_pkgdown.yml

title: MSEtool Functions
icon: logo.png
url: "https://msetool.openmse.com"
template:
  bootstrap: 5

reference:
- title: internal
  contents:
  - CheckDuplicate
  - DLMDataDir
  - DataDir
  - getMP
  - makemov2
  - simmov2
  - MPCalcsNAs
  - NIL
  - OMinit
  - OMexample
  - LHdatabase
  - OMDescription
  - DataDescription
  - StockDescription
  - FleetDescription
  - ObsDescription
  - ImpDescription
  - HistDescription
  - MSEDescription
  - ReqData
  - SIL
  - TEG
  - Taxa_Table
  - getclass
  - getDataList
  - getfirstlev
  - getnIVs
  - hist2
  - iSCAM
  - iSCAMcomps
  - iSCAMinds
  - initialize-methods
  - ldim
  - movfit_Rcpp
  - show,MSE-method
  - show-MSEtool
  - show,Rec-method
  - show,PMobj-method

- title: Operating model

- subtitle: General functions
  contents:
  - OM-class
  - OMdoc
  - testOM
  - plot.Stock

- subtitle: Import
  desc: Convert stock assessment output, i.e., stock, fleet, and some observation error parameters, into an operating model
  contents:
  - ASAP2OM
  - Assess2MOM
  - Assess2OM
  - Awatea2OM
  - BAM2MOM
  - iSCAM2OM
  - SS2MOM
  - WHAM2OM
  
- subtitle: Manual configuration
  desc: Manually parameterize the operating model
  contents:
  - Choose
  - LH2OM
  - ML2D
  - SketchFun
  - Turing
  - XL2Fleet
  - XL2OM
  - XL2Stock
  - makemov

- title: OM components
- subtitle: Stock
  desc: Object specifying biology and stock dynamics
  contents:
  - Stock-class-objects
  - Stock-class

- subtitle: Fleet
  desc: Object specifying fishing dynamics
  contents:
  - Fleet-class-objects
  - Fleet-class

- subtitle: Obs
  desc: Object specifying observation model (how data are simulated)
  contents:
  - Obs-class-objects
  - Obs-class

- subtitle: Imp
  desc: Object specifying the extent of error in MP implementation
  contents:
  - Imp-class-objects
  - Imp-class

- subtitle: Hist
  desc: Object generated from the historical reconstruction of the system dynamics (output of `runMSE(Hist = TRUE)`)
  contents:
  - Hist-class

- title: Data objects
  desc: Includes functions to import and export Data objects, data frames describing slots, manipulate Data objects, and generate examples.
  contents:
  - Data-class-objects
  - Data-class
  - Data2csv
  - DataInit
  - DataSlots
  - Data_xl
  - Lag_Data
  - Report
  - SS2Data
  - SS2DataMOM
  - XL2Data
  - SimulatedData
  - boxplot.Data
  - plot.Data
  - plotOFL
  - summary,Data-method
  - select_MP

- title: Management procedures
  desc: Calculate advice from management procedures

- subtitle: General
  contents:
  - Can
  - Fease
  - Input
  - MPtype
  - RealFease
  - Required
  - Sense
  - TAC
  - TACfilter
  - tune_MP
  - Uses
  - runInMP
  - runMP

- subtitle: Reference management procedures
  desc: Management procedures reflecting idealized management, e.g., perfect knowledge of stock productivity, no fishing scenario, etc.
  contents:
  - FMSYref
  
- subtitle: Other management procedures
  contents:
  - Emp

- subtitle: Rec object
  desc: Output of management procedures to implement in the MSE simulation
  contents:
  - Rec-class

- title: Run MSE simulation
  contents:
  - runCOSEWIC
  - runMSE
  - setup

- title: Evaluate MSE results

- subtitle: Performance metrics
  contents:
  - PMobj-class
  - PerformanceMetric

- subtitle: General and diagnostic functions
  contents:
  - MSE-class
  - Converge
  - Dom
  - VOI
  - VOI2
  - summary,MSE-method

- subtitle: Plot MSE output (general)
  contents:
  - Cplot
  - Kplot
  - PMLimit
  - Pplot
  - Pplot2
  - PWhisker
  - Splot
  - SSBrefplot
  - TradePlot
  - VOIplot
  - plot.MSE
  - wormplot

- subtitle: Plot MSE output (specific to management areas)
  desc:
  contents:
  - DFO_bar
  - DFO_hist
  - DFO_plot
  - DFO_plot2
  - DFO_quant
  - DFO_proj
  - DFO_report
  - DFO_spider
  - DFO_tab
  - DFO_tab_formatted
  - Cos_thresh_tab
  - Thresh_tab
  - NOAA_plot

- title: multiMSE
  desc: Multi-population (two-sex or multi-stock), multi-fleet operating models (class MOM) and corresponding MSE object (class MMSE)
  contents:
  - MOM-class-objects
  - MOM-class
  - MMSE-class
  - makeMOM
  - makeRel
  - multiMSE
  - multidebug
  - plot.MMSE
  - plot.MOM
  - plotRel
  - plotmulti
  - summary,MMSE-method

- title: Miscellaneous
  desc: Convenient user functions to process various objects
  contents:
  - avail
  - optCPU
  - tinyErr
  - writeCSV

- subtitle: OM
  contents:
  - CheckOM
  - Replace
  - MSEextra
  - SubCpars
  - SubOM
  - validcpars

- subtitle: Data
  contents:
  - CALsimp
  - CheckMPs
  - replic8

- subtitle: MP
  contents:
  - MPtype
  - CombineMMP
  - doHCR
  - doIfreq
  - doRec
  - smoothy

- subtitle: MSE
  contents:
  - Sub
  - checkMSE
  - joinData

- subtitle: Internal functions
  desc: Populations dynamics functions and other processing functions
  contents:
  - MSYCalcs
  - applyMP
  - applyMMP
  - calcRefYield
  - cparscheck
  - dnormal
  - getmov2
  - getsel
  - hconv
  - movestockCPP
  - simCAA
  - simCAL
  - simmov

- subtitle: Internal multiMSE
  contents:
  - expandHerm
  - multiData
  - multiDataS

- subtitle: Figures
  contents:
  - join_plots
  - makeTransparent
  - plotFun
  - plotquant
  - quantile_plot