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/>.

Install the latest version of this package by entering the following in R:
AuthorDerek Ogle [aut, cre]
Date of publication2017-03-12 09:02:00
MaintainerDerek Ogle <derek@derekogle.com>
LicenseGPL (>= 2)

View on CRAN

Man pages

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

addZeroCatch: Adds zeros 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...


addRadCap Man page
addZeroCatch Man page
ageBias Man page
agePrecision Man page
alkAgeDist Man page
alkIndivAge Man page
alkMeanVar Man page
alkPlot Man page
anova.catchCurve Man page
anova.depletion Man page
bcFuns Man page
binCI Man page
BluegillJL Man page
bootstrap Man page
BrookTroutTH Man page
capFirst Man page
capHistConvert Man page
capHistSum Man page
catchCurve Man page
catchCurve.default Man page
catchCurve.formula Man page
chapmanRobson Man page
chapmanRobson.default Man page
chapmanRobson.formula Man page
ChinookArg Man page
chooseColors Man page
CodNorwegian Man page
coef.catchCurve Man page
coef.chapmanRobson Man page
coef.depletion Man page
col2rgbt Man page
compIntercepts Man page
compSlopes Man page
confint.bootCase Man page
confint.catchCurve Man page
confint.chapmanRobson Man page
confint.depletion Man page
confint.mrClosed1 Man page
confint.mrClosed2 Man page
confint.mrOpen Man page
confint.nlsboot Man page
confint.nlsBoot Man page
confint.removal Man page
CutthroatAL Man page
depletion Man page
diags Man page
dunnTest Man page
dunnTest.default Man page
dunnTest.formula Man page
Ecoli Man page
expandCounts Man page
expandLenFreq Man page
extraSS Man page
extraTests Man page
fact2num Man page
filterD Man page
fishR Man page
fitPlot Man page
fitPlot.glm Man page
fitPlot.IVR Man page
fitPlot.lm Man page
fitPlot.logreg Man page
fitPlot.nls Man page
fitPlot.ONEWAY Man page
fitPlot.POLY Man page
fitPlot.SLR Man page
fitPlot.TWOWAY Man page
FSA Man page
fsaNews Man page
FSANews Man page
FSA-package Man page
FSAUtils Man page
gConvert Man page
geomean Man page
geosd Man page
GompertzFuns Man page
growthFunShow Man page
growthModels Man page
headtail Man page
hist.bootCase Man page
hist.formula Man page
histFromSum Man page
histFromSum.default Man page
histFromSum.formula Man page
histFromSum.table Man page
hoCoef Man page
htest Man page
htest.bootCase Man page
htest.nlsBoot Man page
hyperCI Man page
iAddLoessLine Man page
iCheckALK Man page
iCheckStartcatW Man page
iCILabel Man page
iGetDecimals Man page
iGetVarFromFormula Man page
iHndlCols2UseIgnore Man page
iHndlFormula Man page
iHndlMultWhat Man page
iLegendHelp Man page
iListSpecies Man page
iMakeColor Man page
iPlotExists Man page
is.even Man page
is.odd Man page
is.wholenumber Man page
iTypeoflm Man page
jolly Man page
kCounts Man page
kPvalue Man page
ksTest Man page
ksTest.default Man page
ksTest.formula Man page
lagratio Man page
lencat Man page
lencat.default Man page
lencat.formula Man page
logbtcf Man page
logisticFuns Man page
lrt Man page
lwCompPreds Man page
mapvalues Man page
metaM Man page
Mirex Man page
Mmethods Man page
mrClosed Man page
mrOpen Man page
nlsTracePlot Man page
oddeven Man page
.onAttach Man page
paletteChoices Man page
pcumsum Man page
perc Man page
PikeNY Man page
PikeNYPartial1 Man page
plot.ageBias Man page
plot.agePrec Man page
plotBinResp Man page
plotBinResp.default Man page
plotBinResp.formula Man page
plot.bootCase Man page
plot.CapHist Man page
plot.catchCurve Man page
plot.chapmanRobson Man page
plot.depletion Man page
plot.mrClosed2 Man page
poiCI Man page
predict.bootCase Man page
predict.nlsBoot Man page
print.compIntercepts Man page
print.compSlopes Man page
print.dunnTest Man page
print.extraTest Man page
print.metaM Man page
psdAdd Man page
psdAdd.default Man page
psdAdd.formula Man page
psdCalc Man page
psdCI Man page
PSDlit Man page
psdPlot Man page
psdVal Man page
purl2 Man page
rcumsum Man page
removal Man page
reproInfo Man page
residPlot Man page
residPlot.IVR Man page
residPlot.lm Man page
residPlot.nlme Man page
residPlot.nls Man page
residPlot.ONEWAY Man page
residPlot.POLY Man page
residPlot.SLR Man page
residPlot.TWOWAY Man page
RichardsFuns Man page
Schnute Man page
se Man page
SMBassLS Man page
SMBassWB Man page
SpotVA1 Man page
srFuns Man page
srFunShow Man page
srStarts Man page
stockRecruitment Man page
STOP Man page
Subset Man page
Summarize Man page
Summarize.default Man page
Summarize.formula Man page
summary.ageBias Man page
summary.agePrec Man page
summary.catchCurve Man page
summary.chapmanRobson Man page
summary.depletion Man page
summary.mrClosed1 Man page
summary.mrClosed2 Man page
summary.mrOpen Man page
summary.removal Man page
sumTable Man page
sumTable.formula Man page
tictactoe Man page
validn Man page
vbFuns Man page
vbStarts Man page
WARN Man page
WhitefishLC Man page
WR79 Man page
wrAdd Man page
wrAdd.default Man page
wrAdd.formula Man page
WSlit Man page
wsVal Man page


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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.