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fishmethods (version 1.12-1)
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
1.12-1
License
GPL (>= 2)
Maintainer
Gary Nelson
Last Published
April 27th, 2023
Functions in fishmethods (1.12-1)
Search functions
bheq
Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator
bhnoneq
Length-based Beverton-Holt Nonequilibrium Z Estimator
agesurv
Age-based Survival Estimators
alkD
Sample Size Determination for Age Subsampling Using the D statistic
alkss
Sample Size Determination for Age Subsampling
alkdata
Age-Length Key for Gulf of Hauraki snapper, 1992-1993
agesurvcl
Age-Based Survival and Mortality Estimators for Cluster Sampling
alkprop
Age-Length Key Proportions-At-Age
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.
buffalo
Life Table Data for African Buffalo
catch.select
Selectivity Ogive from a Catch Curve
clus.rho
Intracluster Correlation Coefficients for Clustered Data
clus.mean
Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Sampling
catch
Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985
clus.lf
Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling
bt.log
Back-transformation of log-transformed mean and variance
catchsurvey
Catch-Survey Analysis
catchmsy
Estimating MSY from catch and resilience
clus.t.test
Correcting a Two-Sample Test for Clustering
compare2
Comparisons of two age readers or two aging methods
codcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985.
clus.rho.g
Calculate A Common Intracluster Correlation Coefficient Among Groups
combinevar
Combining Mean and Variances from Multiple Samples
clus.str.lf
Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
compare.lrt.plus
Comparison of growthlrt.plus model objects
clus.vb.fit
Fit a Von Bertalanffy growth equation to clustered data via bootstrapping
deltadist
Delta Distribution Mean and Variance Estimators
codstrcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985.
ep.data
A sub-sample of data from a simulated population collected via length-stratified age sampling
ep_growth
Fitting the von Bertalanffy growth model to length-stratified age samples
dbsra
Depletion-Based Stock Reduction Analysis
deplet
Catch-Effort Depletion Methods For a Closed Population
dlproj
This function performs projections for dbsra and catchmsy objects
cpuekapp
Trawl survey based abundance estimation using data sets with unusually large catches
darter
Catch Removal Data For Fantail Darter
counts
Run size data for alewife (
Alosa pseudoharengus
)
cowcod
Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008
fm_model_avg
Model Averaging for the Telemetry Method of Hightower et al. (2001)
goosefish
Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002
grotagplus
Flexible maximum likelihood estimation of growth from multiple tagging datasets.
fpc
Fishing Power Correction Factor from Experimental Fishing
epr
Eggs-Per-Recruit Analysis
convmort
Conversion of Mortality Rates
gap
Tukey's Gapping
grotag
Maximum likelihood estimation of growth and growth variability from tagging data - Francis (1988)
growhamp
von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation
fm_telemetry
Estimation of Fishing and Natural Mortality from Telemetry Data
growth_sel
Fitting a von Bertalanffy curve to length and age data biased by gear selectivity
growthResid
Plot residuals of growth model fitted to tag data
growthTraject
Plot growth trajectories obtained from tagging data
growth
Fitting Growth Curves to Length- or Weight-at-Age Data
growthlrt.plus
Likelihood Methods for Comparing Multiple Growth Curves
fm_checkdesign
Check parameter structure of Hightower et al. (2001) models
menhaden
Biological data for menhaden (Brevoortia tyrannus)
growthmultifit
Fit a Multi-Group Growth Model
growtrans
Growth Transition Matrix for a Size-Structured Population Dynamics Model
growthlrt
Likelihood Ratio Tests for Comparing Multiple Growth Curves
kappenman
Pacific cod catch per effort from Table 1 in Kappenman (1999)
lifetable
Life Table Construction
irm_h
Age-Independent Instantaneous Rates Tag Return Model of Hoenig et al. (1998)
maki
Data from Maki et al. 2001
haddock
Biological data for haddock (Melanogrammus aeglefinus)
irm_cr
Age-Independent Instantaneous Rates Model of Jiang et al. (2007) Incorporating Catch and Release Tag Returns
mort.al
Estimation of Mortality using Times-At-Large Data from Tagging
mature
Estimation of proportion mature at age when immature fish are unavailable
pgen
Probability of a Management Parameter Exceeding a Reference Point
remp
Random Number Generation from an Empirical Distribution
nshrimp
Data for Gulf of Maine northern shrimp
rig
Tagging data from a growth study of rig
mrN.single
Estimate of Population Size from a Single Mark-Recapture Experiment
pwpop
Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression
print.grotagplus
Printing Tagging-Growth Objects
simulus
Age and size data for the growth_sel function
schnabel
Population Size Estimates from Repeated Mark-Recapture Experiments
sr
Estimation and Model Comparison of Stock-Recruitment Relationships
rockbass
Age Frequency Data for Rock Bass
sblen
Total length (inches) of striped bass collected by Massachusetts volunteer anglers in 2014
vbfr
Francis' re-parameterization of the von Bertalanffy growth equation for length-age data
striper
Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
trout
Mark-recapture data for Kenai River trout trout
pinfish
Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida
ypr
Yield-Per-Recruit Analysis
surveyref
Quantitative reference points from stock abundance indices based on research surveys
zt
Z-transform or center a time series
surveyfit
Estimating the Relative Abundance of Fish From a Trawl Survey
lingcod
Catch data (metric tons) for lingcod 1889 to 2001
slca
A Weakly Parametric Method for the Analysis of Length Composition Data
opt_slot
Optimum Slot and Trophy Size Limits for Recreational Fisheries
opt_trophy
Optimum Trophy Size Limits for Recreational Fisheries
wolffish
Spring untransformed mean catch per tow for wolffish (Anarhichas lupus)
yellowtail
Fall average catch per tow for southern New England yellowtail flounder
powertrend
Power Analysis For Detecting Trends
sole
Flathead sole CPUEs
plot.grotagplus
Plotting Tagging-Growth Objects
tanaka
Simulated alfonsino data for Tanaka (2006
tag_model_avg
Model Averaging for Instantaneous Rates Tag Return Models
sbotos
Otolith ages of striped bass made by two age readers
sbpr
Spawning Stock Biomass-Per-Recruit Analysis
Hightower
Original data used in Hightower et al. (2001)
Jiang
Tag Data from Jiang (2005)
Shepherd
Seasonal Length Frequencies for Raja clavata
Gerking
Mark-Recapture Data for Sunfish in an Indiana Lake
AtkaMack
Length and Age Data For Male and Female Atka Mackerel
Hoenig
Tag Data from Hoenig et al. (1998)
P.donacina
Data from a growth study of New Zealand intertidal clams.
Jensen
Age Frequency Data for Lake Whitefish By Individual Haul
Kimura
Length and Age Data For Male and Female Pacific Hake
M.empirical
Estimation of Natural Mortality Rates from Life History Parameters