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).

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.

bootCase() confint(<bootCase>) predict(<bootCase>) htest(<bootCase>) hist(<bootCase>) plot(<bootCase>)

Case bootstrapping and associated S3 methods.

compIntercepts() print(<compIntercepts>)

Tests for significant differences among all pairs of intercepts in a dummy variable regression.

compSlopes() print(<compSlopes>)

Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).

dunnTest() print(<dunnTest>)

Dunn's Kruskal-Wallis Multiple Comparisons.

lrt() extraSS() print(<extraTest>)

Likelihood ratio and extra sum-of-squares tests.

fitPlot()

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

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.

hoCoef()

Performs a hypothesis test that a linear model parameter is equal to a specific value.

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.

plotBinResp()

Plots a binary response variable versus a quantitative explanatory variable.

residPlot()

Construct a residual plot from lm or nls objects.

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.

capFirst()

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

chooseColors() paletteChoices()

Create a list of colors from among a variety of color palettes.

col2rgbt()

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

diags()

Extract diagonals from a matrix.

fact2num()

Converts "numeric" factor levels to numeric values.

Subset() filterD()

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

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.

lagratio()

Ratio of lagged observations.

mapvalues

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

perc()

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

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.