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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