Learn R Programming

⚠️There's a newer version (0.9.6) of this package.Take me there.

FSA (version 0.8.1)

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.

Copy Link

Version

Install

install.packages('FSA')

Monthly Downloads

25,045

Version

0.8.1

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/droglenc/FSA

Homepage

http://derekogle.com/fishR/

Maintainer

Last Published

October 10th, 2015

Functions in FSA (0.8.1)

Internal functions.

Age and length of spot.

Gabelhouse five-cell length categories for various species.

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

Population growth of Escherichia coli.

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

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.

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

Plots to visualize age-length keys.

All known standard weight equations.

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

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

Catch-effort data for Little Silver Lake Smallmouth Bass.

Creates separate histograms by levels.

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

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

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

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

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

Length-frequency histogram with Gabelhouse lengthshighlighted.

Confidence interval for Poisson rate parameter.

Creates a function for a specific back-calculation model.

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

Convert between capture history data.frame formats.

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

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

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

Finds reasonable starting values for parameters in specific paramaterizations of common stock-recruitment models.

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

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

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

Mortality estimates from the descending limb of a catch curve.

Fisheries stock assessment methods and data.

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

Confidence intervals for binomial probability of success.

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

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

Opens web pages associated with the fishR website.

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

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

Read news and changes for the 'FSA' package.

Construct a residual plot from lm or nls objects.

Summary statistics for a numeric or factor variable.

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

Constructs length class/category variable.

Tests for significant differences among all pairs of intercepts in a dummy variable regression.

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

Compute and view possible biases between paired sets of ages.

Estimate natural mortality from a variety of empirical methods.

Growth increment data for West Bearskin Lake Smallmouth Bass.

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

Dunn's Kruskal-Wallis Multiple Comparisons.

Converts "numeric" factor levels to numeric values.

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

Ratio of lagged observations.

Kolmogorov-Smirnov Tests.

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

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

Likelihood ratio and extra sum-of-squares tests.

Determine if a number is odd or even.

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

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

Proportions-at-age from an Age-Length Key

Computes Chapman-Robson estimates of S and Z.

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

Computes standard error of the mean.

Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.

Summarize capture histories in individual fish format.

Find reasonable starting values for a von Bertalanffy growth function.

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

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

Compute measures of precision among sets of ages.

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

stockRecruitment

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

Associated S3 methods for bootCase from car.

Converts between types of measurements from calcified structures.

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

Specific utilities for use in a knitr document.

Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).

Expands a length frequency based on a subsample.

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

Plots a binary response variable versus a quantitative explanatory variable.

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

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

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

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

Finds standard weight equation coefficients for a particular species.