| Albacore_TwoFleet | A two-fleet Albacore operating model |
| Assessment-class | Class-'Assessment' |
| avail | What objects of this class are available |
| Awatea2OM | Reads MCMC estimates from Awatea (Paul Starr) processed r... |
| CASAL2OM | Reads MLE estimates from CASAL file structure into an... |
| CASALpars | Rips MLE estimates from CASAL file structure |
| cDD | Continuous Delay-differential assessment model |
| compare_models | Compare output from several assessment models |
| DD_TMB | Delay - Difference Stock Assessment in TMB |
| diagnostic_AM | diagnostic_AM (diagnostic of Assessments in MSE): Did Assess... |
| expandHerm | Expand the Herm list in SexPars to a matrix of fractions at... |
| fetch.file.names | Reads iSCAM Data, Control and Projection files |
| getinds | Characterize posterior predictive data |
| getnIVs | Count independent variables for a MICE relationship at... |
| getq_multi | optimize for catchability (q) |
| getq_multi_MICE | optimize for catchability (q) and fishing dist for a MICE... |
| HCR_FB | A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC... |
| HCRlin | Generic linear harvest control rule based on biomass |
| HCR_MSY | Harvest control rule to fish at some fraction of maximum... |
| HCR_ramp | Linearly ramped harvest control rules |
| HistMICE | Reconstruct historical dynamics |
| hrate | Derives the rate of exchange from one sex to another based on... |
| iSCAM2Data | Reads data from iSCAM file structure into a DLMtool Data... |
| iSCAM2OM | Reads MLE estimates from iSCAM file structure into an... |
| iSCAMcomps | Combines all iSCAM age composition data across fleets |
| iSCAMinds | Combines indices into a single index using linear modelling |
| ldim | Dimensions of a hierarchical list object |
| load.iscam.files | Reads iSCAM files into a hierarchical R list object |
| mahplot | Plot statistical power of the indicator with increasing time... |
| makemov | Calculates movement matrices from user inputs for fraction in... |
| make_MP | Make a custom management procedure (MP) |
| MMSE-class | Class "MMSE" |
| Model-based-MP | Model-based management procedures |
| MOM-class | Class "MOM" |
| MPCalcsNAs | Fill any NAs arising from MPCalcs (hermaphroditism mode) |
| MSEtool-package | Management Strategy Evaluation |
| multiData | Combine data among fleets |
| multiDataS | Combine data among stocks |
| multidebug | A basic comparison of runMSE output (MSE) and multiMSE (MMSE) |
| multiMSE | Run a multi-fleet multi-stock Management Strategy Evaluation |
| NIL | Item in list: get the list values from a list of lists |
| optQ_multi | Optimize q for a single simulation |
| plot.Assessment | Plot Assessment object |
| plot_betavar | Plots a beta variable |
| plot_composition | Plot composition data |
| plot_crosscorr | Produce a cross-correlation plot of the derived data arising... |
| plot_lognormalvar | Plots a lognormal variable |
| plot.MMSE | Standard plot for an object of class MMSE (multi MSE) |
| plot.MOM | Standard plot for an object of class MOM |
| plotmulti | A basic SSB plot for debugging runMSE output |
| plot.prof | Plot profile object |
| plotquant | A fairly tidy time-series quantile plot |
| plotRel | Plot a relationship between stocks |
| plot_residuals | Plot residuals |
| plot.retro | Methods for retro object |
| plot_SR | Plot stock-recruitment function |
| plot.SRA | Plot SRA scope output |
| plot_steepness | Plots probability distribution function of stock-recruit... |
| plot_timeseries | Plot time series of data |
| popdynMICE | Population dynamics for a MICE model (multiyear) |
| popdynOneMICE | Population dynamics for a MICE model (single year) |
| PRBcalc | Calculate mahalanobis distance (null and alternative MSEs)... |
| prelim_AM | Preliminary Assessments in MSE |
| Probs | Calculates mahalanobis distance and rejection of the Null... |
| prof-class | Class-'prof' |
| profile | Profile likelihood of assessment models |
| project-class | Class-'project' |
| projection | Projections for assessment models |
| qestMICE | Internal function for optimizing catchability (q) for a MICE... |
| read.control.file | Reads iSCAM control file |
| read.data.file | Reads iSCAM dat file |
| read.mcmc | Reads iSCAM mcmc output files |
| read.par.file | Reads iSCAM parameter file |
| read.projection.file | Reads iSCAM projection file |
| read.report.file | Reads iSCAM Rep file |
| ResFromRel | Returns Results of a set of MICE relationships |
| retro-class | Class-'retro' |
| retrospective | Retrospective analysis of assessment models |
| retrospective_AM | retrospective_AM (retrospective of Assessment model in MSE) |
| SCA | Statistical catch-at-age (SCA) model |
| SIL | Slot in list: get the slot values from a list of objects |
| simmov | Calculates movement matrices from user inputs |
| SOL | Sum over list: get the list values from a list of lists |
| SP | Surplus production model with FMSY and MSY as leading... |
| SP_production | Find the production parameter based on depletion that... |
| SRA-class | Class-'SRA' |
| SRA_scope | Stock-reduction analysis (SRA) for conditioning operating... |
| SS2Data | Reads data Stock Synthesis file structure into a Data object... |
| SS2MOM | Import Stock Synthesis to multi-fleet 2-sex MOM |
| SS2OM | Reads MLE estimates from Stock Synthesis file structure into... |
| SSS | Simple Stock Synthesis |
| summary.Assessment | Summary of Assessment object |
| swordfish | North Atlantic Swordfish dataset |
| TAC_MSY | Calculate MSY-based TAC from Assessment object |
| TEG | Toms expand grid |
| tinyErr | Remove observation error, process error, implementation error... |
| userguide | Get the MSEtool vignettes |
| VPA | Virtual population analysis (VPA) |
| VPA2OM | Reads bootstrap estimates from a VPA stock assessment into an... |
