Function reference • FSA

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 (Campana-like) age-bias plots.

Age-Length Keys

Process age-length keys including assigning ages to indvidual fish and visualizing a key.

alkIndivAge(): Use an age-length key to assign age to individuals in the unaged sample.

alkPlot(): Plots to visualize age-length keys.

alkAgeDist(): Proportions-at-age from an age-length key

alkMeanVar(): Mean Values-at-age from an age-length key

Size Structure

Efficiently calculate and summarize proportional size distribution (PSD) data.

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

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

psdPlot(): Length-frequency histogram with Gabelhouse lengths highlighted.

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

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

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

tictactoe(): Construct a base tic-tac-toe plot for presenting predator-prey PSD values.

Condition and Weight-Length

Efficiently calculate and summarize relative weight and visualize weight-length 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 (Capture-Recapture)

Estimate abundance with capture-recapture 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 mark-recapture data.

jolly() mrOpen() summary(<mrOpen>) confint(<mrOpen>): Jolly-Seber analysis from multiple mark-recapture 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.

Abundance (Depletion)

Estimate abundance with depletion and removal data.

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 2-pass 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 four-parameter growth function from Schnute (1981).

SchnuteRichards(): The five-parameter growth function from Schnute and Richards (1990).

Mortality Rates

Estimate mortality rates from catch curve data and empirical models.

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 Chapman-Robson estimates of S and Z.

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

Stock-Recruiment

Fit various (Beverton-Holt, Ricker, Shepherd) stock-recruitment functions.

srFuns() srFunShow(): Creates a function for a specific parameterization of a common stock-recruitment function .

srStarts(): Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.

Utilities (Fisheries-Specific)

Utilities that are likely useful only to fisheries scientists.

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 Kruskal-Wallis Multiple Comparisons.

lrt() extraSS() print(<extraTest>): Likelihood ratio and extra sum-of-squares tests.

geomean() geosd(): Calculates the geometric mean or geometric standard deviation.

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(): Kolmogorov-Smirnov Tests.

logbtcf(): Constructs the correction-factor used when back-transforming log-transformed values.

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

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

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 two-way table of summary statistics.

Utilities (Other)

Miscellaneous utilities.

FSA FSA-package: 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.

is.odd() is.even(): Determine if a number is odd or even.

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 non-repeated consecutive rows in a data.frame.

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

Data

Data files.

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

BrookTroutTH: Catch-at-age 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, 1937-1960.

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 mark-recapture 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 five-cell length categories for various species.

SMBassLS: Catch-effort 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.

Defunct

Defunct functions.

bootCase() chooseColors() compIntercepts() compSlopes() diags() filterD() fitPlot() fsaNews() hoCoef() mapvalues() plotBinResp() residPlot() Subset(): DEFUNCT functions.