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FSA (version 0.8.17)

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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Install

install.packages('FSA')

Monthly Downloads

16,224

Version

0.8.17

License

GPL (>= 2)

Issues

4

Pull Requests

0

Stars

66

Forks

22

Maintainer

Derek Ogle

Last Published

October 29th, 2017

Functions in FSA (0.8.17)

.onAttach

Internal functions.
PSDlit

Gabelhouse five-cell length categories for various species.
PikeNY

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

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

Plots to visualize age-length keys.
FSA

Fisheries stock assessment methods and data.
capHistSum

Summarize capture histories in individual fish format.
catchCurve

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

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

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

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

Specific utilities for use in a knitr document.
lwCompPreds

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

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

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

Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
SpotVA1

Age and length of spot.
Subset

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

Compute and view possible differnces between paired sets of ages.
agePrecision

Compute measures of precision among sets of ages.
chapmanRobson

Computes Chapman-Robson estimates of S and Z.
chooseColors

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

Likelihood ratio and extra sum-of-squares tests.
fact2num

Converts "numeric" factor levels to numeric values.
geomean

Calculates the geometric mean or geometric standard deviation.
growthModels

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

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

Associated S3 methods for nlsBoot from nlstools.
psdCI

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

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

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

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

Summary statistics for a numeric variable.
WR79

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

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

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

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

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

Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
PikeNYPartial1

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

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

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

Adds zeros for catches of species not collected in some sampling events.
col2rgbt

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

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

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

Converts between types of measurements from calcified structures.
psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.
psdVal

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

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

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

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

Associated S3 methods for bootCase from car.
capHistConvert

Convert between capture history data.frame formats.
diags

Extract diagonals from a matrix.
dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.
headtail

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

Creates separate histograms by levels.
lencat

Constructs length class/category variable.
logbtcf

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

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

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

Creates a function for a specific back-calculation model.
binCI

Confidence intervals for binomial probability of success.
fishR

Opens web pages associated with the fishR website.
residPlot

Construct a residual plot from lm or nls objects.
se

Computes standard error of the mean.
wrAdd

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

Finds standard weight equation coefficients for a particular species.
fitPlot

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

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

Population growth of Escherichia coli.
SMBassWB

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

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

All known standard weight equations.
WhitefishLC

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

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

Expands a length frequency based on a subsample.
histFromSum

Create a histogram from a frequency table.
hoCoef

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

Kolmogorov-Smirnov Tests.
lagratio

Ratio of lagged observations.
poiCI

Confidence interval for Poisson counts.
mrClosed

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

Adds model fits from nls iterations to active plot.
oddeven

Determine if a number is odd or even.
validn

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

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

Estimate natural mortality from a variety of empirical methods.
psdAdd

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