add Baranov catch equation

DESCRIPTION

@@ -28,6 +28,7 @@ Imports:
   mvtnorm,
   mlogit,
   nloptr,
+  nleqslv,
   triangle,
   arrayhelpers,
   dplyr,
@@ -131,6 +132,7 @@ Collate:
     "OM_2a_Effort_Dynamics_MaxProf.R"
     "OM_2a_Effort_Dynamics_SMFB.R"
     "OM_2a_Effort_Dynamics_SMFB_VarEffortShare.R"
+    "OM_2a_b_Effort_Dynamics_Catch_update_Baranov_SMFB.R"
     "OM_2a1_Catch_Production_Functions.R"
     "OM_2a1_catchability2zero.R"
     "OM_2b_EffDyn_TAC_OverS_Func.R"

NAMESPACE

@@ -1,177 +1,178 @@
-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"
-)
-
+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("nleqslv", "nleqslv")
+#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"
+)
+