NAMESPACE

import("ggplot2")
import("FLCore")
import("FLFleet")
import("methods")
import("tidyverse")
import("arrayhelpers")
importFrom("dplyr", "as_tibble", "%>%", "bind_cols", "bind_rows", "filter", "full_join", "group_by", "mutate","mutate_at", "select", "summarise_at", "ungroup", "if_else", 
           "everything", "case_when", "lag", "left_join")
importFrom("tidyr", "spread", "gather", "unnest")
importFrom("grDevices", "dev.off", "pdf")
importFrom("stats", "aggregate", "anova", "as.formula", "coef", "cor",
  "reshape", "formula", "lm", "mad", "optimize", "terms", "uniroot", "optim", "na.pass",
  "lag", "model.matrix", "setNames")
importFrom("utils", "data", "installed.packages")
importFrom("utils", "read.csv")
import("FLXSA")
import("FLa4a")
import("FLash")
import("Matrix")
import("plyr")
importFrom("mvtnorm", "rmvnorm")
importFrom("triangle", "rtriangle")
importFrom("mlogit", "mlogit.data")
importFrom("nloptr", "nloptr")
#importFrom("nnet", "predict.multinom")
importFrom("purrr", "map", "partial", "set_names")
importFrom("tibble", "tibble")
importFrom("Rcpp", "sourceCpp")

useDynLib(FLBEIA, .registration = TRUE)

export(
"advSum",
"advSumQ",
  "aneHCRE",
  "annualTAC",
  "annexIVHCR",
  "B_flbeia",
  "biolfleets2flstock",
  "bioSum",
"bioSumQ",
  "C_flbeia",
"calculate.q.sel.flrObjs",
  "catchStock",
  "catchStock.f",
  "catchWStock",
  "catchWStock.f",
  "checkAdvice",
  "checkBDs",
  "checkBiols",
  "checkFLBEIAData",
  "checkFleets",
  "checkObsctrl",
  "checkSRs",
  "CFPMSYHCR", 
  "costs_flbeia",
  "create.advice.ctrl",
  "create.assess.ctrl",
  "create.biols.ctrl",
  "create.ecoData",
  "create.fleets.ctrl",
  "create.covars.ctrl", 
  "create.obs.ctrl",
  "create.advice.data",    
  "create.BDs.data",       
  "create.biols.data", 
  "create.biol.arrays",
  "create.fleets.data",
  "create.fleets.arrays",
#  "create.F2CatchHCR.ctrl",    
  "create.indices.data",   
 # "calculate.CDparam",     
 # "create.list.stks.flq",  
 # "create.list.stks.flqa", 
  "create.SRs.data",       
  "D_flbeia",
  #"discnStock",
  "discStock",
  "discStock.f",
  "discWStock",
  "discWStock.f",
  "ecoSum_damara",
  "extractBRP",
  "F2CatchHCR",
  "F_flbeia",
  "FLBEIA",
   "FLBDsim",
"fltSum",
"fltSumQ",
"fltStkSum",
"fltStkSumQ",
  "FLSRsim",
  "FroeseHCR",
  "ghlHCR",
# "initPop_lifeHist",
  "IcesHCR",
  "joinIter",
  "L_flbeia",
  "landStock",
  "landStock.f",
  "landWStock",
  "landWStock.f",
"little2011HCR",
"MAPHCR",
"mtSum",
"mtSumQ",
"mtStkSum",
"mtStkSumQ",
"MultiStockHCR", 
  "neaMAC_ltmp",
"npv",
"npvQ",
  "pidHCR",
  "pidHCRItarg",
  "plotFLBiols",
  "plotFLFleets",
  "plotbioSum", 
  "plotfltSum", 
  "plotfltStkSum",
  "plotfltSum",
  "plotfltStkSum", 
  "plotEco",
  "price_flbeia",
  "R_flbeia",
  "riskSum",
  "revenue_flbeia",
  "segregmix",
  "SelAtAge",
  "SSB_flbeia",
  "stock.fleetInfo",
  "summary_flbeia",
  "tdiscStock",
  "tlandStock",
  "totfcost_flbeia", 
  "totvcost_flbeia",
  "updateFLBiols",
"vesselSum",
"vesselSumQ",
"vesselStkSum",
"vesselStkSumQ",
   "unit2age",
  "wtadStock",
  "wtalStock",
  #"XSAboot",
  "xtabs2",
  "brpsson",
  "plotBRPsson"
)

exportMethods(
  "dimnames<-", # to be deleted after next FLCore release
  "addFLCatch",
  "catchNames",
  "catchNames<-",
  "FLCatchesExt",
  "FLCatchExt",
  "FLFleetExt",
  "FLFleetsExt",
  "FLMetierExt",
  "FLMetiersExt",
  "is.FLCatchesExt",
  "is.FLFleetsExt",
  "is.FLMetiersExt", 
  "setUnitsNA"
)

exportClasses(
  "FLBDsim",
  "FLSRsim",
  "FLCatchesExt",
  "FLCatchExt",
  "FLFleetExt",
  "FLFleetsExt",
  "FLMetierExt",
  "FLMetiersExt"
)