_pkgdown.yml

title: MSEtool Functions
icon: logo.png
url: "https://msetool.openmse.com"
template:
  bootstrap: 5
#   
# reference:
# - title: internal
#   contents:
#   - CheckDuplicate
#   - DLMDataDir
#   - DataDir
#   - 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
#   - SS2MOM
#   - WHAM2OM
#   - iSCAM2OM
#   
# - 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
#   
# - title: Management procedures
#   desc: Calculate advice from management procedures
# 
# - subtitle: General
#   contents:
#   - Can
#   - Fease
#   - Input
#   - MPtype
#   - RealFease
#   - Required
#   - Sense
#   - TAC
#   - TACfilter
#   - Uses
#   - runInMP
#   - runMP
#   
# - subtitle: Reference managment procedures
#   desc: Management procedures reflecting idealized management, e.g., perfect knowledge of stock productivity, no fishing scenario, etc.
#   contents: 
#   - FMSYref
#   
# - 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
#   - 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
#   
# - 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
#