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| spict-package | Fits a continuous-time surplus production model to data |
| acf.signf | Check whether ACF of residuals is significant in any lags. |
| add.catchunit | Add catch unit to label |
| add.col.legend | Add a legend explaining colors of points (vertical orientation) |
| add.col.legend.hor | Add a legend explaining colors of points (horizontal orientation) |
| annual | Convert from quarterly (or other sub-annual) data to annual means or sums. |
| arrow.line | Draw a line with arrow heads. |
| calc.EBinf | Calculate E(Binfinity), i.e. the fished equilibrium. |
| calc.gamma | Calculate gamma from n |
| calc.influence | Calculates influence statistics of observations. |
| calc.osa.resid | Calculate one-step-ahead residuals. |
| check.inp | Check list of input variables |
| extract.simstats | Extracts relevant statistics from the estimation of a simulated data set. |
| fd | Format date |
| fit.aspic | Fits aspic to the data contained in the input file |
| fit.jags | Fit the Meyer & Millar model using rjags |
| fit.meyermillar | Fit the model of Meyer & Millar (1999) |
| fit.spict | Fit a continuous-time surplus production model to data. |
| get.AIC | Calculate AIC from a rep list. |
| get.colnms | Get column names for data.frames. |
| get.cov | Get covariance matrix of two reported quantities not of fixed model parameters. Covariance of fixed model parameters can be found in rep$cov.fixed. |
| get.EBinf | Calculate E(Binfinity) the fished equilibrium. |
| get.msyvec | If multiple growth rates (r) are used (e.g. for a seasonal model), return specified reference point for all instances of r. |
| get.order | Get order of printed quantities. |
| get.osar.pvals | Check whether ACF of catch and index residuals is significant in any lags. |
| get.par | Extract parameters from a result report as generated by fit.spict. |
| get.spline | Get the values of the seasonal spline for F. |
| get.version | Get version of spict including git sha1 version if available. |
| guess.m | Use a simple linear regression to guess m (MSY). |
| invlogit | Inverse logit transform. |
| invlogp1 | Inverse log "plus one" transform |
| latex.figure | Generate latex code for including a figure. |
| likprof.spict | Create profile likelihood |
| list.possible.priors | List parameters to which priors can be added |
| make.datin | Create data list used as input to TMB::MakeADFun. |
| make.ellipse | Calculate confidence ellipsis. |
| make.obj | Create TMB obj using TMB::MakeADFun and squelch screen printing. |
| make.report | Creates a pdf file containing the summary output and result plots |
| make.splinemat | Make a spline design matrix |
| manage | Calculate predictions under different management scenarios |
| mansummary | Print management summary. |
| meanvar2shaperate | Convert mean and variance to shape and rate of gamma distribution |
| plot.col | Plot model points colored depending on the quarter to which they belong. |
| plot.priors | Plot priors of Meyer & Millar model |
| plot.spictcls | Plot summarising spict results. |
| plotmm.priors | Plot priors of Meyer & Millar model |
| plotspict.bbmsy | Plot estimated B/Bmsy. |
| plotspict.biomass | Plot estimated biomass. |
| plotspict.btrend | Plot the expected biomass trend |
| plotspict.catch | Plot observed catch and predictions. |
| plotspict.ci | Plot catch and index data. |
| plotspict.data | Plot input data |
| plotspict.diagnostic | Plot model diagnostic (data, residuals, and more) |
| plotspict.f | Plot estimated fishing mortality. |
| plotspict.fb | Plot fishing mortality versus biomass. |
| plotspict.ffmsy | Plot estimated relative fishing mortality. |
| plotspict.infl | Plots influence statistics of observations. |
| plotspict.inflsum | Plots summary of influence statistics of observations. |
| plotspict.likprof | Plots result of likelihood profiling. |
| plotspict.osar | Plot one-step-ahead residuals |
| plotspict.priors | Plot priors and posterior distribution. |
| plotspict.production | Plot theoretical production curve and estimates. |
| plotspict.retro | Plot results of retrospective analysis |
| plotspict.season | Plot the mean F cycle |
| plotspict.tc | Plot time constant. |
| pol | Fisheries data included in Polacheck et al. (1993). |
| predict.b | Helper function for sim.spict(). |
| predict.logf | Helper function for sim.spict(). |
| print.spictcls | Output a summary of a fit.spict() run. |
| prop.F | Calculate management for changing F by a given factor. |
| put.ax | Adds the x-axis to influence plots |
| put.xax | Adds the x-axis to influence plots |
| read.aspic | Reads ASPIC input file. |
| read.aspic.res | Reads the parameter estimates of an Aspic result file. |
| refpointci | Draw CI around a reference point using polygon |
| res.diagn | Helper function for calc.osar.resid that calculates residual statistics. |
| retro | Conduct retrospective analysis |
| season.cols | Load season colors. |
| shaperate2meanvar | Convert shape and rate of gamma distribution to mean and variance |
| sim.spict | Simulate data from Pella-Tomlinson model |
| spict | Fits a continuous-time surplus production model to data |
| spictcls | An S4 class to represent output from a SPiCT fit. |
| spictcls-class | An S4 class to represent output from a SPiCT fit. |
| summary.spictcls | Output a summary of a fit.spict() run. |
| sumspict.diagnostics | Diagnostics table |
| sumspict.drefpoints | Deternistic reference points of a fit.spict() run. |
| sumspict.fixedpars | Fixed paramters table. |
| sumspict.parest | Parameter estimates of a fit.spict() run. |
| sumspict.predictions | Predictions of a fit.spict() run. |
| sumspict.priors | Fixed parameters table. |
| sumspict.srefpoints | Stochastic reference points of a fit.spict() run. |
| sumspict.states | State estimates of a fit.spict() run. |
| take.c | Calculate management when taking a constant catch (proxy for setting a TAC). |
| test.spict | Example of a spict analysis. |
| trans2real | Get real parameter values from transformed ones. |
| true.col | Load color of true values from simulation. |
| txt.stamp | Add spict version to plot |
| validate.spict | Simulate data and reestimate parameters |
| validation.data.frame | Collect results from the output of running validate.spict. |
| warning.stamp | Add warning sign to plot |
| write.aspic | Takes a SPiCT input list and writes it as an Aspic input file. |
| write.bug.file | Write the BUGS code to a text file |