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FSA (version 0.8.20)

Simple Fisheries Stock Assessment Methods

Description

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

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Version

Install

install.packages('FSA')

Monthly Downloads

11,140

Version

0.8.20

License

GPL (>= 2)

Issues

4

Pull Requests

0

Stars

66

Forks

21

Maintainer

Derek Ogle

Last Published

May 18th, 2018

Functions in FSA (0.8.20)

WR79

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

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

Plots to visualize age-length keys.
WSlit

All known standard weight equations.
expandLenFreq

Expands a length frequency based on a subsample.
col2rgbt

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

Specific utilities for use in a knitr document.
compIntercepts

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

Confidence intervals for binomial probability of success.
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.
ksTest

Kolmogorov-Smirnov Tests.
expandCounts

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

Read news and changes for the 'FSA' package.
fitPlot

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

Summarize capture histories in individual fish format.
fishR

Opens web pages associated with the fishR website.
addZeroCatch

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

Compute and view possible differences between paired sets of ages.
catchCurve

Mortality estimates from the descending limb of a catch curve.
oddeven

Determine if a number is odd or even.
geomean

Calculates the geometric mean or geometric standard deviation.
psdAdd

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

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

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

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

Compute measures of precision among sets of ages.
compSlopes

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

Case bootstrapping and associated S3 methods.
alkIndivAge

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

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

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

Likelihood ratio and extra sum-of-squares tests.
capHistConvert

Convert between capture history data.frame formats.
fact2num

Converts "numeric" factor levels to numeric values.
headtail

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

Proportions-at-age from an Age-Length Key
mrClosed

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

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

Extract diagonals from a matrix.
dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.
mapvalues

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

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

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

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

Create a histogram from a frequency table.
hist.formula

Creates separate histograms by levels.
psdCalc

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

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

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

Estimate natural mortality from a variety of empirical methods.
vbStarts

Find reasonable starting values for a von Bertalanffy growth function.
chapmanRobson

Computes Chapman-Robson estimates of S and Z.
psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.
plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.
stockRecruitment

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

Confidence interval for Poisson counts.
rcumsum

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

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

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

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

Ratio of lagged observations.
tictactoe

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

Adds model fits from nls iterations to active plot.
wsVal

Finds standard weight equation coefficients for a particular species.
confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.
lencat

Constructs length class/category variable.
wrAdd

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

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

Extract the coefficient of determination from a linear model object.
residPlot

Construct a residual plot from lm or nls objects.
se

Computes standard error of the mean.
FSA

Fisheries stock assessment methods and data.
Ecoli

Population growth of Escherichia coli.
CutthroatAL

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

Internal functions.
ChinookArg

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

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

Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
SpotVA1

Age and length of spot.
Mirex

Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
PikeNYPartial1

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

Summary statistics for a numeric variable.
SMBassLS

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

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

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

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

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

Gabelhouse five-cell length categories for various species.
PikeNY

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