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FSA (version 0.8.8)

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

21,693

Version

0.8.8

License

GPL (>= 2)

Issues

2

Pull Requests

0

Stars

74

Forks

27

Maintainer

Derek Ogle

Last Published

July 18th, 2016

Functions in FSA (0.8.8)

bcFuns

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

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

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

Confidence intervals for binomial probability of success.
agePrecision

Compute measures of precision among sets of ages.
ageBias

Compute and view possible biases between paired sets of ages.
addRadCap

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

Plots to visualize age-length keys.
addZeroCatch

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

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

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

Computes Chapman-Robson estimates of S and Z.
capHistSum

Summarize capture histories in individual fish format.
chooseColors

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

Associated S3 methods for bootCase from car.
capHistConvert

Convert between capture history data.frame formats.
ChinookArg

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

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

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

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

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

Population growth of Escherichia coli.
depletion

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

Expands a length frequency based on a subsample.
expandCounts

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

Dunn's Kruskal-Wallis Multiple Comparisons.
col2rgbt

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

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

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

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

Fisheries stock assessment methods and data.
fsaNews

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

Capitalizes the first letter of first or all words in a string.
fact2num

Converts "numeric" factor levels to numeric values.
gConvert

Converts between types of measurements from calcified structures.
fishR

Opens web pages associated with the fishR website.
ksTest

Kolmogorov-Smirnov Tests.
lagratio

Ratio of lagged observations.
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.
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.
hoCoef

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

Create a histogram from a frequency table.
mapvalues

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

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

Internal functions.
headtail

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

Creates separate histograms by levels.
confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.
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.
logbtcf

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

Constructs length class/category variable.
PikeNY

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

Confidence interval for Poisson rate parameter.
psdAdd

Creates a vector of Gabelhouse lengths for each species in an entire data frame.
PikeNYPartial1

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

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

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

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

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

Construct a residual plot from lm or nls objects.
se

Computes standard error of the mean.
Schnute

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

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

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

Gabelhouse five-cell length categories for various species.
psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.
psdVal

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

Estimate natural mortality from a variety of empirical methods.
Mirex

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

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

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

Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
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.
WR79

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

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

All known standard weight equations.
Subset

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

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

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

Estimate initial population size for single or multiple census mark-recapture data.
SpotVA1

Age and length of spot.
srStarts

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

Summary statistics for a numeric or factor variable.
sumTable

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