Check whether ACF of residuals is significant in any lags.
Add a legend explaining colors of points (vertical orientation)
Add a legend explaining colors of points (horizontal orientation)
Convert from quarterly (or other sub-annual) data to annual means or sums.
Calculate E(Binfinity), i.e. the fished equilibrium.
Calculates influence statistics of observations.
Extracts relevant statistics from the estimation of a simulated data set.
Fits aspic to the data contained in the input file
Fit the Meyer & Millar model using rjags
Fit a continuous-time surplus production model to data.
Calculate E(Binfinity) the fished equilibrium.
Get covariance matrix of two reported quantities not of fixed model parameters. Covariance of fixed model parameters can be found in rep$cov.fixed.
If multiple growth rates (r) are used (e.g. for a seasonal model), return specified reference point for all instances of r.
Check whether ACF of catch and index residuals is significant in any lags.
Extract parameters from a result report as generated by fit.spict.
Get the values of the seasonal spline for F.
Get version of spict including git sha1 version if available.
Use a simple linear regression to guess m (MSY).
Generate latex code for including a figure.
List parameters to which priors can be added
Create data list used as input to TMB::MakeADFun.
Create TMB obj using TMB::MakeADFun and squelch screen printing.
Creates a pdf file containing the summary output and result plots
Calculate predictions under different management scenarios
Convert mean and variance to shape and rate of gamma distribution
Plot model points colored depending on the quarter to which they belong.
Plot model diagnostic (data, residuals, and more)
Plot estimated relative fishing mortality.
Plots influence statistics of observations.
Plots summary of influence statistics of observations.
Plot theoretical production curve and estimates.
Fisheries data included in Polacheck et al. (1993).
Calculate management for changing F by a given factor.
Reads the parameter estimates of an Aspic result file.
Draw CI around a reference point using polygon
Helper function for calc.osar.resid that calculates residual statistics.
Convert shape and rate of gamma distribution to mean and variance
Simulate data from Pella-Tomlinson model
Fits a continuous-time surplus production model to data
An S4 class to represent output from a SPiCT fit.
Deternistic reference points of a fit.spict() run.
Parameter estimates of a fit.spict() run.
Stochastic reference points of a fit.spict() run.
Calculate management when taking a constant catch (proxy for setting a TAC).
Get real parameter values from transformed ones.
Load color of true values from simulation.
Collect results from the output of running validate.spict.
Takes a SPiCT input list and writes it as an Aspic input file.