A B C D E F G H I J K L M N P R S T V W
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. |
boot | Associated S3 methods for bootstrap results from car::Boot. |
bootCase | DEFUNCT functions. |
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 | DEFUNCT functions. |
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 | DEFUNCT functions. |
compSlopes | DEFUNCT functions. |
confint.boot | Associated S3 methods for bootstrap results from car::Boot. |
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.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 | DEFUNCT functions. |
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 | DEFUNCT functions. |
fishR | Opens web pages associated with the fishR website. |
fitPlot | DEFUNCT functions. |
FSA-defunct | DEFUNCT functions. |
fsaNews | DEFUNCT functions. |
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.boot | Associated S3 methods for bootstrap results from car::Boot. |
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 | DEFUNCT functions. |
htest | Associated S3 methods for nlsBoot from nlstools. |
htest.boot | Associated S3 methods for bootstrap results from car::Boot. |
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 | Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions. |
lrt | Likelihood ratio and extra sum-of-squares tests. |
lwCompPreds | Constructs plots of predicted weights at given lengths among different groups. |
mapvalues | DEFUNCT functions. |
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. |
nlsBoot | Associated S3 methods for nlsBoot from nlstools. |
nlsTracePlot | Adds model fits from nls iterations to active plot. |
pcumsum | Computes the prior to or reverse cumulative sum of a vector. |
peek | Peek into (show a subset of) a data frame or matrix. |
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.boot | Associated S3 methods for bootstrap results from car::Boot. |
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 | DEFUNCT functions. |
poiCI | Confidence interval for Poisson counts. |
predict.boot | Associated S3 methods for bootstrap results from car::Boot. |
predict.nlsBoot | Associated S3 methods for nlsBoot from nlstools. |
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 | DEFUNCT functions. |
RichardsFuns | Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions. |
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. |
Subset | DEFUNCT functions. |
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 | 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. |
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. |