Age ComparisonsSummarize and visualize bias and precision among multiple estimates of age for individual fish. |
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Compute and view possible differences between paired sets of ages. |
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Compute measures of precision among sets of ages. |
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Construct traditional (Campana-like) age-bias plots. |
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Age-Length KeysProcess age-length keys including assigning ages to indvidual fish and visualizing a key. |
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Use an age-length key to assign age to individuals in the unaged sample. |
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Plots to visualize age-length keys. |
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Proportions-at-age from an age-length key |
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Mean Values-at-age from an age-length key |
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Size StructureEfficiently calculate and summarize proportional size distribution (PSD) data. |
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Gabelhouse five-cell length categories for various species. |
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Finds Gabelhouse lengths (for PSD calculations) for a species. |
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Length-frequency histogram with Gabelhouse lengths highlighted. |
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Convenience function for calculating PSD-X and PSD X-Y values. |
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Compute confidence intervals for PSD-X and PSD X-Y values. |
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Creates a vector of Gabelhouse lengths for each species in an entire data frame. |
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Construct a base tic-tac-toe plot for presenting predator-prey PSD values. |
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Condition and Weight-LengthEfficiently calculate and summarize relative weight and visualize weight-length data among groups with different slopes. |
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All known standard weight equations. |
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Finds standard weight equation coefficients for a particular species. |
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Computes a vector of relative weights specific to a species in an entire data frame. |
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Constructs plots of predicted weights at given lengths among different groups. |
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Abundance (Capture-Recapture)Estimate abundance with capture-recapture data, including handling and summarizing data in a capture history format. |
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Estimate initial population size for single or multiple census mark-recapture data. |
Jolly-Seber analysis from multiple mark-recapture events from an open population. |
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Convert between capture history data.frame formats. |
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Summarize capture histories in individual fish format. |
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Abundance (Depletion)Estimate abundance with depletion and removal data. |
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Computes the Leslie or DeLury population estimate from catch and effort data. |
Population estimates for k-, 3-, or 2-pass removal data. |
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Individual GrowthFit various growth models (von Bertalanffy, Gompertz, logistic, Richards, Schnute) to individual fish. |
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Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions. |
Find reasonable starting values for a von Bertalanffy growth function. |
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The four-parameter growth function from Schnute (1981). |
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Mortality RatesEstimate mortality rates from catch curve data and empirical models. |
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Mortality estimates from the descending limb of a catch curve. |
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Computes Chapman-Robson estimates of S and Z. |
Estimate natural mortality from a variety of empirical methods. |
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Stock-RecruimentFit various (Beverton-Holt, Ricker, Shepherd) stock-recruitment functions. |
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Creates a function for a specific parameterization of a common stock-recruitment function . |
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Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models. |
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Utilities (Fisheries-Specific)Utilities that are likely useful only to fisheries scientists. |
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Adds zeros for catches of species not collected in some sampling events. |
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Repeat individual fish data (including lengths) from tallied counts. |
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Expands a length frequency based on a subsample. |
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Constructs length class/category variable. |
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Utilities (General Statistics)Utilities of a statistical nature that are likely to be useful to a fisheries scientist. |
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Confidence intervals for binomial probability of success. |
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Confidence interval for population size (N) in hypergeometric distribution. |
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Confidence interval for Poisson counts. |
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Case bootstrapping and associated S3 methods. |
Tests for significant differences among all pairs of intercepts in a dummy variable regression. |
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Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR). |
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Dunn's Kruskal-Wallis Multiple Comparisons. |
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Likelihood ratio and extra sum-of-squares tests. |
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Fitted model plot for an lm, glm, or nls object. |
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Calculates the geometric mean or geometric standard deviation. |
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Creates separate histograms by levels. |
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Create a histogram from a frequency table. |
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Performs a hypothesis test that a linear model parameter is equal to a specific value. |
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Associated S3 methods for nlsBoot from nlstools. |
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Kolmogorov-Smirnov Tests. |
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Constructs the correction-factor used when back-transforming log-transformed values. |
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Adds model fits from nls iterations to active plot. |
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Computes the prior to or reverse cumulative sum of a vector. |
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Plots a binary response variable versus a quantitative explanatory variable. |
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Construct a residual plot from lm or nls objects. |
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Extract the coefficient of determination from a linear model object. |
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Computes standard error of the mean. |
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Summary statistics for a numeric variable. |
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Creates a one- or two-way table of summary statistics. |
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Utilities (Other)Miscellaneous utilities. |
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Capitalizes the first letter of first or all words in a string. |
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Create a list of colors from among a variety of color palettes. |
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Converts an R color to RGB (red/green/blue) including a transparency (alpha channel). |
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Extract diagonals from a matrix. |
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Converts "numeric" factor levels to numeric values. |
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Subsets/filters a data frame and drops the unused levels. |
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Shows rows from the head and tail of a data frame or matrix. |
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Determine if a number is odd or even. |
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Ratio of lagged observations. |
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Replace specified values in a vector or factor with new values. |
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Computes the percentage of values in a vector less than or greater than (and equal to) some value. |
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Finds the number of valid (non-NA) values in a vector. |
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DataData files. |
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Capture histories (2 samples) of Bluegill from Jewett Lake, MI. |
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Catch-at-age for Tobin Harbor, Isle Royale Brook Trout. |
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Lengths and weights for Chinook Salmon from three locations in Argentina. |
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Stock and recruitment data for Norwegian cod, 1937-1960. |
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Capture histories (9 samples) of Cutthroat Trout from Auke Lake. |
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Population growth of Escherichia coli. |
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Mirex concentration, weight, capture year, and species of Lake Ontario salmon. |
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Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY. |
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Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY. |
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Gabelhouse five-cell length categories for various species. |
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Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass. |
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Growth increment data for West Bearskin Lake, MN, Smallmouth Bass. |
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Age and length of spot. |
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Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain. |
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Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979). |
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All known standard weight equations. |