A B C D F G H I L M N O P Q R S T U V W misc
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 |
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 |
countNAs | countNAs used in apply to count the number of NAs 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 |
domed | domed calculates domed selectivity curves |
do_MCMC | do_MCMC conducts an MCMC using Gibbs within Metropolis |
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 |
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 |
getMSY | getMSY calculates the MSY for the Polacheck et al 1993 equation |
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 |
Gz | Gz calculates predicted Gompertz length-at-age growth curve |
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 |
LatA | LatA Simulated length-at-age for 358 female fish |
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 |
spmboot | spmboot conducts a bootstrap analysis on a spm model |
spmCE | spmCE - calculates the dynamics for multiple cpue time-series |
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 |
%ni% | '%ni%' identifies which element in x is NOT in y |