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FSA (version 0.8.19)
Simple Fisheries Stock Assessment Methods
A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website
Link to current version
GPL (>= 2)
April 8th, 2018
Functions in FSA (0.8.19)
Proportions-at-age from an Age-Length Key
Adds zeros for catches of species not collected in some sampling events.
Add a total radius-at-capture variable to a data.frame that contains one-fish-per-line increments data.
Replace specified values in a vector or factor with new values.
Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).
Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
Tests for significant differences among all pairs of intercepts in a dummy variable regression.
Likelihood ratio and extra sum-of-squares tests.
Mean Values-at-age from an Age-Length Key
Converts "numeric" factor levels to numeric values.
Read news and changes for the 'FSA' package.
Plots to visualize age-length keys.
Constructs plots of predicted weights at given lengths among different groups.
Create a list of colors from among a variety of color palettes.
Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).
Performs a hypothesis test that a linear model parameter is equal to a specific value.
Create a histogram from a frequency table.
Compute measures of precision among sets of ages.
Computes Chapman-Robson estimates of S and Z.
Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
Computes the Leslie or DeLury population estimate from catch and effort data.
Confidence interval for Poisson counts.
Converts between types of measurements from calcified structures.
Constructs the correction-factor used when back-transforming log-transformed values.
Confidence intervals for binomial probability of success.
Creates a function for a specific back-calculation model.
Constructs length class/category variable.
Creates a vector of Gabelhouse lengths for each species in an entire data frame.
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
All known standard weight equations.
Use an age-length key to assign age to individuals in the unaged sample.
Case bootstrapping and associated S3 methods.
Opens web pages associated with the fishR website.
Population estimates for k-, 3-, or 2-pass removal data.
Summarize capture histories in individual fish format.
Mortality estimates from the descending limb of a catch curve.
Fitted model plot for an lm, glm, or nls object.
Calculates the geometric mean or geometric standard deviation.
Computes the percentage of values in a vector less than or greater than (and equal to) some value.
Plots a binary response variable versus a quantitative explanatory variable.
Jolly-Seber analysis from multiple mark-recapture events from an open population.
Repeat individual fish data (including lengths) from tallied counts.
Expands a length frequency based on a subsample.
Confidence interval for population size (N) in hypergeometric distribution.
Specific utilities for use in a knitr document.
Computes standard error of the mean.
Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
Finds standard weight equation coefficients for a particular species.
Associated S3 methods for nlsBoot from nlstools.
Convert between capture history data.frame formats.
Length-frequency histogram with Gabelhouse lengths highlighted.
Dunn's Kruskal-Wallis Multiple Comparisons.
Creates separate histograms by levels.
Extract diagonals from a matrix.
Shows rows from the head and tail of a data frame or matrix.
Estimate initial population size for single or multiple census mark-recapture data.
Estimate natural mortality from a variety of empirical methods.
Compute confidence intervals for PSD-X and PSD X-Y values.
Ratio of lagged observations.
Convenience function for calculating PSD-X and PSD X-Y values.
Extract the coefficient of determination from a linear model object.
Computes the prior to or reverse cumulative sum of a vector.
Construct a residual plot from lm or nls objects.
Adds model fits from nls iterations to active plot.
Find reasonable starting values for a von Bertalanffy growth function.
Determine if a number is odd or even.
Computes a vector of relative weights specific to a species in an entire data frame.
Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
Finds the number of valid (non-NA) values in a vector.
Finds Gabelhouse lengths (for PSD calculations) for a species.
Creates a function for a specific parameterization of a common stock-recruitment function .
Creates a one- or two-way table of summary statistics.
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
Compute and view possible differences between paired sets of ages.
Capitalizes the first letter of first or all words in a string.
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
Population growth of Escherichia coli.
Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
Lengths and weights for Chinook Salmon from three locations in Argentina.
Stock and recruitment data for Norwegian cod, 1937-1960.
Fisheries stock assessment methods and data.
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
The four-parameter growth function from Schnute (1981).
Age and length of spot.
Subsets/filters a data frame and drops the unused levels.
Summary statistics for a numeric variable.
Gabelhouse five-cell length categories for various species.