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FSA (version 0.8.30)
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
9,602
Version
0.8.30
License
GPL (>= 2)
Issues
3
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Stars
65
Forks
20
Repository
https://github.com/droglenc/FSA
Maintainer
Derek Ogle
Last Published
March 9th, 2020
Functions in FSA (0.8.30)
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CodNorwegian
Stock and recruitment data for Norwegian cod, 1937-1960.
FSAUtils
Capitalizes the first letter of first or all words in a string.
PSDlit
Gabelhouse five-cell length categories for various species.
BrookTroutTH
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
WhitefishLC
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
PikeNY
Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
addZeroCatch
Adds zeros for catches of species not collected in some sampling events.
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.
.onAttach
Internal functions.
FSA
Fisheries stock assessment methods and data.
SMBassWB
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
SMBassLS
Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
Schnute
The four-parameter growth function from Schnute (1981).
compIntercepts
Tests for significant differences among all pairs of intercepts in a dummy variable regression.
compSlopes
Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).
ageBias
Compute and view possible differences between paired sets of ages.
agePrecision
Compute measures of precision among sets of ages.
alkMeanVar
Mean Values-at-age from an age-length key
alkPlot
Plots to visualize age-length keys.
dunnTest
Dunn's Kruskal-Wallis Multiple Comparisons.
expandCounts
Repeat individual fish data (including lengths) from tallied counts.
binCI
Confidence intervals for binomial probability of success.
bootstrap
Case bootstrapping and associated S3 methods.
SchnuteRichards
The five-parameter growth function from Schnute and Richards (1990).
SpotVA1
Age and length of spot.
catchCurve
Mortality estimates from the descending limb of a catch curve.
confint.nlsBoot
Associated S3 methods for nlsBoot from nlstools.
jolly
Jolly-Seber analysis from multiple mark-recapture events from an open population.
hyperCI
Confidence interval for population size (N) in hypergeometric distribution.
kCounts
Specific utilities for use in a knitr document.
chapmanRobson
Computes Chapman-Robson estimates of S and Z.
plotAB
Construct traditional (Campana-like) age-bias plots.
Summarize
Summary statistics for a numeric variable.
Subset
Subsets/filters a data frame and drops the unused levels.
alkAgeDist
Proportions-at-age from an age-length key
plotBinResp
Plots a binary response variable versus a quantitative explanatory variable.
residPlot
Construct a residual plot from lm or nls objects.
alkIndivAge
Use an age-length key to assign age to individuals in the unaged sample.
expandLenFreq
Expands a length frequency based on a subsample.
se
Computes standard error of the mean.
depletion
Computes the Leslie or DeLury population estimate from catch and effort data.
extraTests
Likelihood ratio and extra sum-of-squares tests.
wsVal
Finds standard weight equation coefficients for a particular species.
WSlit
All known standard weight equations.
diags
Extract diagonals from a matrix.
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.
capHistConvert
Convert between capture history data.frame formats.
capHistSum
Summarize capture histories in individual fish format.
chooseColors
Create a list of colors from among a variety of color palettes.
histFromSum
Create a histogram from a frequency table.
col2rgbt
Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
hoCoef
Performs a hypothesis test that a linear model parameter is equal to a specific value.
nlsTracePlot
Adds model fits from nls iterations to active plot.
oddeven
Determine if a number is odd or even.
poiCI
Confidence interval for Poisson counts.
psdAdd
Creates a vector of Gabelhouse lengths for each species in an entire data frame.
sumTable
Creates a one- or two-way table of summary statistics.
fact2num
Converts "numeric" factor levels to numeric values.
fitPlot
Fitted model plot for an lm, glm, or nls object.
tictactoe
Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
fishR
Opens web pages associated with the fishR website.
fsaNews
Read news and changes for the 'FSA' package.
ksTest
Kolmogorov-Smirnov Tests.
headtail
Shows rows from the head and tail of a data frame or matrix.
mapvalues
Replace specified values in a vector or factor with new values.
geomean
Calculates the geometric mean or geometric standard deviation.
lagratio
Ratio of lagged observations.
lencat
Constructs length class/category variable.
peek
Peek into (show a subset of) a data frame or matrix.
perc
Computes the percentage of values in a vector less than or greater than (and equal to) some value.
lwCompPreds
Constructs plots of predicted weights at given lengths among different groups.
Mmethods
Estimate natural mortality from a variety of empirical methods.
growthModels
Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
mrClosed
Estimate initial population size for single or multiple census mark-recapture data.
rSquared
Extract the coefficient of determination from a linear model object.
srStarts
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
psdCalc
Convenience function for calculating PSD-X and PSD X-Y values.
psdVal
Finds Gabelhouse lengths (for PSD calculations) for a species.
hist.formula
Creates separate histograms by levels.
logbtcf
Constructs the correction-factor used when back-transforming log-transformed values.
psdPlot
Length-frequency histogram with Gabelhouse lengths highlighted.
stockRecruitment
Creates a function for a specific parameterization of a common stock-recruitment function .
psdCI
Compute confidence intervals for PSD-X and PSD X-Y values.
vbStarts
Find reasonable starting values for a von Bertalanffy growth function.
rcumsum
Computes the prior to or reverse cumulative sum of a vector.
removal
Population estimates for k-, 3-, or 2-pass removal data.
repeatedRows2Keep
Find non-repeated consecutive rows in a data.frame.
validn
Finds the number of valid (non-NA) values in a vector.
ChinookArg
Lengths and weights for Chinook Salmon from three locations in Argentina.
Ecoli
Population growth of Escherichia coli.
CutthroatAL
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
BluegillJL
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.