%ni%                    '%ni%' identifies which element in x is NOT in
                        y
Gz                      Gz calculates predicted Gompertz length-at-age
                        growth curve
LatA                    LatA Simulated length-at-age for 358 female
                        fish
abdat                   abdat A list of fishery data for blacklip
                        abalone
addcontours             addcontours simplifies adding contours to an xy
                        plot of points
addlnorm                addlnorm estimates a log-normal distribution
                        from output of hist
addnorm                 addnorm adds a normal distribution to a
                        histogram of a data set.
aicbic                  aicbic returns the AIC and BIC for a given
                        model
altnegLL                altnegLL calculate the Normal negative
                        log-likelihood
bce                     bce Baranov catch equation
bh                      bh represents one version of Beverton-Holt
                        recruitment
blackisland             blackisland tagging data from a blacklip
                        abalone population
bracket                 bracket bounds a value on the x-axis and y-axis
calcprior               calcprior return the sum of a vector of
                        constant values as priors
chapter2                chapter2 The 15 R-code chunks from A
                        Non-Introduction to R
chapter3                chapter3 The 27 R-code chunks from Simple
                        Population Models
chapter4                chapter4 The 47 R-code chunks from Model
                        Parameter Estimation
chapter5                chapter5 The 23 R-code chunks from Static
                        Models
chapter6                chapter6 The 53 R-code chunks from On
                        Uncertainty
chapter7                chapter7 The 67 R-code chunks from Surplus
                        Production Models
countNAs                countNAs used in apply to count the number of
                        NAs in a vector
countgtone              countgtone used in apply to count the number >
                        1 in a vector
countgtzero             countgtzero used in apply to count numbers >
                        zero in a vector
countones               countones used in apply to count the number of
                        ones in a vector
countzeros              countzeros used in apply to count the number of
                        zeros in a vector
dataspm                 dataspm A data.frame of fisheries catch and
                        cpue data
discretelogistic        discretelogistic example and figure 3.2
                        Discrete logistic model
do_MCMC                 do_MCMC conducts an MCMC using Gibbs within
                        Metropolis
domed                   domed calculates domed selectivity curves
fabens                  fabens calculates predicted growth increment
                        for tagging data
facttonum               facttonum converts a vector of numeric factors
                        into numbers
fitSPM                  fitSPM fits a surplus production model
freqMean                freqMean calculates the mean and stdev of count
                        data
getMSY                  getMSY calculates the MSY for the Polacheck et
                        al 1993 equation
getlag                  getlag is used to look for the response of cpue
                        to previous catches
getmax                  getmax can be used to define the upper bound
                        for a plot
getmin                  getmin can be used to define the lower bound
                        for a plot
getname                 getname returns the name of a variable as
                        character
getrmse                 getrmse calculates the rmse of the input
                        'invar' series
getseed                 getseed generates a random number seed
getsingle               getsingle extracts one number from an input
                        line of characters
gettime                 gettime calculates time in seconds passed each
                        day
getvector               getvector extracts a vector of numbers from a
                        line of characters
halftable               halftable halves the height of a tall narrow
                        data.frame for printing
inthist                 inthist a replacement for the hist function for
                        use with integers
invl                    invl calculates growth increments for the
                        inverse logistic
iscol                   incol is a utility to determine if a column is
                        present in a matrix
likeratio               likeratio conducts a likelihood ratio test
linter                  linter finds a value in a series using its
                        location in another
logist                  logist Logistic selectivity function
magnitude               magnitude returns the magnitude of numbers in
                        base 10
makelabel               makelabel generates a label from text and
                        values
mature                  mature alternative logistic function commonly
                        used for maturity
minnow                  minnow contains weekly growth data for use with
                        seasonal growth curves
mm                      mm calculates the predicted Michaelis-Menton
                        length-at-age
mnnegLL                 mnnegLL generic multinomial negative
                        log-likelihoods
negLL                   negLL calculate log-normal log-likelihoods
negLL1                  negLL1 calculate log-normal log-likelihoods
                        with a penalty
negLLM                  negLLM -ve log-normal likelihoods for multiple
                        index time-series
negLLP                  negLLP -ve log-likelihood for normally
                        distributed variables
negNLL                  negNLL -ve log-likelihood for normally
                        distributed variables
negnormL                negnormL an alternative -log-likelihood for
                        normal errors
npf                     npf fishery catch data from Northern Prawn
                        Fishery 1970-1992
outfit                  outfit tidy print of output from optim, nlminb,
                        or nlm
panel.cor               panel.cor is a version of a function given in
                        the help for pairs
parasympt               parasympt generates N vectors from a
                        multi-variate normal
parset                  parset alters the current base graphics par
                        settings
parsyn                  parsyn types the standard par command syntax to
                        the console
penalty0                penalty0 enables the adding of a large penalty
                        as one approaches 0.0
penalty1                penalty1 adds an increasingly large penalty as
                        a value approaches 1.0
plot.dynpop             plot.dynpop an S3 method for plotting dynpop
                        objects
plot1                   plot1 a quick way to plot an xy line or point
                        plot
plotfishM               plotfishM plots the catch and optionally the
                        cpue
plotlag                 plotlag plots the effect of a lag between two
                        variables
plotprep                plotprep sets up a window and the par values
                        for plotting
plotprofile             plotprofile simplifies plotting single
                        likelihood profiles
plotproj                plotproj generate a plot of a matrix of biomass
                        projections
plotspmdat              plotspmdat plots the fish data containing
                        catches and cpue
plotspmmod              plotspmmod plots an spm model fit given
                        parameters and data
predfreq                predfreq is used for modal analysis of count
                        data
printV                  printV returns a vector cbinded to
                        1:length(invect)
properties              properties - used to examine the properties of
                        a data.frame
pttuna                  pttuna is yellowfin tuna fishery data from
                        Pella-Tomlinson 1969
quants                  quants used in apply to estimate quantiles
                        across a vector
removeEmpty             removeEmpty removes empty strings from a vector
                        of strings
ricker                  ricker one version of the Ricker stock
                        recruitment
robustSPM               robustSPM does a robustness test on quality of
                        fit of an SPM
schaef                  schaef is yellowfin tuna fishery data from
                        Schaefer 1957
setpalette              setpalette is a shortcut for altering the
                        palette to R4
simpspm                 simpspm calculates only the predicted log(CE)
                        for an SPM
simpspmM                simpspmM calculates predicted CE when multiple
                        indices are present
spm                     spm calculates the dynamics of a Schaefer or
                        Fox model
spmCE                   spmCE - calculates the dynamics for multiple
                        cpue time-series
spmboot                 spmboot conducts a bootstrap analysis on a spm
                        model
spmphaseplot            spmphaseplot - plots the phase plot of harvest
                        rate vs biomass
spmproj                 spmproj calculates biomass trajectories for
                        replicate parameters
spmprojDet              spmprojDet conducts forward projections from
                        known conditions
srug                    srug is the Schnute and Richards Unified Growth
                        Curve
ssq                     ssq a generalized function for summing squared
                        residuals
summspm                 summspm extracts critical statistics from
                        output of plotspmmod
tasab                   tasab is a matrix of abalone maturity-at-length
                        data
tigers                  tigers is tiger prawn recruitment data from
                        Penn & Caputi 1986
twoindex                twoindex has orange roughy catches with
                        hypothetical cpue
uphist                  uphist a histogram with an upper limit on the
                        x-axis
vB                      vB calculates the predicted von Bertalanffy
                        length at age
which.closest           which.closest find a number in a vector closest
                        to a given value
