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FSA (version 0.8.0)
Functions for Simple Fisheries Stock Assessment Methods
Description
Functions to perform a variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website listed below.
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Install
install.packages('FSA')
Monthly Downloads
9,832
Version
0.8.0
License
GPL (>= 2)
Issues
3
Pull Requests
0
Stars
63
Forks
20
Repository
https://github.com/droglenc/FSA
Homepage
http://derekogle.com/fishR/
Maintainer
Derek Ogle
Last Published
October 8th, 2015
Functions in FSA (0.8.0)
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SMBassWB
Growth increment data for West Bearskin Lake Smallmouth Bass.
PikeNYPartial1
Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckthorn Marsh.
ageKey
Use an age-length key to assign age to individuals in the unaged sample.
addRadCap
Add a total radius-at-capture variable to a data.frame that contains one-fish-per-line increments data.
PSDlit
Gabelhouse five-cell length categories for various species.
logbtcf
Constructs the correction-factor used when back-transforming log-transformed values.
ageBias
Compute and view possible biases between paired sets of ages.
removal
Population estimates for k-, 3-, or 2-pass removal data.
lwCompPreds
Constructs plots of predicted weights at given lengths among different groups.
PikeNY
Summarized multiple mark-recapture data for all Northern Pike from Buckthorn Marsh.
BluegillJL
Capture histories (2 samples) of Bluegill from Jewett Lake.
agePrecision
Compute measures of precision among sets of ages.
ChinookArg
Lengths and weights of Chinook Salmon from three locations in Argentina.
Ecoli
Population growth of Escherichia coli.
WSlit
All known standard weight equations.
BrookTroutTH
Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
capHistSum
Summarize capture histories in individual fish format.
capHistConvert
Convert between capture history data.frame formats.
WR79
Age and length for a hypothetical sample from Westerheim and Ricker (1979).
Schnute
The four-parameter growth function from Schnute (1981).
catchCurve
Mortality estimates from the descending limb of a catch curve.
SpotVA1
Age and length of spot.
chapmanRobson
Computes Chapman-Robson estimates of S and Z.
depletion
Computes the Leslie or Delury population estimate from catch and effort data.
SMBassLS
Catch-effort data for Little Silver Lake Smallmouth Bass.
WhitefishLC
Assessed ages from two readers on three structures for Lake Whitefish from Lake Champlain.
Summarize
Summary statistics for a numeric or factor variable.
plotBinResp
Plots a binary response variable versus a quantitative explanatory variable.
CutthroatAL
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
alkAgeDist
Proportions-at-age from an Age-Length Key
gConvert
Converts between types of measurements from calcified structures.
tictactoe
Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
hyperCI
Confidence interval for population size (N) in hypergeometric distribution.
mrClosed
Estimate initial population size for single or multiple census mark-recapture data.
psdVal
Finds Gabelhouse lengths (for PSD calculations) for a species.
FSAUtils
Capitalizes the first letter of first or all words in a string.
confint.nlsBoot
Associated S3 methods for nlsBoot from nlstools.
addZeroCatch
Adds zeroes for catches of species not collected in some sampling events.
jolly
Jolly-Seber analysis from multiple mark-recapture events from an open population.
FSA
Fisheries stock assessment methods and data.
expandCounts
Repeat individual fish data (including lengths) from tallied counts.
dunnTest
Dunn's Kruskal-Wallis Multiple Comparisons.
chooseColors
Create a list of colors from among a variety of color palettes.
psdCalc
Convenience function for calculating PSD-X and PSD X-Y values.
alkMeanVar
Mean Values-at-age from an Age-Length Key
ageKeyPlot
Plots to visualize age-length keys.
bootstrap
Associated S3 methods for bootCase from car.
extraTests
Likelihood ratio and extra sum-of-squares tests.
kCounts
Specific utilities for use in a knitr document.
ksTest
Kolmogorov-Smirnov Tests.
fishR
Opens web pages associated with the fishR website.
residPlot
Construct a residual plot from lm or nls objects.
headtail
Shows rows from the head and tail of a data frame or matrix.
lencat
Constructs length class/category variable.
.onAttach
Internal functions.
se
Computes standard error of the mean.
psdAdd
Create vector of Gabelhouse lengths for each species from an entire data frame.
bcFuns
Creates a function for a specific back-calculation model.
psdPlot
Length-frequency histogram with Gabelhouse lengthshighlighted.
mapvalues
Replace specified values in a vector or factor with new values.
psdCI
Compute confidence intervals for PSD-X and PSD X-Y values.
lenFreqExpand
Expands a length frequency based on a subsample.
Mmethods
Estimate natural mortality from a variety of empirical methods.
stockRecruitment
Creates a function for a specific parameterization of a common stock-recruitment model .
oddeven
Determine if a number is odd or even.
fitPlot
Fitted model plot for an lm, glm, or nls object.
perc
Computes the percentage of values in a vector less than or greater than (and equal to) some value.
Subset
Subsets/filters a data frame and drops the unused levels.
Mirex
Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
fsaNews
Read news and changes for the 'FSA' package.
growthModels
Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
srStarts
Finds reasonable starting values for parameters in specific paramaterizations of common stock-recruitment models.
fact2num
Converts "numeric" factor levels to numeric values.
sumTable
Creates a one- or two-way table of summary statistics.
vbStarts
Find reasonable starting values for a von Bertalanffy growth function.
wrAdd
Computes a vector of relative weights specific to a species in an entire data frame.
poiCI
Confidence interval for Poisson rate parameter.
hoCoef
Performs a hypothesis test that a linear model parameter is equal to a specific value.
binCI
Confidence intervals for binomial probability of success.
wsVal
Finds standard weight equation coefficients for a particular species.
CodNorwegian
Stock and recruitment data for Norwegian cod,1937-1960.
hist.formula
Creates separate histograms by levels.
lagratio
Ratio of lagged observations.
rcumsum
Computes the prior to or reverse cumulative sum of a vector.
validn
Finds the number of valid (non-NA) values in a vector.