| abdat | abdat A list of fishery data for blacklip abalone |
| addcontours | addcontours simplifies adding contours to an xy plot of... |
| addlnorm | addlnorm estimates a log-normal distribution from output of... |
| addnorm | addnorm adds a normal distribution to a histogram of a data... |
| 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... |
| 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... |
| countzeros | countzeros used in apply to count the number of zeros in a... |
| dataspm | dataspm A data.frame of fisheries catch and cpue data |
| discretelogistic | discretelogistic example and figure 3.2 Discrete logistic... |
| 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 |
| getlag | getlag is used to look for the response of cpue to previous... |
| 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... |
| 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... |
| gettime | gettime calculates time in seconds passed each day |
| getvector | getvector extracts a vector of numbers from a line of... |
| grapes-ni-grapes | '%ni%' identifies which element in x is NOT in y |
| Gz | Gz calculates predicted Gompertz length-at-age growth curve |
| halftable | halftable halves the height of a tall narrow data.frame for... |
| inthist | inthist a replacement for the hist function for use with... |
| invl | invl calculates growth increments for the inverse logistic |
| iscol | incol is a utility to determine if a column is present in a... |
| 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... |
| 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... |
| minnow | minnow contains weekly growth data for use with seasonal... |
| mm | mm calculates the predicted Michaelis-Menton length-at-age |
| mnnegLL | mnnegLL generic multinomial negative log-likelihoods |
| MQMF | MQMF functions for Using R for Modelling and Quantitative... |
| 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... |
| 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... |
| 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... |
| penalty1 | penalty1 adds an increasingly large penalty as a value... |
| plot1 | plot1 a quick way to plot an xy line or point plot |
| plot.dynpop | plot.dynpop an S3 method for plotting dynpop objects |
| 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... |
| 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... |
| 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... |
| spmproj | spmproj calculates biomass trajectories for replicate... |
| 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... |
| tasab | tasab is a matrix of abalone maturity-at-length data |
| tigers | tigers is tiger prawn recruitment data from Penn & Caputi... |
| 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... |
