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fishmethods (version 1.11-2)
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
1,123
Version
1.11-2
License
GPL (>= 2)
Maintainer
Gary Nelson
Last Published
July 16th, 2021
Functions in fishmethods (1.11-2)
Search functions
Hoenig
Tag Data from Hoenig et al. (1998)
Shepherd
Seasonal Length Frequencies for Raja clavata
M.empirical
Estimation of Natural Mortality Rates from Life History Parameters
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
Jensen
Age Frequency Data for Lake Whitefish By Individual Haul
P.donacina
Data from a growth study of New Zealand intertidal clams.
Jiang
Tag Data from Jiang (2005)
bhnoneq
Length-based Beverton-Holt Nonequilibrium Z Estimator
alk
Create An Age-Length Key
bonito
Data from an age and growth study of the pacific bonito.
catchmsy
Estimating MSY from catch and resilience
catchsurvey
Catch-Survey Analysis
astrocalc4r
Solar zenith angles for biological research
clus.rho
Intracluster Correlation Coefficients for Clustered Data
bheq
Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator
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
growtrans
Growth Transition Matrix for a Size-Structured Population Dynamics Model
menhaden
Biological data for menhaden (Brevoortia tyrannus)
growhamp
von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation
growthmultifit
Fit a Multi-Group Growth Model
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
alkD
Sample Size Determination for Age Subsampling Using the D statistic
rockbass
Age Frequency Data for Rock Bass
mort.al
Estimation of Mortality using Times-At-Large Data from Tagging
cowcod
Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008
compare2
Comparisons of two age readers or two aging methods
sole
Flathead sole CPUEs
sr
Estimation and Model Comparison of Stock-Recruitment Relationships
clus.rho.g
Calculate A Common Intracluster Correlation Coefficient Among Groups
clus.lf
Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling
Kimura
Length and Age Data For Male and Female Pacific Hake
sblen
Total length (inches) of striped bass collected by Massachusetts volunteer anglers in 2014
alkprop
Age-Length Key Proportions-At-Age
goosefish
Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002
combinevar
Combining Mean and Variances from Multiple Samples
grotag
Maximum likelihood estimation of growth and growth variability from tagging data - Francis (1988)
alkdata
Age-Length Key for Gulf of Hauraki snapper, 1992-1993
convmort
Conversion of Mortality Rates
yellowtail
Fall average catch per tow for southern New England yellowtail flounder
clus.mean
Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Sampling
deplet
Catch-Effort Depletion Methods For a Closed Population
sbotos
Otolith ages of striped bass made by two age readers
counts
Run size data for alewife (
Alosa pseudoharengus
)
alkss
Sample Size Determination for Age Subsampling
fm_checkdesign
Check parameter structure of Hightower et al. (2001) models
gap
Tukey's Gapping
darter
Catch Removal Data For Fantail Darter
cpuekapp
Trawl survey based abundance estimation using data sets with unusually large catches
opt_trophy
Optimum Trophy Size Limits for Recreational Fisheries
catch
Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985
zt
Z-transform or center a time series
opt_slot
Optimum Slot and Trophy Size Limits for Recreational Fisheries
dlproj
This function performs projections for dbsra and catchmsy objects
pgen
Probability of a Management Parameter Exceeding a Reference Point
growthlrt
Likelihood Ratio Tests for Comparing Multiple Growth Curves
catch.select
Selectivity Ogive from a Catch Curve
vbfr
Francis' re-parameterization of the von Bertalanffy growth equation for length-age data
growthTraject
Plot growth trajectories obtained from tagging data
powertrend
Power Analysis For Detecting Trends
clus.str.lf
Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
mature
Estimation of proportion mature at age when immature fish are unavailable
bt.log
Back-transformation of log-transformed mean and variance
grotagplus
Flexible maximum likelihood estimation of growth from multiple tagging datasets.
lifetable
Life Table Construction
lingcod
Catch data (metric tons) for lingcod 1889 to 2001
irm_cr
Age-Independent Instantaneous Rates Model of Jiang et al. (2007) Incorporating Catch and Release Tag Returns
epr
Eggs-Per-Recruit Analysis
haddock
Biological data for haddock (Melanogrammus aeglefinus)
irm_h
Age-Independent Instantaneous Rates Tag Return Model of Hoenig et al. (1998)
nshrimp
Data for Gulf of Maine northern shrimp
clus.t.test
Correcting a Two-Sample Test for Clustering
mrN.single
Estimate of Population Size from a Single Mark-Recapture Experiment
kappenman
Pacific cod catch per effort from Table 1 in Kappenman (1999)
growth
Fitting Growth Curves to Length- or Weight-at-Age Data
buffalo
Life Table Data for African Buffalo
codstrcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985.
growthResid
Plot residuals of growth model fitted to tag data
deltadist
Delta Distribution Mean and Variance Estimators
print.grotagplus
Printing Tagging-Growth Objects
tanaka
Simulated alfonsino data for Tanaka (2006
schnabel
Population Size Estimates from Repeated Mark-Recapture Experiments
dbsra
Depletion-Based Stock Reduction Analysis
fpc
Fishing Power Correction Factor from Experimental Fishing
maki
Data from Maki et al. 2001
pinfish
Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida
surveyref
Quantitative reference points from stock abundance indices based on research surveys
surveyfit
Estimating the Relative Abundance of Fish From a Trawl Survey
ypr
Yield-Per-Recruit Analysis
sbpr
Spawning Stock Biomass-Per-Recruit Analysis
remp
Random Number Generation from an Empirical Distribution
striper
Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
pwpop
Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression
wolffish
Spring untransformed mean catch per tow for wolffish (Anarhichas lupus)
trout
Mark-recapture data for Kenai River trout trout
plot.grotagplus
Plotting Tagging-Growth Objects
slca
A Weakly Parametric Method for the Analysis of Length Composition Data
rig
Tagging data from a growth study of rig
tag_model_avg
Model Averaging for Instantaneous Rates Tag Return Models