| Check whether ACF of residuals is significant in any lags. | acf.signf |
| Add catch unit to label | add.catchunit |
| Add a legend explaining colors of points (vertical orientation) | add.col.legend |
| Add a legend explaining colors of points (horizontal orientation) | add.col.legend.hor |
| Define management scenario | add.man.scenario get.TAC get.TAC, make.man.inp |
| Add lines to plot indicating result of management scenarios. | add.manlines |
| Convert from quarterly (or other sub-annual) data to annual means, sums or a custom function. | annual |
| Draw a line with arrow heads. | arrow.line |
| Calculates the Bmsy/K ratio | calc.bmsyk |
| Calculate E(Binfinity), i.e. the fished equilibrium. | calc.EBinf |
| Calculate gamma from n | calc.gamma |
| Calculates influence statistics of observations. | calc.influence |
| Calculate Mean Absolute Scaled Error (MASE) | calc.mase |
| Calculates the order of magnitude for the relative reference levels B/Bmsy and F/Fmsy | calc.om |
| Calculate one-step-ahead residuals. | calc.osa.resid |
| Calculate process residuals | calc.process.resid |
| Calculate Total Allowable Catch (TAC) | calc.tac |
| Check catch list | check.catchList |
| Check sensitivity of fit to initial parameter values | check.ini |
| Check list of input variables | check.inp |
| Check the consistency of management scenarios in rep | check.man |
| Checks and corrects management time to be within model time | check.man.time |
| Check rep list | check.rep |
| Extract hindcast info from a fitted spict object | extract.hindcast.info |
| Extracts relevant statistics from the estimation of a simulated data set. | extract.simstats |
| Format date | fd |
| Fits aspic to the data contained in the input file | fit.aspic |
| Fit the Meyer & Millar model using rjags | fit.jags |
| Fit the model of Meyer & Millar (1999) | fit.meyermillar |
| Fit a continuous-time surplus production model to data. | fit.spict |
| Calculate AIC from a rep list. | get.AIC |
| Find observations of catch and index that overlap | get.catchindexoverlap |
| Get column names for data.frames. | get.colnms |
| Get covariance matrix of two reported quantities not of fixed model parameters. Covariance of fixed model parameters can be found in rep$cov.fixed. | get.cov |
| Calculate E(Binfinity) the fished equilibrium. | get.EBinf |
| Estimate fishing mortality factor minimising probability of specified model variable hitting a specified reference level under given fishing mortality | get.ffac |
| Estimate catch for management period based on last catch observations | get.manC |
| Get limts of any parameter considering all spict objects in rep$man | get.manlimits |
| Get spict object in rep$man with longest time series | get.manmax |
| Get mfrow from the number of plots to be plotted | get.mfrow |
| If multiple growth rates (r) are used (e.g. for a seasonal model), return specified reference point for all instances of r. | get.msyvec |
| Get number of active priors | get.no.active.priors |
| Get order of printed quantities. | get.order |
| Check whether ACF of catch and index residuals is significant in any lags. | get.osar.pvals |
| Extract parameters from a result report as generated by fit.spict. | get.par list.quantities |
| Get the values of the seasonal spline for F. | get.spline |
| Get version of spict including git sha1 version if available. | get.version |
| Use a simple linear regression to guess m (MSY). | guess.m |
| Conduct hindcasting analysis | hindcast |
| Inverse logit transform. | invlogit |
| Inverse log "plus one" transform | invlogp1 |
| Generate latex code for including a figure. | latex.figure |
| Create profile likelihood | likprof.spict |
| List parameters to which priors can be added | list.possible.priors |
| Create data list used as input to TMB::MakeADFun. | make.datin |
| Make fcon vector | make.fconvec |
| Make ffac vector | make.ffacvec |
| Create TMB obj using TMB::MakeADFun and squelch screen printing. | make.obj |
| Creates a pdf file containing the summary output and result plots | make.report |
| Calculate confidence ellipsis for reference points. | make.rpellipse |
| Make a spline design matrix | make.splinemat |
| Load color of management scenarios. | man.cols |
| Select management scenarios | man.select |
| Get the TAC for the management scenarios | man.tac |
| Print a schematic to the console visualising the management timeline | man.timeline |
| Calculate predictions under 8 default management scenarios | manage |
| Convert mean and variance to shape and rate of gamma distribution | meanvar2shaperate |
| Convert mode and fractile to shape and rate in Gamma distribution (only for mode>0, i.e. shape >= 1) | modefrac2shaperate |
| Calculate Mohn's rho for different estimates | mohns_rho |
| Plot osar acf | osar.acf.plot |
| Plot osar qq | osar.qq.plot |
| Plot model points colored depending on the quarter to which they belong. | plot.col |
| Plot summarising spict results. | plot.spictcls |
| Plot summarising spict results (alternative plot composition) | plot2 |
| Plot priors of Meyer & Millar model | plot.priors plotmm.priors |
| Plot estimated B/Bmsy. | plotspict.bbmsy |
| Plot estimated biomass. | plotspict.biomass |
| Plot the expected biomass trend | plotspict.btrend |
| Plot observed catch and predictions. | plotspict.catch |
| Plot catch and index data. | plotspict.ci |
| Compare different spict fits | plotspict.compare |
| Compare one variable of different spict fits | plotspict.compare.one |
| Plot input data | plotspict.data |
| Plot model diagnostic (data, residuals, and more) | plotspict.diagnostic |
| Plot model diagnostics regarding processes and process residuals | plotspict.diagnostic.process |
| Plot estimated fishing mortality. | plotspict.f |
| Plot fishing mortality versus biomass. | plotspict.fb |
| Plot estimated relative fishing mortality. | plotspict.ffmsy |
| Plot estimated time-varying growth | plotspict.growth |
| Comparison plot of aavailable management scenarios | plotspict.hcr |
| Hindcasting plot for indices | plotspict.hindcast |
| Plots influence statistics of observations. | plotspict.infl |
| Plots summary of influence statistics of observations. | plotspict.inflsum |
| Plots result of likelihood profiling. | plotspict.likprof |
| Plot one-step-ahead residuals | plotspict.osar |
| Plot priors and posterior distribution. | plotspict.priors |
| Plot theoretical production curve and estimates. | plotspict.production |
| Plot results of retrospective analysis | plotspict.retro plotspict.retro.fixed |
| Plot the mean F cycle | plotspict.season |
| Plot time constant. | plotspict.tc |
| Fisheries data included in Polacheck et al. (1993). | pol |
| Helper function for sim.spict(). | predict.b |
| Helper function for sim.spict(). | predict.logf |
| Helper function for sim.spict(). | predict.logmre |
| Output a summary of a fit.spict() run. | print.spictcls |
| Estimate deviation between targeted and realised probability of specified model variable hitting a specified reference level under given fishing mortality | probdev |
| Prune a fitted spict object to the core elements | prune.baserun |
| Adds the x-axis to influence plots | put.ax put.xax |
| Reads ASPIC input file. | read.aspic |
| Reads the parameter estimates of an Aspic result file. | read.aspic.res |
| Draw CI around a reference point using polygon | refpointci |
| Helper function for calc.osar.resid that calculates residual statistics. | res.diagn |
| Retape a fitted spict model based on an updated input list | retape.spict |
| Conduct retrospective analysis | retro |
| Load season colors. | season.cols |
| Convert shape and rate of gamma distribution to mean and variance | shaperate2meanvar |
| Shorten time series of input data to specified range | shorten.inp |
| Simulate data from Pella-Tomlinson model | sim.spict |
| Stochastic surplus Production model in Continuous-Time (SPiCT) | spict |
| An S4 class to represent output from a SPiCT fit. | spictcls spictcls-class |
| Output a summary of a fit.spict() run. | summary.spictcls |
| Diagnostics table | sumspict.diagnostics |
| Deternistic reference points of a fit.spict() run. | sumspict.drefpoints |
| Fixed parameters table. | sumspict.fixedpars |
| Sensitivity to the initial parameter values | sumspict.ini |
| Print management summary. | mansummary sumspict.manage |
| Parameter estimates of a fit.spict() run. | sumspict.parest |
| Predictions of a fit.spict() run. | sumspict.predictions |
| Fixed parameters table. | sumspict.priors |
| Stochastic reference points of a fit.spict() run. | sumspict.srefpoints |
| State estimates of a fit.spict() run. | sumspict.states |
| Example of a spict analysis. | test.spict |
| Get real parameter values from transformed ones. | trans2real |
| Load color of true values from simulation. | true.col |
| Add spict version to plot | txt.stamp |
| Simulate data and reestimate parameters | validate.spict |
| Collect results from the output of running validate.spict. | validation.data.frame |
| Add warning sign to plot | warning.stamp |
| Takes a SPiCT input list and writes it as an Aspic input file. | write.aspic |
| Write the BUGS code to a text file | write.bug.file |
