Package: fishmethods 1.13-1

fishmethods: Fishery Science Methods and Models

Functions for applying a wide range of fisheries stock assessment methods.

Authors:Gary A. Nelson [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fishmethods/json (API)

# Install 'fishmethods' in R:
install.packages('fishmethods', repos = c('https://gnelson12.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • alkdata - Age-Length Key for Gulf of Hauraki snapper, 1992-1993
  • AtkaMack - Length and Age Data For Male and Female Atka Mackerel
  • bonito - Data from an age and growth study of the pacific bonito.
  • buffalo - Life Table Data for African Buffalo
  • 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.
  • codstrcluslen - Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985.
  • counts - Run size data for alewife
  • cowcod - Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008
  • darter - Catch Removal Data For Fantail Darter
  • ep.data - A sub-sample of data from a simulated population collected via length-stratified age sampling
  • Gerking - Mark-Recapture Data for Sunfish in an Indiana Lake
  • goosefish - Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002
  • haddock - Biological data for haddock
  • Hightower - Original data used in Hightower et al.
  • Hoenig - Tag Data from Hoenig et al.
  • hohe - Age-length key and length frequency data from Hoenig and Heisey
  • Jensen - Age Frequency Data for Lake Whitefish By Individual Haul
  • Jiang - Tag Data from Jiang
  • kappenman - Pacific cod catch per effort from Table 1 in Kappenman
  • Kimura - Length and Age Data For Male and Female Pacific Hake
  • lepdata - Simulated data based on parameters estimated from corrected 1980s bluefin tuna data used in Laslett et al.
  • lingcod - Catch data (metric tons) for lingcod 1889 to 2001
  • maki - Data from Maki et al. 2001
  • menhaden - Biological data for menhaden
  • nshrimp - Data for Gulf of Maine northern shrimp
  • P.donacina - Data from a growth study of New Zealand intertidal clams.
  • pinfish - Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Florida
  • rig - Tagging data from a growth study of rig
  • rockbass - Age Frequency Data for Rock Bass
  • 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
  • Shepherd - Seasonal Length Frequencies for Raja clavata
  • simulus - Age and size data for the growth_sel function
  • sole - Flathead sole CPUEs
  • striper - Recruitment Numbers and Female Spawning Stock Biomass for Striped Bass
  • tanaka - Simulated alfonsino data for Tanaka (2006
  • trout - Mark-recapture data for Kenai River trout trout
  • wolffish - Spring untransformed mean catch per tow for wolffish
  • yellowtail - Fall average catch per tow for southern New England yellowtail flounder

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.15 score 6 stars 1 packages 173 scripts 1.5k downloads 3 mentions 74 exports 18 dependencies

Last updated from:cb5c9ac846. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK214
linux-devel-x86_64OK216
source / vignettesOK198
linux-release-arm64OK214
linux-release-x86_64OK201
macos-release-arm64OK309
macos-release-x86_64OK300
macos-oldrel-arm64OK205
macos-oldrel-x86_64OK549
windows-develOK192
windows-releaseOK218
windows-oldrelOK201
wasm-releaseFAIL133

Exports:agesurvagesurvclalkalkDalkpropalkssastrocalc4rbheqbhnoneqbt.logcatch.selectcatchmsycatchsurveyclus.lfclus.meanclus.rhoclus.rho.gclus.str.lfclus.t.testclus.vb.fitcombinevarcompare.lrt.pluscompare2convmortcpuekappdbsradeltadistdepletdlprojep_growtheprfm_checkdesignfm_model_avgfm_telemetryfpcgapgrotaggrotagplusgrowhampgrowthgrowth_LEPgrowth_selgrowthlrtgrowthlrt.plusgrowthmultifitgrowthResidgrowthTrajectgrowtransinverse_alkirm_crirm_hlifetableM.empiricalmaturemort.almrN.singleopt_slotopt_trophypgenplot.grotagpluspowertrendprint.grotagpluspwpoprempsbprschnabelslcasrsurveyfitsurveyreftag_model_avgvbfryprzt

Dependencies:bootbootstrapdata.tablelatticelme4MASSMatrixminqanlmenloptrnumDerivrbibutilsRcppRcppEigenRdpackreformulasrlangTMB

Readme and manuals

Help Manual

Help pageTopics
Age-based Survival Estimatorsagesurv
Age-Based Survival and Mortality Estimators for Cluster Samplingagesurvcl
Create An Age-Length Keyalk
Sample Size Determination for Age Subsampling Using the D statisticalkD
Age-Length Key for Gulf of Hauraki snapper, 1992-1993alkdata
Age-Length Key Proportions-At-Agealkprop
Sample Size Determination for Age Subsamplingalkss
Solar zenith angles for biological researchastrocalc4r
Length and Age Data For Male and Female Atka MackerelAtkaMack
Length-based Beverton-Holt Equilibrium Total Instantaneous Mortality Estimatorbheq
Length-based Beverton-Holt Nonequilibrium Z Estimatorbhnoneq
Data from an age and growth study of the pacific bonito.bonito
Back-transformation of log-transformed mean and variancebt.log
Life Table Data for African Buffalobuffalo
Number of cod captured in 10 standardized bottom trawl hauls from Massachusetts, 1985catch
Selectivity Ogive from a Catch Curvecatch.select
Estimating MSY from catch and resiliencecatchmsy
Catch-Survey Analysiscatchsurvey
Statistical Comparison of Length Frequencies from Simple Random Cluster Samplingclus.lf
Estimation of Population Attributes and Effective Sample Size for Fishes Collected Via Cluster Samplingclus.mean
Intracluster Correlation Coefficients for Clustered Dataclus.rho
Calculate A Common Intracluster Correlation Coefficient Among Groupsclus.rho.g
Statistical Comparison of Length Frequencies from Stratified Random Cluster Samplingclus.str.lf
Correcting a Two-Sample Test for Clusteringclus.t.test
Fit a Von Bertalanffy growth equation to clustered data via bootstrappingclus.vb.fit
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries bottom trawl survey, spring 1985.codcluslen
Lengths of Atlantic cod caught during Massachusetts Division of Marine Fisheries stratified random bottom trawl survey, spring 1985.codstrcluslen
Combining Mean and Variances from Multiple Samplescombinevar
Comparison of growthlrt.plus model objectscompare.lrt.plus
Comparisons of two age readers or two aging methodscompare2
Conversion of Mortality Ratesconvmort
Run size data for alewife (_Alosa pseudoharengus_)counts
Catch data (metric tons) for cowcod Sebastes levis 1900 to 2008cowcod
Trawl survey based abundance estimation using data sets with unusually large catchescpuekapp
Catch Removal Data For Fantail Darterdarter
Depletion-Based Stock Reduction Analysisdbsra
Delta Distribution Mean and Variance Estimatorsdeltadist
Catch-Effort Depletion Methods For a Closed Populationdeplet
This function performs projections for dbsra and catchmsy objectsdlproj
Fitting the von Bertalanffy growth model to length-stratified age samplesep_growth
A sub-sample of data from a simulated population collected via length-stratified age samplingep.data
Eggs-Per-Recruit Analysisepr
Check parameter structure of Hightower et al. (2001) modelsfm_checkdesign
Model Averaging for the Telemetry Method of Hightower et al. (2001)fm_model_avg
Estimation of Fishing and Natural Mortality from Telemetry Datafm_telemetry
Fishing Power Correction Factor from Experimental Fishingfpc
Tukey's Gappinggap
Mark-Recapture Data for Sunfish in an Indiana LakeGerking
Mean Length and Numbers of Lengths for Northern Goosefish, 1963-2002goosefish
Maximum likelihood estimation of growth and growth variability from tagging data - Francis (1988)grotag
Flexible maximum likelihood estimation of growth from multiple tagging datasets.grotagplus
von Bertalanffy Growth Models for Tagging Data Incorporating Individual Variationgrowhamp
Fitting Growth Curves to Length- or Weight-at-Age Datagrowth
A flexible maximum likelihood approach for fitting growth curves to tag-recapture datagrowth_LEP
Fitting a von Bertalanffy curve to length and age data biased by gear selectivitygrowth_sel
Likelihood Ratio Tests for Comparing Multiple Growth Curvesgrowthlrt
Likelihood Methods for Comparing Multiple Growth Curvesgrowthlrt.plus
Fit a Multi-Group Growth Modelgrowthmultifit
Plot residuals of growth model fitted to tag datagrowthResid
Plot growth trajectories obtained from tagging datagrowthTraject
Growth Transition Matrix for a Size-Structured Population Dynamics Modelgrowtrans
Biological data for haddock (Melanogrammus aeglefinus)haddock
Original data used in Hightower et al. (2001)Hightower
Tag Data from Hoenig et al. (1998)Hoenig
age-length key and length frequency data from Hoenig and Heisey (1987)hohe
Inverse Age-Length Key Method of Hoenig and Heisey (1987)inverse_alk
Age-Independent Instantaneous Rates Model of Jiang et al. (2007) Incorporating Catch and Release Tag Returnsirm_cr
Age-Independent Instantaneous Rates Tag Return Model of Hoenig et al. (1998)irm_h
Age Frequency Data for Lake Whitefish By Individual HaulJensen
Tag Data from Jiang (2005)Jiang
Pacific cod catch per effort from Table 1 in Kappenman (1999)kappenman
Length and Age Data For Male and Female Pacific HakeKimura
Simulated data based on parameters estimated from corrected 1980s bluefin tuna data used in Laslett et al.(2002)lepdata
Life Table Constructionlifetable
Catch data (metric tons) for lingcod 1889 to 2001lingcod
Estimation of Natural Mortality Rates from Life History ParametersM.empirical
Data from Maki et al. 2001maki
Estimation of proportion mature at age when immature fish are unavailablemature
Biological data for menhaden (Brevoortia tyrannus)menhaden
Estimation of Mortality using Times-At-Large Data from Taggingmort.al
Estimate of Population Size from a Single Mark-Recapture ExperimentmrN.single
Data for Gulf of Maine northern shrimpnshrimp
Optimum Slot and Trophy Size Limits for Recreational Fisheriesopt_slot
Optimum Trophy Size Limits for Recreational Fisheriesopt_trophy
Data from a growth study of New Zealand intertidal clams.P.donacina
Probability of a Management Parameter Exceeding a Reference Pointpgen
Length, age and sex data for pinfish (Lagodon rhomboides) from Tampa Bay, Floridapinfish
Plotting Tagging-Growth Objectsplot.grotagplus
Power Analysis For Detecting Trendspowertrend
Printing Tagging-Growth Objectsprint.grotagplus
Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regressionpwpop
Random Number Generation from an Empirical Distributionremp
Tagging data from a growth study of rigrig
Age Frequency Data for Rock Bassrockbass
Total length (inches) of striped bass collected by Massachusetts volunteer anglers in 2014sblen
Otolith ages of striped bass made by two age readerssbotos
Spawning Stock Biomass-Per-Recruit Analysissbpr
Population Size Estimates from Repeated Mark-Recapture Experimentsschnabel
Seasonal Length Frequencies for Raja clavataShepherd
Age and size data for the growth_sel functionsimulus
A Weakly Parametric Method for the Analysis of Length Composition Dataslca
Flathead sole CPUEssole
Estimation and Model Comparison of Stock-Recruitment Relationshipssr
Recruitment Numbers and Female Spawning Stock Biomass for Striped Bassstriper
Estimating the Relative Abundance of Fish From a Trawl Surveysurveyfit
Quantitative reference points from stock abundance indices based on research surveyssurveyref
Model Averaging for Instantaneous Rates Tag Return Modelstag_model_avg
Simulated alfonsino data for Tanaka (2006tanaka
Mark-recapture data for Kenai River trout trouttrout
Francis' re-parameterization of the von Bertalanffy growth equation for length-age datavbfr
Spring untransformed mean catch per tow for wolffish (Anarhichas lupus)wolffish
Fall average catch per tow for southern New England yellowtail flounderyellowtail
Yield-Per-Recruit Analysisypr
Z-transform or center a time serieszt