FSA: Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.

AuthorDerek Ogle [aut, cre]
Date of publication2016-12-13 15:49:34
MaintainerDerek Ogle <derek@derekogle.com>
LicenseGPL (>= 2)
Version0.8.11
https://github.com/droglenc/FSA

View on CRAN

Man pages

addRadCap: Add a total radius-at-capture variable to a data.frame that...

addZeroCatch: Adds zeroes for catches of species not collected in some...

ageBias: Compute and view possible biases between paired sets of ages.

agePrecision: Compute measures of precision among sets of ages.

alkAgeDist: Proportions-at-age from an Age-Length Key

alkIndivAge: Use an age-length key to assign age to individuals in the...

alkMeanVar: Mean Values-at-age from an Age-Length Key

alkPlot: Plots to visualize age-length keys.

bcFuns: Creates a function for a specific back-calculation model.

binCI: Confidence intervals for binomial probability of success.

BluegillJL: Capture histories (2 samples) of Bluegill from Jewett Lake,...

bootCase: Associated S3 methods for bootCase from car.

BrookTroutTH: Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.

capHistConvert: Convert between capture history data.frame formats.

capHistSum: Summarize capture histories in individual fish format.

catchCurve: Mortality estimates from the descending limb of a catch...

chapmanRobson: Computes Chapman-Robson estimates of S and Z.

ChinookArg: Lengths and weights for Chinook Salmon from three locations...

chooseColors: Create a list of colors from among a variety of color...

CodNorwegian: Stock and recruitment data for Norwegian cod, 1937-1960.

col2rgbt: Converts an R color to RGB (red/green/blue) including a...

compIntercepts: Tests for significant differences among all pairs of...

compSlopes: Tests for significant differences among all pairs of slopes...

CutthroatAL: Capture histories (9 samples) of Cutthroat Trout from Auke...

depletion: Computes the Leslie or Delury population estimate from catch...

diags: Extract diagonals from a matrix.

dunnTest: Dunn's Kruskal-Wallis Multiple Comparisons.

Ecoli: Population growth of Escherichia coli.

expandCounts: Repeat individual fish data (including lengths) from tallied...

expandLenFreq: Expands a length frequency based on a subsample.

extraTests: Likelihood ratio and extra sum-of-squares tests.

fact2num: Converts "numeric" factor levels to numeric values.

fishR: Opens web pages associated with the fishR website.

fitPlot: Fitted model plot for an lm, glm, or nls object.

FSA: Fisheries stock assessment methods and data.

FSA-internals: Internal functions.

fsaNews: Read news and changes for the 'FSA' package.

FSAUtils: Capitalizes the first letter of first or all words in a...

gConvert: Converts between types of measurements from calcified...

geomean: Calculates the geometric mean or geometric standard...

growthModels: Creates a function for a specific parameterization of the von...

headtail: Shows rows from the head and tail of a data frame or matrix.

hist.formula: Creates separate histograms by levels.

histFromSum: Create a histogram from a frequency table.

hoCoef: Performs a hypothesis test that a linear model parameter is...

hyperCI: Confidence interval for population size (N) in hypergeometric...

knitUtil: Specific utilities for use in a knitr document.

ksTest: Kolmogorov-Smirnov Tests.

lagratio: Ratio of lagged observations.

lencat: Constructs length class/category variable.

logbtcf: Constructs the correction-factor used when back-transforming...

lwCompPreds: Constructs plots of predicted weights at given lengths among...

mapvalues: Replace specified values in a vector or factor with new...

metaM: Estimate natural mortality from a variety of empirical...

Mirex: Mirex concentration, weight, capture year, and species of...

mrClosed: Estimate initial population size for single or multiple...

mrOpen: Jolly-Seber analysis from multiple mark-recapture events from...

nlsBoot: Associated S3 methods for nlsBoot from nlstools.

nlsTracePlot: Adds model fits from nls iterations to active plot.

oddeven: Determine if a number is odd or even.

perc: Computes the percentage of values in a vector less than or...

PikeNY: Summarized multiple mark-recapture data for all Northern Pike...

PikeNYPartial1: Capture histories (4 samples), in capture history format, of...

plotBinResp: Plots a binary response variable versus a quantitative...

poiCI: Confidence interval for Poisson counts.

psdAdd: Creates a vector of Gabelhouse lengths for each species in an...

psdCalc: Convenience function for calculating PSD-X and PSD X-Y...

psdCI: Compute confidence intervals for PSD-X and PSD X-Y values.

PSDlit: Gabelhouse five-cell length categories for various species.

psdPlot: Length-frequency histogram with Gabelhouse lengths...

psdVal: Finds Gabelhouse lengths (for PSD calculations) for a...

rcumsum: Computes the prior to or reverse cumulative sum of a vector.

removal: Population estimates for k-, 3-, or 2-pass removal data.

residPlot: Construct a residual plot from lm or nls objects.

Schnute: The four-parameter growth function from Schnute (1981).

se: Computes standard error of the mean.

SMBassLS: Catch-effort data for Little Silver Lake (Ont) Smallmouth...

SMBassWB: Growth increment data for West Bearskin Lake, MN, Smallmouth...

SpotVA1: Age and length of spot.

srStarts: Finds reasonable starting values for parameters in specific...

stockRecruitment: Creates a function for a specific parameterization of a...

Subset: Subsets/filters a data frame and drops the unused levels.

Summarize: Summary statistics for a numeric variable.

sumTable: Creates a one- or two-way table of summary statistics.

tictactoe: Construct a base tic-tac-toe plot for presenting...

validn: Finds the number of valid (non-NA) values in a vector.

vbStarts: Find reasonable starting values for a von Bertalanffy growth...

WhitefishLC: Assigned ages from two readers on three structures for Lake...

WR79: Ages and lengths for a hypothetical sample from Westerheim...

wrAdd: Computes a vector of relative weights specific to a species...

WSlit: All known standard weight equations.

wsVal: Finds standard weight equation coefficients for a particular...

Files in this package

FSA
FSA/COPYING
FSA/inst
FSA/inst/CITATION
FSA/inst/extdata
FSA/inst/extdata/bootCase1.RData
FSA/inst/extdata/PSDWR_testdata.csv
FSA/inst/extdata/nlsBoot1.RData
FSA/tests
FSA/tests/testthat
FSA/tests/testthat/test_WSWR_OUT.R
FSA/tests/testthat/test_expandCounts_OUT_VALIDATE.R
FSA/tests/testthat/test_addZeroCatch_MSG.R
FSA/tests/testthat/test_mrOpen_MSG.R
FSA/tests/testthat/test_StockRecruit_MSG.R
FSA/tests/testthat/Rplots.pdf
FSA/tests/testthat/test_FSAUtils_OUT.R
FSA/tests/testthat/test_LWCompPreds_MSG.R
FSA/tests/testthat/test_addZeroCatch_VALIDATE.R
FSA/tests/testthat/test_bcFuns_OUT.R
FSA/tests/testthat/test_ciDists_MSG.R
FSA/tests/testthat/test_ksTest_OUT.R
FSA/tests/testthat/test_extraTests_MSG.R
FSA/tests/testthat/test_VonBertalanffy_VALIDATE.R
FSA/tests/testthat/EXS_growthUtils.R
FSA/tests/testthat/test_growthUtils_MSG.R
FSA/tests/testthat/test_comparisonsDVR_OUT.R
FSA/tests/testthat/test_expandLenFreq_MSG.R
FSA/tests/testthat/test_capHist_OUT.R
FSA/tests/testthat/test_metaM_OUT.R
FSA/tests/testthat/test_AgeLengthKey_OUT.R
FSA/tests/testthat/EXS_mrOpen.R
FSA/tests/testthat/test_Summarize_OUT_VALIDATE.R
FSA/tests/testthat/test_VonBertalanffy_OUT.R
FSA/tests/testthat/EXS_AgeLengthKey.R
FSA/tests/testthat/test_extraTests_VALIDATE.R
FSA/tests/testthat/EXS_sumTable.R
FSA/tests/testthat/test_metaM_MSG.R
FSA/tests/testthat/test_metaM_VALIDATE.R
FSA/tests/testthat/test_dunnTest_MSG.R
FSA/tests/testthat/test_WSWR_VALIDATE.R
FSA/tests/testthat/test_histFormula_MSG.R
FSA/tests/testthat/test_LWCompPreds_OUT.R
FSA/tests/testthat/test_fitResidPlots_OUT.R
FSA/tests/testthat/test_CatchCurve_MSG.R
FSA/tests/testthat/test_mrOpen_VALIDATE.R
FSA/tests/testthat/EXS_Summarize.R
FSA/tests/testthat/EXS_growthFuns.R
FSA/tests/testthat/test_growthUtils_OUT.R
FSA/tests/testthat/test_sumTable_OUT_VALIDATE.R
FSA/tests/testthat/test_removal_VALIDATE.R
FSA/tests/testthat/test_PSD_VALIDATE.R
FSA/tests/testthat/EXS_bootstrap.R
FSA/tests/testthat/test_growthFuns_MSG.R
FSA/tests/testthat/test_removal_OUT.R
FSA/tests/testthat/EXS_lencat.R
FSA/tests/testthat/test_dunnTest_VALIDATE.R
FSA/tests/testthat/EXS_CatchCurve.R
FSA/tests/testthat/test_ksTest_VALIDATE.R
FSA/tests/testthat/test_histFromSum_MSG.R
FSA/tests/testthat/test_CatchCurve_OUT.R
FSA/tests/testthat/EXS_capHist.R
FSA/tests/testthat/test_lencat_MSG.R
FSA/tests/testthat/test_mrOpen_OUT.R
FSA/tests/testthat/test_sumTable_MSG.R
FSA/tests/testthat/test_Summarize_MSG.R
FSA/tests/testthat/test_AgeLengthKey_MSG.R
FSA/tests/testthat/test_depletion_MSG.R
FSA/tests/testthat/test_capHist_MSG.R
FSA/tests/testthat/test_comparisonsDVR_MSG.R
FSA/tests/testthat/test_lencat_VALIDATE.R
FSA/tests/testthat/test_Internals.R
FSA/tests/testthat/test_ciDists_OUT.R
FSA/tests/testthat/test_extraTests_OUT.R
FSA/tests/testthat/test_histFormula_OUT.R
FSA/tests/testthat/test_mrClosed_VALIDATE.R
FSA/tests/testthat/test_fitResidPlots_MSG.R
FSA/tests/testthat/test_FSAUtils_MSG.R
FSA/tests/testthat/EXS_extraTests.R
FSA/tests/testthat/EXS_dunnTest.R
FSA/tests/testthat/test_capHist_VALIDATE.R
FSA/tests/testthat/test_nlsTracePlot_MSG.R
FSA/tests/testthat/test_nlsTracePlot_OUT.R
FSA/tests/testthat/test_lencat_OUT.R
FSA/tests/testthat/EXS_comparisonsDVR.R
FSA/tests/testthat/test_AgeComparisons_OUT.R
FSA/tests/testthat/test_ciDists_VALIDATE.R
FSA/tests/testthat/test_knitUtil_OUT.R
FSA/tests/testthat/test_expandLenFreq_OUT_VALIDATE.R
FSA/tests/testthat/test_depletion_OUT.R
FSA/tests/testthat/test_removal_MSG.R
FSA/tests/testthat/EXS_PSD.R
FSA/tests/testthat/test_AgeComparisons_VALIDATE.R
FSA/tests/testthat/test_PSD_MSG.R
FSA/tests/testthat/test_addZeroCatch_OUT.R
FSA/tests/testthat/EXS_addZeroCatch.R
FSA/tests/testthat/test_ksTest_MSG.R
FSA/tests/testthat/test_dunnTest_OUT.R
FSA/tests/testthat/test_growthFuns_OUT.R
FSA/tests/testthat/test_depletion_VALIDATE.R
FSA/tests/testthat/test_AgeLengthKey_VALIDATE.R
FSA/tests/testthat/test_StockRecruit_OUT.R
FSA/tests/testthat/test_mrClosed_OUT.R
FSA/tests/testthat/test_WSWR_MSG.R
FSA/tests/testthat/test_AgeComparisons_MSG.R
FSA/tests/testthat/test_expandCounts_MSG.R
FSA/tests/testthat/test_bcFuns_MSG.R
FSA/tests/testthat/test_mrClosed_MSG.R
FSA/tests/testthat/test_bootstrap_MSG.R
FSA/tests/testthat/test_PSD_OUT.R
FSA/tests/testthat/EXS_fitResidPlots.R
FSA/tests/testthat/test_bootstrap_OUT.R
FSA/tests/testthat/test_VonBertalanffy_MSG.R
FSA/tests/testthat/test_CatchCurve_VALIDATE.R
FSA/tests/test-all.R
FSA/NAMESPACE
FSA/NEWS.md
FSA/data
FSA/data/CodNorwegian.rdata
FSA/data/PikeNYPartial1.rdata
FSA/data/SMBassWB.rdata
FSA/data/CutthroatAL.rdata
FSA/data/ChinookArg.rdata
FSA/data/SMBassLS.rdata
FSA/data/WSlit.rdata
FSA/data/PSDlit.rdata
FSA/data/BrookTroutTH.rdata
FSA/data/Mirex.rdata
FSA/data/Ecoli.rdata
FSA/data/WhitefishLC.rdata
FSA/data/SpotVA1.rdata
FSA/data/WR79.rdata
FSA/data/BluegillJL.rdata
FSA/data/PikeNY.rdata
FSA/R
FSA/R/plotBinResp.R FSA/R/residPlot.R FSA/R/expandCounts.R FSA/R/nlsTracePlot.R FSA/R/capHistConvert.R FSA/R/alkIndivAge.R FSA/R/bootstrap.R FSA/R/SpotVA1.R FSA/R/depletion.R FSA/R/stockRecruitment.R FSA/R/alkPlot.R FSA/R/mrClosed.R FSA/R/WR79.R FSA/R/Summarize.R FSA/R/bcFuns.R FSA/R/WhitefishLC.R FSA/R/BluegillJL.R FSA/R/growthModels.R FSA/R/hist.formula.R FSA/R/growthDataUtils.R FSA/R/alkSummaries.R FSA/R/expandLenFreq.R FSA/R/PikeNY.R FSA/R/FSA.R FSA/R/vbStarts.R FSA/R/Mirex.R FSA/R/mrOpen.R FSA/R/lencat.R FSA/R/ageComparisons.R FSA/R/comparisonsDVR.R FSA/R/extraTests.R FSA/R/fitPlot.R FSA/R/removal.R FSA/R/wsVal.R FSA/R/lwCompPreds.R FSA/R/tictactoe.R FSA/R/CIDists.R FSA/R/knitUtil.R FSA/R/BrookTroutTH.R FSA/R/WSlit.R FSA/R/wrAdd.R FSA/R/chapmanRobson.R FSA/R/FSA-internals.R FSA/R/srStarts.R FSA/R/SMBassLS.R FSA/R/catchCurve.R FSA/R/SMBassWB.R FSA/R/FSAUtils.R FSA/R/ksTest.R FSA/R/sumTable.R FSA/R/histFromSum.R FSA/R/dunnTest.R FSA/R/PikeNYPartial1.R FSA/R/Ecoli.R FSA/R/mapvalues.R FSA/R/capHistSum.R FSA/R/PSDlit.R FSA/R/psdVal.R FSA/R/psdPlot.R FSA/R/ChinookArg.R FSA/R/CodNorwegian.R FSA/R/psdCI.R FSA/R/CutthroatAL.R FSA/R/metaM.R FSA/R/psdAdd.R FSA/R/psdCalc.R FSA/R/addZeroCatch.R
FSA/MD5
FSA/DESCRIPTION
FSA/man
FSA/man/PikeNY.Rd FSA/man/col2rgbt.Rd FSA/man/Summarize.Rd FSA/man/logbtcf.Rd FSA/man/alkMeanVar.Rd FSA/man/poiCI.Rd FSA/man/compSlopes.Rd FSA/man/growthModels.Rd FSA/man/geomean.Rd FSA/man/histFromSum.Rd FSA/man/binCI.Rd FSA/man/lencat.Rd FSA/man/WR79.Rd FSA/man/alkPlot.Rd FSA/man/psdAdd.Rd FSA/man/psdPlot.Rd FSA/man/FSAUtils.Rd FSA/man/perc.Rd FSA/man/chooseColors.Rd FSA/man/CutthroatAL.Rd FSA/man/vbStarts.Rd FSA/man/hyperCI.Rd FSA/man/ChinookArg.Rd FSA/man/fishR.Rd FSA/man/mrOpen.Rd FSA/man/plotBinResp.Rd FSA/man/rcumsum.Rd FSA/man/dunnTest.Rd FSA/man/chapmanRobson.Rd FSA/man/FSA-internals.Rd FSA/man/diags.Rd FSA/man/validn.Rd FSA/man/SMBassWB.Rd FSA/man/capHistConvert.Rd FSA/man/nlsTracePlot.Rd FSA/man/expandCounts.Rd FSA/man/FSA.Rd FSA/man/BluegillJL.Rd FSA/man/mrClosed.Rd FSA/man/ksTest.Rd FSA/man/lagratio.Rd FSA/man/addRadCap.Rd FSA/man/se.Rd FSA/man/mapvalues.Rd FSA/man/depletion.Rd FSA/man/hoCoef.Rd FSA/man/psdCalc.Rd FSA/man/catchCurve.Rd FSA/man/PSDlit.Rd FSA/man/PikeNYPartial1.Rd FSA/man/WhitefishLC.Rd FSA/man/headtail.Rd FSA/man/extraTests.Rd FSA/man/bootCase.Rd FSA/man/capHistSum.Rd FSA/man/gConvert.Rd FSA/man/Subset.Rd FSA/man/wrAdd.Rd FSA/man/removal.Rd FSA/man/Schnute.Rd FSA/man/knitUtil.Rd FSA/man/alkAgeDist.Rd FSA/man/nlsBoot.Rd FSA/man/srStarts.Rd FSA/man/compIntercepts.Rd FSA/man/WSlit.Rd FSA/man/agePrecision.Rd FSA/man/CodNorwegian.Rd FSA/man/Ecoli.Rd FSA/man/bcFuns.Rd FSA/man/oddeven.Rd FSA/man/fact2num.Rd FSA/man/residPlot.Rd FSA/man/tictactoe.Rd FSA/man/Mirex.Rd FSA/man/addZeroCatch.Rd FSA/man/SpotVA1.Rd FSA/man/hist.formula.Rd FSA/man/fsaNews.Rd FSA/man/psdCI.Rd FSA/man/expandLenFreq.Rd FSA/man/sumTable.Rd FSA/man/alkIndivAge.Rd FSA/man/psdVal.Rd FSA/man/fitPlot.Rd FSA/man/ageBias.Rd FSA/man/lwCompPreds.Rd FSA/man/BrookTroutTH.Rd FSA/man/wsVal.Rd FSA/man/SMBassLS.Rd FSA/man/metaM.Rd FSA/man/stockRecruitment.Rd

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