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FSA (version 0.9.5)
Simple Fisheries Stock Assessment Methods
A variety of simple fish stock assessment methods.
Link to current version
GPL (>= 2)
August 26th, 2023
Functions in FSA (0.9.5)
Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
Summary statistics for a numeric variable.
The five-parameter growth function from Schnute and Richards (1990).
Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).
Population growth of Escherichia coli.
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
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.
The four-parameter growth function from Schnute (1981).
Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
Gabelhouse five-cell length categories for various species.
Age and length of spot.
Plots to visualize age-length keys.
Adds zeros for catches of species not collected in some sampling events.
All known standard weight equations.
Confidence intervals for binomial probability of success.
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
Compute and view possible differences between paired sets of ages.
Proportions-at-age from an age-length key
Compute measures of precision among sets of ages.
Mean Values-at-age from an age-length key
Use an age-length key to assign age to individuals in the unaged sample.
Summarize capture histories in individual fish format.
Dunn's Kruskal-Wallis Multiple Comparisons.
Associated S3 methods for bootstrap results from car::Boot.
Repeat individual fish data (including lengths) from tallied counts.
Convert between capture history data.frame formats.
Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
Computes Chapman-Robson estimates of S and Z.
Computes the Leslie or DeLury population estimate from catch and effort data.
Mortality estimates from the descending limb of a catch curve.
Capitalizes the first letter of first or all words in a string.
Converts "numeric" factor levels to numeric values.
Expands a length frequency based on a subsample.
Shows rows from the head and tail of a data frame or matrix.
Calculates the geometric mean or geometric standard deviation.
Creates separate histograms by levels.
Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
Opens web pages associated with the fishR website.
Likelihood ratio and extra sum-of-squares tests.
Confidence interval for population size (N) in hypergeometric distribution.
Create a histogram from a frequency table.
Determine if a number is odd or even.
Ratio of lagged observations.
Specific utilities for use in a knitr document.
Estimate initial population size for single or multiple census mark-recapture data.
Constructs length class/category variable.
Constructs plots of predicted weights at given lengths among different groups.
Estimate natural mortality from a variety of empirical methods.
Jolly-Seber analysis from multiple mark-recapture events from an open population.
Construct traditional (Campana-like) age-bias plots.
Constructs the correction-factor used when back-transforming log-transformed values.
Confidence interval for Poisson counts.
Peek into (show a subset of) a data frame or matrix.
Convenience function for calculating PSD-X and PSD X-Y values.
Associated S3 methods for nlsBoot from nlstools.
Computes the percentage of values in a vector less than or greater than (and equal to) some value.
Length-frequency histogram with Gabelhouse lengths highlighted.
Adds model fits from nls iterations to active plot.
Compute confidence intervals for PSD-X and PSD X-Y values.
Finds Gabelhouse lengths (for PSD calculations) for a species.
Creates a vector of Gabelhouse lengths for each species in an entire data frame.
Creates a one- or two-way table of summary statistics.
Computes a vector of relative weights specific to a species in an entire data frame.
Creates a function for a specific parameterization of a common stock-recruitment function .
Computes the prior to or reverse cumulative sum of a vector.
Population estimates for k-, 3-, or 2-pass removal data.
Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
Find non-repeated consecutive rows in a data.frame.
Computes standard error of the mean.
Finds standard weight equation coefficients for a particular species.
Extract the coefficient of determination from a linear model object.
Finds the number of valid (non-NA) values in a vector.
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
Find reasonable starting values for a von Bertalanffy growth function.
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
Fisheries stock assessment methods and data.
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
Stock and recruitment data for Norwegian cod, 1937-1960.
Lengths and weights for Chinook Salmon from three locations in Argentina.