gulf of Hauraki snapper, 1992-1993
bheq
Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator
clus.rho
Intracluster Correlation Coefficients for Clustered Data
catchmsy
Estimating MSY from catch and resilience
clus.lf
Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling
bt.log
Back-transformation of log-transformed mean and variance
catch
Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985
buffalo
Life Table Data for African Buffalo
compare2
Comparisons of two age readers or two aging methods
clus.mean
Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Sampling
counts
Run size data for alewife (
Alosa pseudoharengus
)
combinevar
Combining Mean and Variances from Multiple Samples
codstrcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985.
clus.rho.g
Calculate A Common Intracluster Correlation Coefficient Among Groups
catch.select
Selectivity Ogive from a Catch Curve
convmort
Conversion of Mortality Rates
catchsurvey
Catch-Survey Analysis
codcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985.
clus.vb.fit
Fit a Von Bertalanffy growth equation to clustered data via bootstrapping
cowcod
Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008
clus.t.test
Correcting a Two-Sample Test for Clustering
clus.str.lf
Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
deplet
Catch-Effort Depletion Methods For a Closed Population
ep.data
A sub-sample of data from a simulated population collected via length-stratified age sampling
darter
Catch Removal Data For Fantail Darter
deltadist
Delta Distribution Mean and Variance Estimators
dbsra
Depletion-Based Stock Reduction Analysis
fm_checkdesign
Check parameter structure of Hightower et al. (2001) models
epr
Eggs-Per-Recruit Analysis
ep_growth
Fitting the von Bertalanffy growth model to length-stratified age samples
cpuekapp
Trawl survey based abundance estimation using data sets with unusually large catches
dlproj
This function performs projections for dbsra and catchmsy objects
fm_telemetry
Estimation of Fishing and Natural Mortality from Telemetry Data
growhamp
von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation
fpc
Fishing Power Correction Factor from Experimental Fishing
fm_model_avg
Model Averaging for the Telemetry Method of Hightower et al. (2001)
grotagplus
Flexible maximum likelihood estimation of growth from multiple tagging datasets.
gap
Tukey's Gapping
goosefish
Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002
grotag
Maximum likelihood estimation of growth and growth variability from tagging data - Francis (1988)
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
lingcod
Catch data (metric tons) for lingcod 1889 to 2001
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)
growtrans
Growth Transition Matrix for a Size-Structured Population Dynamics Model
haddock
Biological data for haddock (Melanogrammus aeglefinus)
lifetable
Life Table Construction
irm_cr
Age-Independent Instantaneous Rates Model of Jiang et al. (2007) Incorporating Catch and Release Tag Returns
growthmultifit
Fit a Multi-Group Growth Model
growthlrt
Likelihood Ratio Tests for Comparing Multiple Growth Curves
pinfish
Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida
maki
Data from Maki et al. 2001
mature
Estimation of proportion mature at age when immature fish are unavailable
pgen
Probability of a Management Parameter Exceeding a Reference Point
menhaden
Biological data for menhaden (Brevoortia tyrannus)
opt_slot
Optimum Slot and Trophy Size Limits for Recreational Fisheries
opt_trophy
Optimum Trophy Size Limits for Recreational Fisheries
mrN.single
Estimate of Population Size from a Single Mark-Recapture Experiment
mort.al
Estimation of Mortality using Times-At-Large Data from Tagging
plot.grotagplus
Plotting Tagging-Growth Objects
nshrimp
Data for Gulf of Maine northern shrimp
pwpop
Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression
print.grotagplus
Printing Tagging-Growth Objects
powertrend
Power Analysis For Detecting Trends
sbotos
Otolith ages of striped bass made by two age readers
rig
Tagging data from a growth study of rig
sbpr
Spawning Stock Biomass-Per-Recruit Analysis
remp
Random Number Generation from an Empirical Distribution
surveyfit
Estimating the Relative Abundance of Fish From a Trawl Survey
striper
Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
tanaka
Simulated alfonsino data for Tanaka (2006
trout
Mark-recapture data for Kenai River trout trout
schnabel
Population Size Estimates from Repeated Mark-Recapture Experiments
slca
A Weakly Parametric Method for the Analysis of Length Composition Data
yellowtail
Fall average catch per tow for southern New England yellowtail flounder
rockbass
Age Frequency Data for Rock Bass
sblen
Total length (inches) of striped bass collected by Massachusetts volunteer anglers in 2014
wolffish
Spring untransformed mean catch per tow for wolffish (Anarhichas lupus)
tag_model_avg
Model Averaging for Instantaneous Rates Tag Return Models
ypr
Yield-Per-Recruit Analysis
surveyref
Quantitative reference points from stock abundance indices based on research surveys
sr
Estimation and Model Comparison of Stock-Recruitment Relationships
sole
Flathead sole CPUEs
zt
Z-transform or center a time series
vbfr
Francis' re-parameterization of the von Bertalanffy growth equation for length-age data
Kimura
Length and Age Data For Male and Female Pacific Hake
agesurv
Age-based Survival Estimators
Hoenig
Tag Data from Hoenig et al. (1998)
Jiang
Tag Data from Jiang (2005)
Jensen
Age Frequency Data for Lake Whitefish By Individual Haul