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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Details
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 |
depends | boot , bootstrap , lme4 , MASS , numDeriv , R (>= 2.7.0) |
Contributors | Gary A Nelson |
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