getAggLoglikeFiles: Processing the loglike.dat files (maybe better for you to use...

In frabas/displaceplot: A suite of R routines to treat DISPLACE simulation output files

Description

This function process the loglike_simu_xxx.dat files

Usage

getAggLoglikeFiles(general = general, what = "weight",
  explicit_pops = c(0, 1, 2, 3, 11, 23, 24, 26, 30, 31, 32),
  implicit_pops = c(0, 1, 2, 4, 5, 6, 8, 9, 11:30),
  selected_vessels_set1 = selected_vessels_set1,
  selected_vessels_set2 = selected_vessels_set2,
  selected_vessels_set3 = selected_vessels_set3)

Arguments

fname	First name
lname	Last name

Examples

## Not run: 
general <- setGeneralOverallVariable (pathToRawInputs =file.path("C:", "Users", "fbas", 
                                                "Documents", "GitHub", paste0("DISPLACE_input_gis_", 
                                                 "DanishFleet")),
                                      pathToDisplaceInputs = file.path("C:", "Users", "fbas", 
                                                "Documents", "GitHub", paste0("DISPLACE_input_", "DanishFleet")),
                                      pathToOutputs =file.path("C:","DISPLACE_outputs"),
                                      caseStudy="DanishFleet",
                                      iGraph=41,
                                      iYear="2015",
                                      iCountry="DEN",
                                      nbPops=39,
                                      nbSzgroup=14,
                                      theScenarios= c("svana_baseline",
                                                      "svana_sub1mx20",
                                                      "svana_sub4mx20",
                                                      "svana_sub4mx5ns20bt",
                                                      "svana_sub4mx20ns5bt",
                                                      "svana_sub4mx5ns5bt" ),
                                      nbSimus=20,
                                      useSQLite=FALSE    
                                      )


 if(FALSE){
 load(file.path(general$main.path.param, "FISHERIES",
          paste("logbooks_DNK_","2015",".RData",sep=''))) 
 eflalo                           <- cbind.data.frame (logbooks, totland=apply(logbooks[, grep("LE_KG", colnames(logbooks))],  1, sum, na.rm=TRUE )  )
 eflalo                           <- cbind(eflalo, ICESrectangle2LonLat(eflalo$LE_RECT))
 eflalo$area                      <- ICESarea2 (eflalo[, c("SI_LONG", "SI_LATI")])
 bottomfishingmets                <- as.character(unique(eflalo$LE_MET)[ unique(
                                            c(grep("OTB", unique(eflalo$LE_MET)),
                                              grep("PTB", unique(eflalo$LE_MET)),
                                              grep("SDN", unique(eflalo$LE_MET)),
                                              grep("PS", unique(eflalo$LE_MET)),
                                              grep("SSC", unique(eflalo$LE_MET)),
                                              grep("TBB", unique(eflalo$LE_MET)),
                                              grep("DRB", unique(eflalo$LE_MET))
                                                )
                                           )])  
                                           
 
 vids_all                         <- unique(eflalo[, "VE_REF"])
 vids_bottomfishing_baltic        <- unique(eflalo[eflalo$area %in% c("2224", "2532") & eflalo$LE_MET %in% bottomfishingmets, "VE_REF"])
 vids_bottomfishing_nseakask      <- unique(eflalo[eflalo$area %in% c("nsea", "kask") & eflalo$LE_MET %in% bottomfishingmets, "VE_REF"])
 
 selected_vessels_set_1  <-  as.character(unique(vids_all[ vids_all %in%  loglike$VE_REF ]))  
 selected_vessels_set_2  <-  as.character(unique(vids_bottomfishing_baltic[ vids_bottomfishing_baltic %in%  vids_bottomfishing_baltic ]))  
 selected_vessels_set_3  <-  as.character(unique(vids_bottomfishing_nseakask[ vids_bottomfishing_nseakask %in%  vids_bottomfishing_nseakask ]))   
 selected_vessels_set_1  <- selected_vessels_set_1[!is.na(selected_vessels_set_1)]
 selected_vessels_set_2  <- selected_vessels_set_2[!is.na(selected_vessels_set_2)]
selected_vessels_set_3  <- selected_vessels_set_3[!is.na(selected_vessels_set_3)]

 write.table(selected_vessels_set_1, file.path(general$main.path, general$case_study,
          paste("selected_vessels_set_1.dat",sep='')), col.names=FALSE, row.names=FALSE)
 write.table(selected_vessels_set_2, file.path(general$main.path, general$case_study,
          paste("selected_vessels_set_2.dat",sep='')), col.names=FALSE, row.names=FALSE)
 write.table(selected_vessels_set_3, file.path(general$main.path, general$case_study,
          paste("selected_vessels_set_3.dat",sep='')), col.names=FALSE, row.names=FALSE)
 } else{
  selected_vessels_set_1 <- as.character(read.table(file.path(general$main.path, general$case_study,
          paste("selected_vessels_set_1.dat",sep='')), header=FALSE)[,1])
  selected_vessels_set_2 <-as.character(read.table(file.path(general$main.path, general$case_study,
          paste("selected_vessels_set_2.dat",sep='')), header=FALSE)[,1])
   selected_vessels_set_3 <- as.character(read.table(file.path(general$main.path, general$case_study,
          paste("selected_vessels_set_3.dat",sep='')), header=FALSE)[,1])
  
 
 }
 
 
 save(selected_vessels_set_1, selected_vessels_set_2, selected_vessels_set_3,
   file=file.path(general$main.path, general$namefolderinput, 
                    paste("selected_vessels.RData", sep='')) )
 



  getAggLoglikeFiles(general=general, what="weight",
            explicit_pops=c(0, 1, 2, 3, 11, 23, 24, 26, 30, 31, 32),
            implicit_pops=c (4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38),
            selected_vessels_set1=selected_vessels_set_1,
           selected_vessels_set2=selected_vessels_set_2,
            selected_vessels_set3=selected_vessels_set_3)  
  
## End(Not run)

frabas/displaceplot documentation built on May 3, 2019, 4:06 p.m.