A B C D E F G H I J K L M N O P R S T V W

FSA-package | Fisheries stock assessment methods and data. |

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

ageBias | Compute and view possible differences 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 unaged sample. |

alkMeanVar | Mean Values-at-age from an age-length key |

alkPlot | Plots to visualize age-length keys. |

anova.catchCurve | Mortality estimates from the descending limb of a catch curve. |

anova.depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

binCI | Confidence intervals for binomial probability of success. |

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

bootCase | Case bootstrapping and associated S3 methods. |

bootstrap | Case bootstrapping and associated S3 methods. |

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

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

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 curve. |

catchCurve.default | Mortality estimates from the descending limb of a catch curve. |

catchCurve.formula | Mortality estimates from the descending limb of a catch curve. |

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

chapmanRobson.default | Computes Chapman-Robson estimates of S and Z. |

chapmanRobson.formula | Computes Chapman-Robson estimates of S and Z. |

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

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

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

coef.catchCurve | Mortality estimates from the descending limb of a catch curve. |

coef.chapmanRobson | Computes Chapman-Robson estimates of S and Z. |

coef.depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

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

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

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

confint.bootCase | Case bootstrapping and associated S3 methods. |

confint.catchCurve | Mortality estimates from the descending limb of a catch curve. |

confint.chapmanRobson | Computes Chapman-Robson estimates of S and Z. |

confint.depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

confint.mrClosed1 | Estimate initial population size for single or multiple census mark-recapture data. |

confint.mrClosed2 | Estimate initial population size for single or multiple census mark-recapture data. |

confint.mrOpen | Jolly-Seber analysis from multiple mark-recapture events from an open population. |

confint.nlsBoot | Associated S3 methods for nlsBoot from nlstools. |

confint.nlsboot | Associated S3 methods for nlsBoot from nlstools. |

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

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

depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

diags | Extract diagonals from a matrix. |

dunnTest | Dunn's Kruskal-Wallis Multiple Comparisons. |

dunnTest.default | Dunn's Kruskal-Wallis Multiple Comparisons. |

dunnTest.formula | Dunn's Kruskal-Wallis Multiple Comparisons. |

Ecoli | Population growth of Escherichia coli. |

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

expandLenFreq | Expands a length frequency based on a subsample. |

extraSS | Likelihood ratio and extra sum-of-squares tests. |

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

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

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

fishR | Opens web pages associated with the fishR website. |

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

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

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

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

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

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

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

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

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

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

FSA | Fisheries stock assessment methods and data. |

FSANews | Read news and changes for the 'FSA' package. |

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

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

geomean | Calculates the geometric mean or geometric standard deviation. |

geosd | Calculates the geometric mean or geometric standard deviation. |

GompertzFuns | Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions. |

growthFunShow | Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions. |

growthModels | Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions. |

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

hist.bootCase | Case bootstrapping and associated S3 methods. |

hist.formula | Creates separate histograms by levels. |

histFromSum | Create a histogram from a frequency table. |

histFromSum.default | Create a histogram from a frequency table. |

histFromSum.formula | Create a histogram from a frequency table. |

histFromSum.table | Create a histogram from a frequency table. |

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

htest | Associated S3 methods for nlsBoot from nlstools. |

htest.bootCase | Case bootstrapping and associated S3 methods. |

htest.nlsBoot | Associated S3 methods for nlsBoot from nlstools. |

htest.nlsboot | Associated S3 methods for nlsBoot from nlstools. |

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

is.CapHist | Summarize capture histories in individual fish format. |

is.even | Determine if a number is odd or even. |

is.odd | Determine if a number is odd or even. |

jolly | Jolly-Seber analysis from multiple mark-recapture events from an open population. |

kCounts | Specific utilities for use in a knitr document. |

kPvalue | Specific utilities for use in a knitr document. |

ksTest | Kolmogorov-Smirnov Tests. |

ksTest.default | Kolmogorov-Smirnov Tests. |

ksTest.formula | Kolmogorov-Smirnov Tests. |

lagratio | Ratio of lagged observations. |

lencat | Constructs length class/category variable. |

lencat.default | Constructs length class/category variable. |

lencat.formula | Constructs length class/category variable. |

logbtcf | Constructs the correction-factor used when back-transforming log-transformed values. |

logisticFuns | |

lrt | Likelihood ratio and extra sum-of-squares tests. |

lwCompPreds | Constructs plots of predicted weights at given lengths among different groups. |

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

metaM | Estimate natural mortality from a variety of empirical methods. |

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

Mmethods | Estimate natural mortality from a variety of empirical methods. |

mrClosed | Estimate initial population size for single or multiple census mark-recapture data. |

mrOpen | Jolly-Seber analysis from multiple mark-recapture events from an open population. |

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

oddeven | Determine if a number is odd or even. |

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

pcumsum | Computes the prior to or reverse cumulative sum of a vector. |

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

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. |

plot.ageBias | Compute and view possible differences between paired sets of ages. |

plot.agePrec | Compute measures of precision among sets of ages. |

plot.bootCase | Case bootstrapping and associated S3 methods. |

plot.CapHist | Summarize capture histories in individual fish format. |

plot.catchCurve | Mortality estimates from the descending limb of a catch curve. |

plot.chapmanRobson | Computes Chapman-Robson estimates of S and Z. |

plot.depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

plot.mrClosed2 | Estimate initial population size for single or multiple census mark-recapture data. |

plotAB | Construct traditional (Campana-like) age-bias plots. |

plotBinResp | Plots a binary response variable versus a quantitative explanatory variable. |

plotBinResp.default | Plots a binary response variable versus a quantitative explanatory variable. |

plotBinResp.formula | Plots a binary response variable versus a quantitative explanatory variable. |

poiCI | Confidence interval for Poisson counts. |

predict.bootCase | Case bootstrapping and associated S3 methods. |

predict.nlsbooot | Associated S3 methods for nlsBoot from nlstools. |

predict.nlsBoot | Associated S3 methods for nlsBoot from nlstools. |

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

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

print.dunnTest | Dunn's Kruskal-Wallis Multiple Comparisons. |

print.extraTest | Likelihood ratio and extra sum-of-squares tests. |

print.metaM | Estimate natural mortality from a variety of empirical methods. |

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

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

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

psdCalc | Convenience function for calculating PSD-X and PSD X-Y values. |

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 highlighted. |

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

purl2 | Specific utilities for use in a knitr document. |

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

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

repeatedRows2Keep | Find non-repeated consecutive rows in a data.frame. |

reproInfo | Specific utilities for use in a knitr document. |

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

residPlot.IVR | Construct a residual plot from lm or nls objects. |

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

residPlot.nlme | Construct a residual plot from lm or nls objects. |

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

residPlot.ONEWAY | Construct a residual plot from lm or nls objects. |

residPlot.POLY | Construct a residual plot from lm or nls objects. |

residPlot.SLR | Construct a residual plot from lm or nls objects. |

residPlot.TWOWAY | Construct a residual plot from lm or nls objects. |

RichardsFuns | |

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

rSquared.catchCurve | Mortality estimates from the descending limb of a catch curve. |

rSquared.default | Extract the coefficient of determination from a linear model object. |

rSquared.depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

rSquared.lm | Extract the coefficient of determination from a linear model object. |

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

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

se | Computes standard error of the mean. |

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. |

srFuns | Creates a function for a specific parameterization of a common stock-recruitment function . |

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. |

stockRecruitment | Creates a function for a specific parameterization of a common stock-recruitment function . |

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

Summarize | Summary statistics for a numeric variable. |

Summarize.default | Summary statistics for a numeric variable. |

Summarize.formula | Summary statistics for a numeric variable. |

summary.ageBias | Compute and view possible differences between paired sets of ages. |

summary.agePrec | Compute measures of precision among sets of ages. |

summary.catchCurve | Mortality estimates from the descending limb of a catch curve. |

summary.chapmanRobson | Computes Chapman-Robson estimates of S and Z. |

summary.depletion | Computes the Leslie or DeLury population estimate from catch and effort data. |

summary.mrClosed1 | Estimate initial population size for single or multiple census mark-recapture data. |

summary.mrClosed2 | Estimate initial population size for single or multiple census mark-recapture data. |

summary.mrOpen | Jolly-Seber analysis from multiple mark-recapture events from an open population. |

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

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

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

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

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

vbFuns | |

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

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). |

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

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

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

WSlit | All known standard weight equations. |

wsVal | Finds standard weight equation coefficients for a particular species. |