readAllResultsSCfunc.R

In torrem/scFunctions:

#setwd("C:/Users/Mike/Documents/Snow Crab/SnowCrabFunctions/ResultsRead")


#resdr = "C:/Users/Mike/Documents/Snow Crab/Dismels Runs/Batch Run/2003"
#resfn = 'results.'

require(RCurl)

source("C:/Users/Mike/Documents/Snow Crab/SnowCrabFunctions/ResultsRead/getStandardAttributes.R");
source("C:/Users/Mike/Documents/Snow Crab/SnowCrabFunctions/ResultsRead/getLifeStageInfo.SnowCrab.R");
#source("https://github.com/torrem/SnowCrabFunctions/raw/master/BeringMap.R"); 

info<-getLifeStageInfo.SnowCrab();
typeNames<-factor(info$lifeStageTypes$typeName,levels=info$lifeStageTypes$typeName);#typeNames as factor levels

readResults <-function(resdr, resfn){
  #read model results by java class and sort by startTime, id and time within a class
  cat("\n\n-----------------\n");
  cat("Reading and sorting results files\n");
  dfrs<-list();
  for  (cls in names(info$classInfo)){
    cat("\tclass name:",cls,"\n");
    csv<-file.path(resdr,paste0(resfn,cls,".csv"));
    tmp<-readr::read_csv(csv,skip=1);
    qry<-"select * from tmp
          order by startTime,id,time;"
    tmps<-sqldf::sqldf(qry);
    tmps$typeName<-factor(tmps$typeName,levels=typeNames);#change typeName from character to factor
    dfrs[[cls]]<-tmps;
  }
  rm(csv,tmp,qry,tmps);
  
  #--reorder model results into list of dataframes by typeName, not java class
  dfrts<-list();
  for (typeName in typeNames){
    dfrt<-NULL;
    for (cls in names(info$classInfo)){
      idx<-dfrs[[cls]]$typeName==typeName;
      if (any(idx)){
        if (sum(idx)==length(dfrs[[cls]]$typeName)) {
          tmp<-dfrs[[cls]];
        } else {
          tmp<-dfrs[[cls]][idx,];
        }
        dfrt<-rbind(dfrt,tmp);
      }
    }
    dfrts[[typeName]]<-dfrt;
  }
  dfrs<-dfrts;#NOTE that dfrs is now dataframes by typename which are ordered by id, startTime, and time
  rm(dfrts,typeName,dfrt,cls,idx,tmp);
  
  print(paste("Saving dfrs to:",resdr,sep=""))
  save(dfrs, file=paste(resdr,"/dfrs.RData", sep=""));
  #return(dfrs)
  }