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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
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Install
install.packages('FSA')
Monthly Downloads
9,832
Version
0.8.32
License
GPL (>= 2)
Issues
3
Pull Requests
0
Stars
63
Forks
20
Repository
https://github.com/droglenc/FSA
Maintainer
Derek Ogle
Last Published
January 15th, 2021
Functions in FSA (0.8.32)
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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.
se
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.