Fishery Science Methods and Models
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Documentation for package ‘fishmethods’ version 1.12-0
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A B C D E F G H I J K L M N O P R S T V W Y Z
-- A --
| agesurv | Age-based Survival Estimators |
| agesurvcl | Age-Based Survival and Mortality Estimators for Cluster Sampling |
| alk | Create An Age-Length Key |
| alkD | Sample Size Determination for Age Subsampling Using the D statistic |
| alkdata | Age-Length Key for Gulf of Hauraki snapper, 1992-1993 |
| alkprop | Age-Length Key Proportions-At-Age |
| alkss | Sample Size Determination for Age Subsampling |
| astrocalc4r | Solar zenith angles for biological research |
-- B --
| 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. |
| bt.log | Back-transformation of log-transformed mean and variance |
| buffalo | Life Table Data for African Buffalo |
-- C --
| catch | Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985 |
| catch.select | Selectivity Ogive from a Catch Curve |
| catchmsy | Estimating MSY from catch and resilience |
| catchsurvey | Catch-Survey Analysis |
| 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.rho | Intracluster Correlation Coefficients for Clustered Data |
| clus.rho.g | Calculate A Common Intracluster Correlation Coefficient Among Groups |
| clus.str.lf | Statistical Comparison of Length Frequencies from Stratified Random Cluster Sampling |
| clus.t.test | Correcting a Two-Sample Test for Clustering |
| clus.vb.fit | Fit a Von Bertalanffy growth equation to clustered data via bootstrapping |
| codcluslen | Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985. |
| 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 |
| compare2 | Comparisons of two age readers or two aging methods |
| convmort | Conversion of Mortality Rates |
| counts | Run size data for alewife (_Alosa pseudoharengus_) |
| cowcod | Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008 |
| cpuekapp | Trawl survey based abundance estimation using data sets with unusually large catches |
-- D --
| darter | Catch Removal Data For Fantail Darter |
| dbsra | Depletion-Based Stock Reduction Analysis |
| deltadist | Delta Distribution Mean and Variance Estimators |
| deplet | Catch-Effort Depletion Methods For a Closed Population |
| dlproj | This function performs projections for dbsra and catchmsy objects |
-- E --
| ep.data | A sub-sample of data from a simulated population collected via length-stratified age sampling |
| epr | Eggs-Per-Recruit Analysis |
| ep_growth | Fitting the von Bertalanffy growth model to length-stratified age samples |
-- F --
| fm_checkdesign | Check parameter structure of Hightower et al. (2001) models |
| 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 |
| fpc | Fishing Power Correction Factor from Experimental Fishing |
-- G --
| gap | Tukey's Gapping |
| Gerking | Mark-Recapture Data for Sunfish in an Indiana Lake |
| goosefish | Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002 |
| 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. |
| growhamp | von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variation |
| growth | Fitting Growth Curves to Length- or Weight-at-Age Data |
| growthlrt | Likelihood Ratio Tests for Comparing Multiple Growth Curves |
| growthmultifit | Fit a Multi-Group Growth Model |
| growthResid | Plot residuals of growth model fitted to tag data |
| growthTraject | Plot growth trajectories obtained from tagging data |
| growtrans | Growth Transition Matrix for a Size-Structured Population Dynamics Model |
-- H --
| haddock | Biological data for haddock (Melanogrammus aeglefinus) |
| Hightower | Original data used in Hightower et al. (2001) |
| Hoenig | Tag Data from Hoenig et al. (1998) |
-- I --
| 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) |
-- J --
| Jensen | Age Frequency Data for Lake Whitefish By Individual Haul |
| Jiang | Tag Data from Jiang (2005) |
-- K --
| kappenman | Pacific cod catch per effort from Table 1 in Kappenman (1999) |
| Kimura | Length and Age Data For Male and Female Pacific Hake |
-- L --
| lifetable | Life Table Construction |
| lingcod | Catch data (metric tons) for lingcod 1889 to 2001 |
-- M --
| M.empirical | Estimation of Natural Mortality Rates from Life History Parameters |
| maki | Data from Maki et al. 2001 |
| mature | Estimation of proportion mature at age when immature fish are unavailable |
| menhaden | Biological data for menhaden (Brevoortia tyrannus) |
| mort.al | Estimation of Mortality using Times-At-Large Data from Tagging |
| mrN.single | Estimate of Population Size from a Single Mark-Recapture Experiment |
-- N --
| nshrimp | Data for Gulf of Maine northern shrimp |
-- O --
| opt_slot | Optimum Slot and Trophy Size Limits for Recreational Fisheries |
| opt_trophy | Optimum Trophy Size Limits for Recreational Fisheries |
-- P --
| P.donacina | Data from a growth study of New Zealand intertidal clams. |
| pgen | Probability of a Management Parameter Exceeding a Reference Point |
| pinfish | Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida |
| plot.grotagplus | Plotting Tagging-Growth Objects |
| powertrend | Power Analysis For Detecting Trends |
| print.grotagplus | Printing Tagging-Growth Objects |
| pwpop | Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression |
-- R --
| remp | Random Number Generation from an Empirical Distribution |
| rig | Tagging data from a growth study of rig |
| rockbass | Age Frequency Data for Rock Bass |
-- S --
| 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 |
| Shepherd | Seasonal Length Frequencies for Raja clavata |
| slca | A Weakly Parametric Method for the Analysis of Length Composition Data |
| sole | Flathead sole CPUEs |
| sr | Estimation and Model Comparison of Stock-Recruitment Relationships |
| striper | Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass |
| surveyfit | Estimating the Relative Abundance of Fish From a Trawl Survey |
| surveyref | Quantitative reference points from stock abundance indices based on research surveys |
-- T --
| tag_model_avg | Model Averaging for Instantaneous Rates Tag Return Models |
| tanaka | Simulated alfonsino data for Tanaka (2006 |
| trout | Mark-recapture data for Kenai River trout trout |
-- V --
| vbfr | Francis' re-parameterization of the von Bertalanffy growth equation for length-age data |
-- W --
| wolffish | Spring untransformed mean catch per tow for wolffish (Anarhichas lupus) |
-- Y --
| yellowtail | Fall average catch per tow for southern New England yellowtail flounder |
| ypr | Yield-Per-Recruit Analysis |
-- Z --
| zt | Z-transform or center a time series |