FSA: Simple Fisheries Stock Assessment Methods

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A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.

Author
Derek Ogle [aut, cre]
Date of publication
2016-09-24 18:04:14
Maintainer
Derek Ogle <derek@derekogle.com>
License
GPL (>= 2)
Version
0.8.10
URLs

View on CRAN

Man pages

addRadCap
Add a total radius-at-capture variable to a data.frame that...
addZeroCatch
Adds zeroes for catches of species not collected in some...
ageBias
Compute and view possible biases between paired sets of ages.
agePrecision
Compute measures of precision among sets of ages.
alkAgeDist
Proportions-at-age from an Age-Length Key
alkIndivAge
Use an age-length key to assign age to individuals in the...
alkMeanVar
Mean Values-at-age from an Age-Length Key
alkPlot
Plots to visualize age-length keys.
bcFuns
Creates a function for a specific back-calculation model.
binCI
Confidence intervals for binomial probability of success.
BluegillJL
Capture histories (2 samples) of Bluegill from Jewett Lake,...
bootCase
Associated S3 methods for bootCase from car.
BrookTroutTH
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
capHistConvert
Convert between capture history data.frame formats.
capHistSum
Summarize capture histories in individual fish format.
catchCurve
Mortality estimates from the descending limb of a catch...
chapmanRobson
Computes Chapman-Robson estimates of S and Z.
ChinookArg
Lengths and weights for Chinook Salmon from three locations...
chooseColors
Create a list of colors from among a variety of color...
CodNorwegian
Stock and recruitment data for Norwegian cod, 1937-1960.
col2rgbt
Converts an R color to RGB (red/green/blue) including a...
compIntercepts
Tests for significant differences among all pairs of...
compSlopes
Tests for significant differences among all pairs of slopes...
CutthroatAL
Capture histories (9 samples) of Cutthroat Trout from Auke...
depletion
Computes the Leslie or Delury population estimate from catch...
diags
Extract diagonals from a matrix.
dunnTest
Dunn's Kruskal-Wallis Multiple Comparisons.
Ecoli
Population growth of Escherichia coli.
expandCounts
Repeat individual fish data (including lengths) from tallied...
expandLenFreq
Expands a length frequency based on a subsample.
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.
fitPlot
Fitted model plot for an lm, glm, or nls object.
FSA
Fisheries stock assessment methods and data.
FSA-internals
Internal functions.
fsaNews
Read news and changes for the 'FSA' package.
FSAUtils
Capitalizes the first letter of first or all words in a...
gConvert
Converts between types of measurements from calcified...
geomean
Calculates the geometric mean or geometric standard...
growthModels
Creates a function for a specific parameterization of the von...
headtail
Shows rows from the head and tail of a data frame or matrix.
hist.formula
Creates separate histograms by levels.
histFromSum
Create a histogram from a frequency table.
hoCoef
Performs a hypothesis test that a linear model parameter is...
hyperCI
Confidence interval for population size (N) in hypergeometric...
knitUtil
Specific utilities for use in a knitr document.
ksTest
Kolmogorov-Smirnov Tests.
lagratio
Ratio of lagged observations.
lencat
Constructs length class/category variable.
logbtcf
Constructs the correction-factor used when back-transforming...
lwCompPreds
Constructs plots of predicted weights at given lengths among...
mapvalues
Replace specified values in a vector or factor with new...
metaM
Estimate natural mortality from a variety of empirical...
Mirex
Mirex concentration, weight, capture year, and species of...
mrClosed
Estimate initial population size for single or multiple...
mrOpen
Jolly-Seber analysis from multiple mark-recapture events from...
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...
PikeNY
Summarized multiple mark-recapture data for all Northern Pike...
PikeNYPartial1
Capture histories (4 samples), in capture history format, of...
plotBinResp
Plots a binary response variable versus a quantitative...
poiCI
Confidence interval for Poisson rate parameter.
psdAdd
Creates a vector of Gabelhouse lengths for each species in an...
psdCalc
Convenience function for calculating PSD-X and PSD X-Y...
psdCI
Compute confidence intervals for PSD-X and PSD X-Y values.
PSDlit
Gabelhouse five-cell length categories for various species.
psdPlot
Length-frequency histogram with Gabelhouse lengths...
psdVal
Finds Gabelhouse lengths (for PSD calculations) for a...
rcumsum
Computes the prior to or reverse cumulative sum of a vector.
removal
Population estimates for k-, 3-, or 2-pass removal data.
residPlot
Construct a residual plot from lm or nls objects.
Schnute
The four-parameter growth function from Schnute (1981).
se
Computes standard error of the mean.
SMBassLS
Catch-effort data for Little Silver Lake (Ont) Smallmouth...
SMBassWB
Growth increment data for West Bearskin Lake, MN, Smallmouth...
SpotVA1
Age and length of spot.
srStarts
Finds reasonable starting values for parameters in specific...
stockRecruitment
Creates a function for a specific parameterization of a...
Subset
Subsets/filters a data frame and drops the unused levels.
Summarize
Summary statistics for a numeric variable.
sumTable
Creates a one- or two-way table of summary statistics.
tictactoe
Construct a base tic-tac-toe plot for presenting...
validn
Finds the number of valid (non-NA) values in a vector.
vbStarts
Find reasonable starting values for a von Bertalanffy growth...
WhitefishLC
Assigned ages from two readers on three structures for Lake...
WR79
Ages and lengths for a hypothetical sample from Westerheim...
wrAdd
Computes a vector of relative weights specific to a species...
WSlit
All known standard weight equations.
wsVal
Finds standard weight equation coefficients for a particular...

Files in this package

FSA
FSA/COPYING
FSA/inst
FSA/inst/CITATION
FSA/inst/extdata
FSA/inst/extdata/bootCase1.RData
FSA/inst/extdata/PSDWR_testdata.csv
FSA/inst/extdata/nlsBoot1.RData
FSA/tests
FSA/tests/testthat
FSA/tests/testthat/test_addZeroCatch.R
FSA/tests/testthat/test_histFromSum.R
FSA/tests/testthat/test_PSD.R
FSA/tests/testthat/Rplots.pdf
FSA/tests/testthat/test_growthFuns.R
FSA/tests/testthat/test_StockRecruit.R
FSA/tests/testthat/test_capHist.R
FSA/tests/testthat/test_mrClosed.R
FSA/tests/testthat/test_mrOpen.R
FSA/tests/testthat/test_WSWR.R
FSA/tests/testthat/test_LWCompPreds.R
FSA/tests/testthat/test_depletion.R
FSA/tests/testthat/test_CatchCurve_ChapmanRobson.R
FSA/tests/testthat/test_dunnTest.R
FSA/tests/testthat/test_sumTable.R
FSA/tests/testthat/test_VonBertalanffy.R
FSA/tests/testthat/test_comparisonsDVR.R
FSA/tests/testthat/test_removal.R
FSA/tests/testthat/test_bcFuns.R
FSA/tests/testthat/test_Internals.R
FSA/tests/testthat/test_metaM.R
FSA/tests/testthat/test_bootstrap.R
FSA/tests/testthat/test_extraTests.R
FSA/tests/testthat/test_expandCounts.R
FSA/tests/testthat/test_histFormula.R
FSA/tests/testthat/test_expandLenFreq.R
FSA/tests/testthat/test_ksTest.R
FSA/tests/testthat/test_fitResidPlots.R
FSA/tests/testthat/test_growthUtils.R
FSA/tests/testthat/test_AgeLengthKey.R
FSA/tests/testthat/test_FSAUtils.R
FSA/tests/testthat/test_Summarize.R
FSA/tests/testthat/test_AgeComparisons.R
FSA/tests/testthat/test_lencat.R
FSA/tests/test-all.R
FSA/NAMESPACE
FSA/NEWS.md
FSA/data
FSA/data/CodNorwegian.rdata
FSA/data/PikeNYPartial1.rdata
FSA/data/SMBassWB.rdata
FSA/data/CutthroatAL.rdata
FSA/data/ChinookArg.rdata
FSA/data/SMBassLS.rdata
FSA/data/WSlit.rdata
FSA/data/PSDlit.rdata
FSA/data/BrookTroutTH.rdata
FSA/data/Mirex.rdata
FSA/data/Ecoli.rdata
FSA/data/WhitefishLC.rdata
FSA/data/SpotVA1.rdata
FSA/data/WR79.rdata
FSA/data/BluegillJL.rdata
FSA/data/PikeNY.rdata
FSA/R
FSA/R/plotBinResp.R
FSA/R/residPlot.R
FSA/R/expandCounts.R
FSA/R/capHistConvert.R
FSA/R/alkIndivAge.R
FSA/R/bootstrap.R
FSA/R/SpotVA1.R
FSA/R/depletion.R
FSA/R/stockRecruitment.R
FSA/R/alkPlot.R
FSA/R/mrClosed.R
FSA/R/WR79.R
FSA/R/Summarize.R
FSA/R/bcFuns.R
FSA/R/WhitefishLC.R
FSA/R/BluegillJL.R
FSA/R/growthModels.R
FSA/R/hist.formula.R
FSA/R/growthDataUtils.R
FSA/R/alkSummaries.R
FSA/R/expandLenFreq.R
FSA/R/PikeNY.R
FSA/R/FSA.R
FSA/R/vbStarts.R
FSA/R/Mirex.R
FSA/R/mrOpen.R
FSA/R/lencat.R
FSA/R/ageComparisons.R
FSA/R/comparisonsDVR.R
FSA/R/extraTests.R
FSA/R/fitPlot.R
FSA/R/removal.R
FSA/R/wsVal.R
FSA/R/lwCompPreds.R
FSA/R/tictactoe.R
FSA/R/CIDists.R
FSA/R/knitUtil.R
FSA/R/BrookTroutTH.R
FSA/R/WSlit.R
FSA/R/wrAdd.R
FSA/R/chapmanRobson.R
FSA/R/FSA-internals.R
FSA/R/srStarts.R
FSA/R/SMBassLS.R
FSA/R/catchCurve.R
FSA/R/SMBassWB.R
FSA/R/FSAUtils.R
FSA/R/ksTest.R
FSA/R/sumTable.R
FSA/R/histFromSum.R
FSA/R/dunnTest.R
FSA/R/PikeNYPartial1.R
FSA/R/Ecoli.R
FSA/R/mapvalues.R
FSA/R/capHistSum.R
FSA/R/PSDlit.R
FSA/R/psdVal.R
FSA/R/psdPlot.R
FSA/R/ChinookArg.R
FSA/R/CodNorwegian.R
FSA/R/psdCI.R
FSA/R/CutthroatAL.R
FSA/R/metaM.R
FSA/R/psdAdd.R
FSA/R/psdCalc.R
FSA/R/addZeroCatch.R
FSA/MD5
FSA/DESCRIPTION
FSA/man
FSA/man/PikeNY.Rd
FSA/man/col2rgbt.Rd
FSA/man/Summarize.Rd
FSA/man/logbtcf.Rd
FSA/man/alkMeanVar.Rd
FSA/man/poiCI.Rd
FSA/man/compSlopes.Rd
FSA/man/growthModels.Rd
FSA/man/geomean.Rd
FSA/man/histFromSum.Rd
FSA/man/binCI.Rd
FSA/man/lencat.Rd
FSA/man/WR79.Rd
FSA/man/alkPlot.Rd
FSA/man/psdAdd.Rd
FSA/man/psdPlot.Rd
FSA/man/FSAUtils.Rd
FSA/man/perc.Rd
FSA/man/chooseColors.Rd
FSA/man/CutthroatAL.Rd
FSA/man/vbStarts.Rd
FSA/man/hyperCI.Rd
FSA/man/ChinookArg.Rd
FSA/man/fishR.Rd
FSA/man/mrOpen.Rd
FSA/man/plotBinResp.Rd
FSA/man/rcumsum.Rd
FSA/man/dunnTest.Rd
FSA/man/chapmanRobson.Rd
FSA/man/FSA-internals.Rd
FSA/man/diags.Rd
FSA/man/validn.Rd
FSA/man/SMBassWB.Rd
FSA/man/capHistConvert.Rd
FSA/man/expandCounts.Rd
FSA/man/FSA.Rd
FSA/man/BluegillJL.Rd
FSA/man/mrClosed.Rd
FSA/man/ksTest.Rd
FSA/man/lagratio.Rd
FSA/man/addRadCap.Rd
FSA/man/se.Rd
FSA/man/mapvalues.Rd
FSA/man/depletion.Rd
FSA/man/hoCoef.Rd
FSA/man/psdCalc.Rd
FSA/man/catchCurve.Rd
FSA/man/PSDlit.Rd
FSA/man/PikeNYPartial1.Rd
FSA/man/WhitefishLC.Rd
FSA/man/headtail.Rd
FSA/man/extraTests.Rd
FSA/man/bootCase.Rd
FSA/man/capHistSum.Rd
FSA/man/gConvert.Rd
FSA/man/Subset.Rd
FSA/man/wrAdd.Rd
FSA/man/removal.Rd
FSA/man/Schnute.Rd
FSA/man/knitUtil.Rd
FSA/man/alkAgeDist.Rd
FSA/man/nlsBoot.Rd
FSA/man/srStarts.Rd
FSA/man/compIntercepts.Rd
FSA/man/WSlit.Rd
FSA/man/agePrecision.Rd
FSA/man/CodNorwegian.Rd
FSA/man/Ecoli.Rd
FSA/man/bcFuns.Rd
FSA/man/oddeven.Rd
FSA/man/fact2num.Rd
FSA/man/residPlot.Rd
FSA/man/tictactoe.Rd
FSA/man/Mirex.Rd
FSA/man/addZeroCatch.Rd
FSA/man/SpotVA1.Rd
FSA/man/hist.formula.Rd
FSA/man/fsaNews.Rd
FSA/man/psdCI.Rd
FSA/man/expandLenFreq.Rd
FSA/man/sumTable.Rd
FSA/man/alkIndivAge.Rd
FSA/man/psdVal.Rd
FSA/man/fitPlot.Rd
FSA/man/ageBias.Rd
FSA/man/lwCompPreds.Rd
FSA/man/BrookTroutTH.Rd
FSA/man/wsVal.Rd
FSA/man/SMBassLS.Rd
FSA/man/metaM.Rd
FSA/man/stockRecruitment.Rd