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fishmethods (version 1.10-4)
Fishery Science Methods and Models in R
Description
Fishery science methods and models from published literature and contributions from colleagues.
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Install
install.packages('fishmethods')
Monthly Downloads
1,429
Version
1.10-4
License
GPL (>= 2)
Maintainer
Gary A Nelson
Last Published
October 16th, 2017
Functions in fishmethods (1.10-4)
Search functions
Jiang
Tag Data from Jiang (2005)
Kimura
Length and Age Data For Male and Female Pacific Hake
Hoenig
Tag Data from Hoenig et al. (1998)
Jensen
Age Frequency Data for Lake Whitefish By Individual Haul
M.empirical
Estimation of Natural Mortality Rates from Life History Parameters
P.donacina
Data from a growth study of New Zealand intertidal clams.
Shepherd
Seasonal Length Frequencies for Raja clavata
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
alk
Create An Age-Length Key
astrocalc4r
Solar zenith angles for biological research
clus.rho
Intracluster Correlation Coefficients for Clustered Data
clus.rho.g
Calculate A Common Intracluster Correlation Coefficient Among Groups
bt.log
Back-transformation of log-transformed mean and variance
buffalo
Life Table Data for African Buffalo
clus.str.lf
Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling
bheq
Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimator
bhnoneq
Length-based Beverton-Holt Nonequilibrium Z Estimator
bonito
Data from an age and growth study of the pacific bonito.
catchmsy
Estimating MSY from catch and resilience
catchsurvey
Catch-Survey Analysis
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)
fm_telemetry
Estimation of Fishing and Natural Mortality from Telemetry Data
growthResid
Plot residuals of growth model fitted to tag data
growthTraject
Plot growth trajectories obtained from tagging data
mature
Estimation of proportion mature at age when immature fish are unavailable
menhaden
Biological data for menhaden (Brevoortia tyrannus)
nshrimp
Data for Gulf of Maine northern shrimp
clus.t.test
Correcting a Two-Sample Test for Clustering
epr
Eggs-Per-Recruit Analysis
fm_checkdesign
Check parameter structure of Hightower et al. (2001) models
opt_slot
Optimum Slot and Trophy Size Limits for Recreational Fisheries
slca
A Weakly Parametric Method for the Analysis of Length Composition Data
sr
Estimation and Model Comparison of Stock-Recruitment Relationships
vbfr
Francis' re-parameterization of the von Bertalanffy growth equation for length-age data
growtrans
Growth Transition Matrix for a Size-Structured Population Dynamics Model
haddock
Biological data for haddock (Melanogrammus aeglefinus)
lingcod
Catch data (metric tons) for lingcod 1889 to 2001
alkprop
Age-Length Key Proportions-At-Age
alkss
Sample Size Determination for Age Subsampling
clus.lf
Statistical Comparison of Length Frequencies from Simple Random Cluster Sampling
clus.mean
Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Sampling
clus.vb.fit
Fit a Von Bertalanffy growth equation to clustered data via bootstrapping
vblrt
Likelihood Ratio Tests for Comparing Multiple von Bertalanffy Growth Curves
maki
Data from Maki et al. 2001
pinfish
Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida
plot.grotagplus
Plotting Tagging-Growth Objects
rig
Tagging data from a growth study of rig
rockbass
Age Frequency Data for Rock Bass
surveyref
Quantitative reference points from stock abundance indices based on research surveys
alkD
Sample Size Determination for Age Subsampling Using the D statistic
alkdata
Age-Length Key for Gulf of Hauraki snapper, 1992-1993
catch
Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985
codcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985.
cpuekapp
Trawl survey based abundance estimation using data sets with unusually large catches
darter
Catch Removal Data For Fantail Darter
growhamp
von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation
growth
Fitting Growth Curves to Length- or Weight-at-Age Data
tag_model_avg
Model Averaging for Instantaneous Rates Tag Return Models
kappenman
Pacific cod catch per effort from Table 1 in Kappenman (1999)
lifetable
Life Table Construction
pwpop
Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression
remp
Random Number Generation from an Empirical Distribution
codstrcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985.
combinevar
Combining Mean and Variances from Multiple Samples
dbsra
Depletion-Based Stock Reduction Analysis
deltadist
Delta Distribution Mean and Variance Estimators
gap
Tukey's Gapping
goosefish
Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002
irm_cr
Age-Independent Instantaneous Rates Model of Jiang et al. (2007) Incorporating Catch and Release Tag Returns
irm_h
Age-Independent Instantaneous Rates Tag Return Model of Hoenig et al. (1998)
catch.select
Selectivity Ogive from a Catch Curve
compare2
Comparisons of two age readers or two aging methods
convmort
Conversion of Mortality Rates
deplet
Catch-Effort Depletion Methods For a Closed Population
dlproj
This function performs projections for dbsra and catchmsy objects
powertrend
Power Analysis For Detecting Trends
print.grotagplus
Printing Tagging-Growth Objects
striper
Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
surveyfit
Estimating the Relative Abundance of Fish From a Trawl Survey
yellowtail
Fall average catch per tow for southern New England yellowtail flounder
grotag
Maximum likelihood estimation of growth and growth variability from tagging data - Francis (1988)
grotagplus
Flexible maximum likelihood estimation of growth from multiple tagging datasets.
mort.al
Estimation of Mortality using Times-At-Large Data from Tagging
mrN.single
Estimate of Population Size from a Single Mark-Recapture Experiment
opt_trophy
Optimum Trophy Size Limits for Recreational Fisheries
pgen
Probability of a Management Parameter Exceeding a Reference Point
sblen
Total length (inches) of striped bass collected by Massachusetts volunteer anglers in 2014
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 Experiments
vbmultifit
Fit a Multi-Group von Bertalanffy Growth Model
ypr
Yield-Per-Recruit Analysis
tanaka
Simulated alfonsino data for Tanaka (2006
trout
Mark-recapture data for Kenai River trout trout
zt
Z-transform or center a time series
wolffish
Spring untransformed mean catch per tow for wolffish (Anarhichas lupus)