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

FSA (version 0.8.32)

Simple Fisheries Stock Assessment Methods

Description

A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website .

Copy Link

Version

Install

install.packages('FSA')

Monthly Downloads

22,961

Version

0.8.32

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

January 15th, 2021

Functions in FSA (0.8.32)

BluegillJL

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

FSA

Fisheries stock assessment methods and data.

ChinookArg

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

FSAUtils

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

.onAttach

Internal functions.

Mirex

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

CutthroatAL

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

BrookTroutTH

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

CodNorwegian

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

Ecoli

Population growth of Escherichia coli.

PSDlit

Gabelhouse five-cell length categories for various species.

SchnuteRichards

The five-parameter growth function from Schnute and Richards (1990).

Subset

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

PikeNY

Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.

WSlit

All known standard weight equations.

alkPlot

Plots to visualize age-length keys.

WR79

Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).

SMBassLS

Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.

alkMeanVar

Mean Values-at-age from an age-length key

PikeNYPartial1

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

SMBassWB

Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.

alkAgeDist

Proportions-at-age from an age-length key

Schnute

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

SpotVA1

Age and length of spot.

Summarize

Summary statistics for a numeric variable.

ageBias

Compute and view possible differences between paired sets of ages.

compSlopes

Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).

compIntercepts

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

agePrecision

Compute measures of precision among sets of ages.

WhitefishLC

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

bootstrap

Case bootstrapping and associated S3 methods.

binCI

Confidence intervals for binomial probability of success.

catchCurve

Mortality estimates from the descending limb of a catch curve.

addZeroCatch

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

capHistConvert

Convert between capture history data.frame formats.

expandLenFreq

Expands a length frequency based on a subsample.

capHistSum

Summarize capture histories in individual fish format.

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

expandCounts

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

fact2num

Converts "numeric" factor levels to numeric values.

fishR

Opens web pages associated with the fishR website.

fsaNews

Read news and changes for the 'FSA' package.

fitPlot

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

histFromSum

Create a histogram from a frequency table.

hyperCI

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

hoCoef

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

alkIndivAge

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

diags

Extract diagonals from a matrix.

chooseColors

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

col2rgbt

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

depletion

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

headtail

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

hist.formula

Creates separate histograms by levels.

kCounts

Specific utilities for use in a knitr document.

ksTest

Kolmogorov-Smirnov Tests.

lagratio

Ratio of lagged observations.

lwCompPreds

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

mapvalues

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

psdCI

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

geomean

Calculates the geometric mean or geometric standard deviation.

psdAdd

Creates a vector of Gabelhouse lengths for each species in an entire data frame.

poiCI

Confidence interval for Poisson counts.

removal

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

stockRecruitment

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

psdCalc

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

srStarts

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

lencat

Constructs length class/category variable.

growthModels

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

logbtcf

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

repeatedRows2Keep

Find non-repeated consecutive rows in a data.frame.

nlsTracePlot

Adds model fits from nls iterations to active plot.

peek

Peek into (show a subset of) a data frame or matrix.

oddeven

Determine if a number is odd or even.

perc

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

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

jolly

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

Mmethods

Estimate natural mortality from a variety of empirical methods.

mrClosed

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

rSquared

Extract the coefficient of determination from a linear model object.

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

residPlot

Construct a residual plot from lm or nls objects.

Computes standard error of the mean.

plotAB

Construct traditional (Campana-like) age-bias plots.

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

sumTable

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

rcumsum

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

psdVal

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

tictactoe

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

validn

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

wsVal

Finds standard weight equation coefficients for a particular species.

wrAdd

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

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.