R/05.02.SDAM.R

In y-yasutomo/maliaver0:

#05.02 Single Data Analysis by MALIA
#'Estimate detection function and calculate density
#'@description Sequence analysis will be conducted
#'
#'@param Voyage.name
#'@param COVARIATE
#'@param key.list
#'@param td
#'@param cp
#'@param area
#'@param save
#'
#'@author Tomoki Yasuhara
#'@export
#'
#'@examples
#'
 SDAM<-function(Voyage.name,COVARIATE=c("conv","occo","weather","size"),key.list=c("hn","hr","hhn","hhr"),
                td=200,cp=10,area=T,control=list(para.scale=0.05,rescale=10^(-3),
                                          ignore=0.01),inits=NULL,save=T){
  ###
  if(F){
    Voyage.name<-"SE18y3"
    key.list<-c("hn","hr","hhn","hhr")
    COVARIATE<-c("conv","occo","weather","size")
    td=200
    cp=10
    control=list(para.scale=0.05,rescale=10^(-3),
                 ignore=0.01)
    inits=NULL
    save=T
   }#IF(F)
   ###
   Voyage.result<-vector("list",length(key.list))
   if(1!=length(key.list))pb<-txtProgressBar(min=1,max=length(key.list),style=3)
   system.time({
     for(i in 1:length(key.list)){
       key<-key.list[i]
       RES.<-vector("list",length(COVARIATE))
       for(j in 1:length(COVARIATE)){
         colist<-COVARIATE[j]
         if(colist=="conv")colist<-NULL
         RES.[[j]]<-TCDM(Voyage.name,type=NULL,key,td,cp=cp,colist=colist,inits=inits,area=area,
                         para.scale=control$para.scale,rescale=control$rescale,ignore=control$ignore)
       }#for(j)
       names(RES.)<-COVARIATE
       Voyage.result[[i]]<-RES.
       if(1!=length(key.list))setTxtProgressBar(pb,i)
     }#for(i)
     names(Voyage.result)<-key.list
   })
     if(save){
       obj.list<-list.files(getwd(),"result.obj")
       ind<-paste(Voyage.name,".result.obj",sep="")%in%obj.list
       if(!ind){
         saveRDS(Voyage.result,paste(Voyage.name,".result.obj",sep=""))
         cat("\n",paste(Voyage.name,".result.obj",sep="")," is created.")
       }else{
         saveRDS(Voyage.result,paste(Voyage.name,".result2.obj",sep=""))
         warning("Since ",paste(Voyage.name,".result.obj",sep=""),
                 " already exists, \n",paste(Voyage.name,".result2.obj",sep=""),
                 " is created.",immediate.=T)
       }
     }#IF(SAVE)
   invisible(Voyage.result)
 }#SDAM