fishmethods v1.10-4

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Fishery Science Methods and Models in R

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

Functions in fishmethods

Name Description
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)
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Date 2017-10-16
License GPL (>= 2)
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-10-16 17:46:20 UTC; gnelson
Repository CRAN
Date/Publication 2017-10-16 18:00:09 UTC

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