Function reference
Age Comparisons
Summarize and visualize bias and precision among multiple estimates of age for individual fish.

ageBias()
summary(<ageBias>)
plot(<ageBias>)
 Compute and view possible differences between paired sets of ages.

agePrecision()
summary(<agePrec>)
 Compute measures of precision among sets of ages.

plotAB()
 Construct traditional (Campanalike) agebias plots.
AgeLength Keys
Process agelength keys including assigning ages to indvidual fish and visualizing a key.

alkIndivAge()
 Use an agelength key to assign age to individuals in the unaged sample.

alkPlot()
 Plots to visualize agelength keys.

alkAgeDist()
 Proportionsatage from an agelength key

alkMeanVar()
 Mean Valuesatage from an agelength key

PSDlit
 Gabelhouse fivecell length categories for various species.

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

psdPlot()
 Lengthfrequency histogram with Gabelhouse lengths highlighted.

psdCalc()
 Convenience function for calculating PSDX and PSD XY values.

psdCI()
 Compute confidence intervals for PSDX and PSD XY values.

psdAdd()
 Creates a vector of Gabelhouse lengths for each species in an entire data frame.

tictactoe()
 Construct a base tictactoe plot for presenting predatorprey PSD values.
Condition and WeightLength
Efficiently calculate and summarize relative weight and visualize weightlength data among groups with different slopes.

WSlit
 All known standard weight equations.

wsVal()
 Finds standard weight equation coefficients for a particular species.

wrAdd()
 Computes a vector of relative weights specific to a species in an entire data frame.

lwCompPreds()
 Constructs plots of predicted weights at given lengths among different groups.
Abundance (CaptureRecapture)
Estimate abundance with capturerecapture data, including handling and summarizing data in a capture history format.

mrClosed()
summary(<mrClosed1>)
confint(<mrClosed1>)
summary(<mrClosed2>)
confint(<mrClosed2>)
plot(<mrClosed2>)
 Estimate initial population size for single or multiple census markrecapture data.

jolly()
mrOpen()
summary(<mrOpen>)
confint(<mrOpen>)
 JollySeber analysis from multiple markrecapture events from an open population.

capHistConvert()
 Convert between capture history data.frame formats.

capHistSum()
is.CapHist()
plot(<CapHist>)
 Summarize capture histories in individual fish format.

depletion()
summary(<depletion>)
coef(<depletion>)
confint(<depletion>)
anova(<depletion>)
rSquared(<depletion>)
plot(<depletion>)
 Computes the Leslie or DeLury population estimate from catch and effort data.

removal()
summary(<removal>)
confint(<removal>)
 Population estimates for k, 3, or 2pass removal data.
Individual Growth
Fit various growth models (von Bertalanffy, Gompertz, logistic, Richards, Schnute) to individual fish.

vbFuns()
GompertzFuns()
RichardsFuns()
logisticFuns()
growthFunShow()
 Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.

vbStarts()
 Find reasonable starting values for a von Bertalanffy growth function.

Schnute()
 The fourparameter growth function from Schnute (1981).

SchnuteRichards()
 The fiveparameter growth function from Schnute and Richards (1990).

catchCurve()
summary(<catchCurve>)
coef(<catchCurve>)
anova(<catchCurve>)
confint(<catchCurve>)
rSquared(<catchCurve>)
plot(<catchCurve>)
 Mortality estimates from the descending limb of a catch curve.

chapmanRobson()
summary(<chapmanRobson>)
coef(<chapmanRobson>)
confint(<chapmanRobson>)
plot(<chapmanRobson>)
 Computes ChapmanRobson estimates of S and Z.

Mmethods()
metaM()
print(<metaM>)
 Estimate natural mortality from a variety of empirical methods.

srFuns()
srFunShow()
 Creates a function for a specific parameterization of a common stockrecruitment function .

srStarts()
 Finds reasonable starting values for parameters in specific parameterizations of common stockrecruitment models.

addZeroCatch()
 Adds zeros for catches of species not collected in some sampling events.

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

expandLenFreq()
 Expands a length frequency based on a subsample.

lencat()
 Constructs length class/category variable.
Utilities (General Statistics)
Utilities of a statistical nature that are likely to be useful to a fisheries scientist.

binCI()
 Confidence intervals for binomial probability of success.

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

poiCI()
 Confidence interval for Poisson counts.

confint(<boot>)
htest(<boot>)
predict(<boot>)
hist(<boot>)
 Associated S3 methods for bootstrap results from car::Boot.

dunnTest()
print(<dunnTest>)
 Dunn's KruskalWallis Multiple Comparisons.

lrt()
extraSS()
print(<extraTest>)
 Likelihood ratio and extra sumofsquares tests.

hist(<formula>)
 Creates separate histograms by levels.

histFromSum()
 Create a histogram from a frequency table.

confint(<nlsBoot>)
predict(<nlsBoot>)
htest()
 Associated S3 methods for nlsBoot from nlstools.

ksTest()
 KolmogorovSmirnov Tests.

logbtcf()
 Constructs the correctionfactor used when backtransforming logtransformed values.

nlsTracePlot()
 Adds model fits from nls iterations to active plot.

rSquared()
 Extract the coefficient of determination from a linear model object.

se()
 Computes standard error of the mean.

Summarize()
 Summary statistics for a numeric variable.

sumTable()
 Creates a one or twoway table of summary statistics.

FSA
FSApackage
 Fisheries stock assessment methods and data.

capFirst()
 Capitalizes the first letter of first or all words in a string.

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

fact2num()
 Converts "numeric" factor levels to numeric values.

fishR()
 Opens web pages associated with the fishR website.

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

kCounts()
kPvalue()
purl2()
reproInfo()
 Specific utilities for use in a knitr document.

lagratio()
 Ratio of lagged observations.

perc()
 Computes the percentage of values in a vector less than or greater than (and equal to) some value.

peek()
 Peek into (show a subset of) a data frame or matrix.

repeatedRows2Keep()
 Find nonrepeated consecutive rows in a data.frame.

validn()
 Finds the number of valid (nonNA) values in a vector.

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

BrookTroutTH
 Catchatage for Tobin Harbor, Isle Royale Brook Trout.

ChinookArg
 Lengths and weights for Chinook Salmon from three locations in Argentina.

CodNorwegian
 Stock and recruitment data for Norwegian cod, 19371960.

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

Ecoli
 Population growth of Escherichia coli.

Mirex
 Mirex concentration, weight, capture year, and species of Lake Ontario salmon.

PikeNY
 Summarized multiple markrecapture data for all Northern Pike from Buckhorn Marsh, NY.

PikeNYPartial1
 Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.

PSDlit
 Gabelhouse fivecell length categories for various species.

SMBassLS
 Catcheffort data for Little Silver Lake (Ont) Smallmouth Bass.

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

SpotVA1
 Age and length of spot.

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

WR79
 Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).

WSlit
 All known standard weight equations.