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FSA (version 0.8.0)

Functions for Simple Fisheries Stock Assessment Methods

Description

Functions to perform a variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website listed below.

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Version

Install

install.packages('FSA')

Monthly Downloads

21,460

Version

0.8.0

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/droglenc/FSA

Homepage

http://derekogle.com/fishR/

Maintainer

Derek Ogle

Last Published

October 8th, 2015

Functions in FSA (0.8.0)

Growth increment data for West Bearskin Lake Smallmouth Bass.

Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckthorn Marsh.

Use an age-length key to assign age to individuals in the unaged sample.

Add a total radius-at-capture variable to a data.frame that contains one-fish-per-line increments data.

Gabelhouse five-cell length categories for various species.

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

Compute and view possible biases between paired sets of ages.

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

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

Summarized multiple mark-recapture data for all Northern Pike from Buckthorn Marsh.

Capture histories (2 samples) of Bluegill from Jewett Lake.

Compute measures of precision among sets of ages.

Lengths and weights of Chinook Salmon from three locations in Argentina.

Population growth of Escherichia coli.

All known standard weight equations.

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

Summarize capture histories in individual fish format.

Convert between capture history data.frame formats.

Age and length for a hypothetical sample from Westerheim and Ricker (1979).

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

Mortality estimates from the descending limb of a catch curve.

Age and length of spot.

Computes Chapman-Robson estimates of S and Z.

Computes the Leslie or Delury population estimate from catch and effort data.

Catch-effort data for Little Silver Lake Smallmouth Bass.

Assessed ages from two readers on three structures for Lake Whitefish from Lake Champlain.

Summary statistics for a numeric or factor variable.

Plots a binary response variable versus a quantitative explanatory variable.

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

Proportions-at-age from an Age-Length Key

Converts between types of measurements from calcified structures.

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

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

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

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

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

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

Adds zeroes for catches of species not collected in some sampling events.

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

Fisheries stock assessment methods and data.

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

Dunn's Kruskal-Wallis Multiple Comparisons.

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

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

Mean Values-at-age from an Age-Length Key

Plots to visualize age-length keys.

Associated S3 methods for bootCase from car.

Likelihood ratio and extra sum-of-squares tests.

Specific utilities for use in a knitr document.

Kolmogorov-Smirnov Tests.

Opens web pages associated with the fishR website.

Construct a residual plot from lm or nls objects.

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

Constructs length class/category variable.

Internal functions.

Computes standard error of the mean.

Create vector of Gabelhouse lengths for each species from an entire data frame.

Creates a function for a specific back-calculation model.

Length-frequency histogram with Gabelhouse lengthshighlighted.

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

Compute confidence intervals for PSD-X and PSD X-Y values.

Expands a length frequency based on a subsample.

Estimate natural mortality from a variety of empirical methods.

stockRecruitment

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

Determine if a number is odd or even.

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

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

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

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

Read news and changes for the 'FSA' package.

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 paramaterizations of common stock-recruitment models.

Converts "numeric" factor levels to numeric values.

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

Find reasonable starting values for a von Bertalanffy growth function.

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

Confidence interval for Poisson rate parameter.

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

Confidence intervals for binomial probability of success.

Finds standard weight equation coefficients for a particular species.

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

Creates separate histograms by levels.

Ratio of lagged observations.

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

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