Package: FSA 0.10.1

Derek H. Ogle

FSA: Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods.

Authors:Derek H. Ogle [aut, cre], Jason C. Doll [aut], A. Powell Wheeler [aut], Alexis Dinno [aut]

FSA_0.10.1.tar.gz
FSA_0.10.1.zip(r-4.7)FSA_0.10.1.zip(r-4.6)FSA_0.10.1.zip(r-4.5)
FSA_0.10.1.tgz(r-4.6-any)FSA_0.10.1.tgz(r-4.5-any)
FSA_0.10.1.tar.gz(r-4.7-any)FSA_0.10.1.tar.gz(r-4.6-any)
FSA_0.10.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FSA/json (API)
NEWS

# Install 'FSA' in R:

install.packages('FSA', repos = c('https://fishr-core-team.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fishr-core-team/fsa/issues

Pkgdown/docs site:https://fishr-core-team.github.io

Datasets:

BluegillJL - Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
BrookTroutTH - Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
ChinookArg - Lengths and weights for Chinook Salmon from three locations in Argentina.
CodNorwegian - Stock and recruitment data for Norwegian cod, 1937-1960.
CutthroatAL - Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
Ecoli - Population growth of Escherichia coli.
GrowthData1 - Hypothetical growth data for testing
GrowthData2 - Hypothetical growth data for testing seasonal age models.
GrowthData3 - Hypothetical growth data for testing
Mirex - Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
PikeNY - Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
PikeNYPartial1 - Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
PSDlit - Gabelhouse five-cell length categories for various species.
PSDWRtest - Hypothetical weight-length data for testing PSD and relative weight functions
SMBassLS - Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
SMBassWB - Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
SpotVA1 - Age and length of spot.
WhitefishLC - Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
WR79 - Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).
WSlit - All known standard weight equations.

On CRAN:

fish fisheries fisheries-management fisheries-stock-assessment population-dynamics stock-assessment

11.57 score 76 stars 13 packages 3.9k scripts 21k downloads 225 mentions 93 exports 87 dependencies

Last updated from:4c266fb361. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	218
source / vignettes	OK	251
linux-release-x86_64	OK	176
macos-release-arm64	OK	176
macos-oldrel-arm64	OK	174
windows-devel	OK	196
windows-release	OK	187
windows-oldrel	OK	180
wasm-release	OK	141

Exports:addZeroCatch ageBias agePrecision alkAgeDist alkIndivAge alkMeanVar alkPlot binCI bootCase capFirst capHistConvert capHistSum catchCurve chapmanRobson chooseColors col2rgbt compIntercepts compSlopes depletion diags dunnTest expandCounts expandLenFreq extraSS fact2num filterD findGrowthStarts fishR fitPlot fsaNews geomean geosd GompertzFuns growthFunShow headtail histFromSum hoCoef htest hyperCI is.CapHist is.even is.odd jolly kCounts kPvalue ksTest lagratio lencat logbtcf logisticFuns lrt lwCompPreds makeGrowthFun mapvalues metaM Mmethods mrClosed mrOpen nlsTracePlot pcumsum peek perc plotAB plotBinResp poiCI psdAdd psdCalc psdCI psdPlot psdVal purl2 rcumsum removal repeatedRows2Keep reproInfo residPlot RichardsFuns rSquared Schnute se showGrowthFun srFuns srFunShow srStarts Subset Summarize sumTable tictactoe validn vbFuns vbStarts wrAdd wsVal

Dependencies:abind backports boot broom ca car carData cli cluster codetools colorspace corrr cowplot cpp11 Deriv doBy dplyr dunn.test farver FlexParamCurve foreach forecast Formula fracdiff gclus generics ggplot2 ggrepel glue gtable isoband iterators labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr nlme nloptr nnet numDeriv pbkrtest permute pillar pkgconfig plotrix purrr qap quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas registry rlang S7 scales scrutiny seriation SparseM stringi stringr survival tibble tidyr tidyselect timeDate TSP urca utf8 vctrs vegan viridisLite withr zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adds zeros for catches of species not collected in some sampling events.	addZeroCatch
Compute and view possible differences between paired sets of ages.	ageBias plot.ageBias summary.ageBias
Compute measures of precision among sets of ages.	agePrecision plot.agePrec summary.agePrec
Proportions-at-age from an age-length key	alkAgeDist
Use an age-length key to assign age to individuals in the unaged sample.	alkIndivAge
Mean Values-at-age from an age-length key	alkMeanVar
Plots to visualize age-length keys.	alkPlot
Confidence intervals for binomial probability of success.	binCI
Capture histories (2 samples) of Bluegill from Jewett Lake, MI.	BluegillJL
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.	BrookTroutTH
Capitalizes the first letter of first or all words in a string.	capFirst
Convert between capture history data.frame formats.	capHistConvert
Summarize capture histories in individual fish format.	capHistSum is.CapHist plot.CapHist
Mortality estimates from the descending limb of a catch curve.	anova.catchCurve catchCurve catchCurve.default catchCurve.formula coef.catchCurve confint.catchCurve plot.catchCurve rSquared.catchCurve summary.catchCurve
Computes Chapman-Robson estimates of S and Z.	chapmanRobson chapmanRobson.default chapmanRobson.formula coef.chapmanRobson confint.chapmanRobson plot.chapmanRobson summary.chapmanRobson
Lengths and weights for Chinook Salmon from three locations in Argentina.	ChinookArg
Stock and recruitment data for Norwegian cod, 1937-1960.	CodNorwegian
Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).	col2rgbt
Associated S3 methods for bootstrap results from car::Boot.	boot confint.boot hist.boot htest.boot plot.boot predict.boot
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.	CutthroatAL
Computes the Leslie or DeLury population estimate from catch and effort data.	anova.depletion coef.depletion confint.depletion depletion depletion.default depletion.formula plot.depletion rSquared.depletion summary.depletion
Dunn's Kruskal-Wallis Multiple Comparisons.	dunnTest dunnTest.default dunnTest.formula print.dunnTest
Population growth of Escherichia coli.	Ecoli
Repeat individual fish data (including lengths) from tallied counts.	expandCounts
Expands a length frequency based on a subsample.	expandLenFreq
Likelihood ratio and extra sum-of-squares tests.	extraSS extraTests lrt print.extraTest
Converts "numeric" factor levels to numeric values.	fact2num
Find reasonable starting values for common fish growth functions.	findGrowthStarts
Opens web pages associated with the fishR website.	fishR
DEFUNCT functions.	bootCase chooseColors compIntercepts compSlopes diags filterD fitPlot FSA-defunct fsaNews hoCoef mapvalues plotBinResp residPlot Schnute Subset
Calculates the geometric mean or geometric standard deviation.	geomean geosd
Hypothetical growth data for testing	GrowthData1
Hypothetical growth data for testing seasonal age models.	GrowthData2
Hypothetical growth data for testing	GrowthData3
DEPRECATED (as of v0.10.0). Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.	GompertzFuns growthFunShow growthModels logisticFuns RichardsFuns vbFuns
Shows rows from the head and tail of a data frame or matrix.	headtail
Creates separate histograms by levels.	hist.formula
Create a histogram from a frequency table.	histFromSum histFromSum.default histFromSum.formula histFromSum.table
Confidence interval for population size (N) in hypergeometric distribution.	hyperCI
Determine if a number is odd or even.	is.even is.odd
Jolly-Seber analysis from multiple mark-recapture events from an open population.	confint.mrOpen jolly mrOpen summary.mrOpen
Specific utilities for use in a knitr document.	kCounts kPvalue purl2 reproInfo
Kolmogorov-Smirnov Tests.	ksTest ksTest.default ksTest.formula
Ratio of lagged observations.	lagratio
Constructs length class/category variable.	lencat lencat.default lencat.formula
Constructs the correction-factor used when back-transforming log-transformed values.	logbtcf
Constructs plots of predicted weights at given lengths among different groups.	lwCompPreds
Creates a function for a specific parameterization of the von Bertalanffy and other common growth functions.	makeGrowthFun
Mirex concentration, weight, capture year, and species of Lake Ontario salmon.	Mirex
Estimate natural mortality from a variety of empirical methods.	metaM Mmethods
Estimate initial population size for single or multiple census mark-recapture data.	confint.mrClosed1 confint.mrClosed2 mrClosed plot.mrClosed2 summary.mrClosed1 summary.mrClosed2
Associated S3 methods for nlsBoot from nlstools.	confint.nlsBoot htest htest.nlsBoot nlsBoot predict.nlsBoot
Adds model fits from nls iterations to active plot.	nlsTracePlot
Peek into (show a subset of) a data frame or matrix.	peek
Computes the percentage of values in a vector less than or greater than (and equal to) some value.	perc
Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.	PikeNY
Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.	PikeNYPartial1
Construct traditional (Campana-like) age-bias plots.	plotAB
Confidence interval for Poisson counts.	poiCI
Creates a vector of Gabelhouse lengths for each species in an entire data frame.	psdAdd psdAdd.default psdAdd.formula
Convenience function for calculating PSD-X and PSD X-Y values.	psdCalc
Compute confidence intervals for PSD-X and PSD X-Y values.	psdCI
Gabelhouse five-cell length categories for various species.	PSDlit
Length-frequency histogram with Gabelhouse lengths highlighted.	psdPlot
Finds Gabelhouse lengths (for PSD calculations) for a species.	psdVal
Hypothetical weight-length data for testing PSD and relative weight functions	PSDWRtest
Computes the prior to or reverse cumulative sum of a vector.	pcumsum rcumsum
Population estimates for k-, 3-, or 2-pass removal data.	coef.removal confint.removal removal removal.default removal.formula summary.removal
Find non-repeated consecutive rows in a data.frame.	repeatedRows2Keep
Extract the coefficient of determination from a linear model object.	rSquared rSquared.default rSquared.lm
Computes standard error of the mean.	se
Creates a string or an expression for a specific growth function.	showGrowthFun
Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.	SMBassLS
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.	SMBassWB
Age and length of spot.	SpotVA1
Creates a function for a specific parameterization of a common stock-recruitment function .	srFuns srFunShow
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.	srStarts
Summary statistics for a numeric variable.	Summarize Summarize.default Summarize.formula
Creates a one- or two-way table of summary statistics.	sumTable sumTable.formula
Construct a base tic-tac-toe plot for presenting predator-prey PSD values.	tictactoe
Finds the number of valid (non-NA) values in a vector.	validn
Find reasonable starting values for a von Bertalanffy growth function.	vbStarts
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.	WhitefishLC
Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).	WR79
Computes a vector of relative weights specific to a species in an entire data frame.	wrAdd wrAdd.default wrAdd.formula
All known standard weight equations.	WSlit
Finds standard weight equation coefficients for a particular species.	wsVal