R/makeFake_release.df.R

In tmcd82070/CAMP_RST: CAMP RST R Routines

#' @export
#'
#' @title makeFake_release.df
#'
#' @description Create a fake \code{release.df} data frame for use when no
#'   trials exist within the time period specified via \code{min.date} and
#'   \code{max.date}.
#'   
#' @param site The identification number of the site for which estimates are 
#'   required.
#'   
#' @param min.date The start date for data to include. This is a text string in 
#'   the format \code{\%Y-\%m-\%d}, or \code{YYYY-MM-DD}.
#'   
#' @param max.date The end date for data to include.  Same format as
#'   \code{min.date}.
#'   
#' @param visit.df A data frame resulting from the catch SQL sequence.
#'
#' @return A data frame with the number of rows equal to the number of days
#'   between \code{min.date} and \code{max.date}, inclusive.
#'
#' @details Days produced depend on the \code{seq.POSIXt} function with
#'   \code{by="1 DSTday"}.
#'
#'   The "fake efficiency trials" produced by this function insert one released
#'   fish and zero captured fish, per unique \code{trapPositionID} found within
#'   the \code{visit.df} data frame.  These numbers are used to minimize the
#'   impact, if any, the construction of these fake data cause.
#'   
#' @seealso \code{F.get.release.data}
makeFake_release.df <- function(site,min.date,max.date,visit.df){

  # site <- 5000
  # min.date <- "2016-03-02"
  # max.date <- "2016-04-01"
  # visit.df <- visit.df[visit.df$trapPositionID == trap,]
  
  pos <- 1
  envir <- as.environment(pos)
  time.zone <- get("time.zone",envir=.GlobalEnv)
  
  
  #   ---- Be sure to make a fake eff trial on a day within the range covered by our enh eff spline days.  
  
  #   ---- Get the temporal spline basis matrix goods.  
  here <- paste0(find.package("campR"),"/enhEffStats")  
  .tmpDataEnv <- new.env(parent=emptyenv()) 
  
  traps <- unique(visit.df$oldtrapPositionID)
  release.df <- NULL
  for(trap in traps){
    theFile <- paste0(here,"/",site,"_",trap,"_splineDays.RData")
    if(!file.exists(theFile)){
       release.df <- NULL
    } else {
      
      load(theFile,envir=.tmpDataEnv)
      splineDays <- .tmpDataEnv$splineDays
    
      #   ---- Remap back to the present.  
      reMap2list <- reMap2(min.date,max.date,splineDays)
      strt.dt <- reMap2list$strt.dt
      end.dt <- reMap2list$end.dt
    
      #   ---- We need to make a fake efficiency trial on a day inside BOTH strt.dt and end.dt (days on 
      #   ---- which we fit an enh eff spline) AND min.date and max.date.  
      min.max.dates  <- as.POSIXlt(seq.POSIXt(as.POSIXct(min.date,format="%Y-%m-%d",tz=time.zone),
                                              as.POSIXct(max.date,format="%Y-%m-%d",tz=time.zone),by="1 DSTday"))
      strt.end.dates <- as.POSIXlt(seq.POSIXt(as.POSIXct(strt.dt ,format="%Y-%m-%d",tz=time.zone),
                                              as.POSIXct(end.dt  ,format="%Y-%m-%d",tz=time.zone),by="1 DSTday"))
    
      #   ---- Check for non-zero intersection.  If so, use last date.  Don't use first, because the 
      #   ---- 4 AM construct pushes the first date back one day -- this could end up being outside 
      #   ---- the true date range we care about.  If empty intersection...we can't do anything?  
      AintB <- intersect(min.max.dates,strt.end.dates)
      
      if(length(AintB) > 0){
      
        release.df.trap <- data.frame(projectDescriptionID=0,
                                      releaseID=0,
                                       IncludeTest=NA,
                                      IncludeCatch=NA,
                                      ReleaseDate=AintB[length(AintB)],
                                      siteID=site,
                                      siteName=visit.df[visit.df$oldtrapPositionID == trap,]$siteName[1],
                                      trapPositionID=trap,
                                      TrapPosition=visit.df[visit.df$trapPositionID == trap,]$TrapPosition[1],
                                      sampleGear=NA,
                                      HalfCone=NA,
                                      nReleased=1,
                                      Recaps=0,
                                      ReleaseComments=NA,
                                      visitTime=.POSIXct(NA),
                                      visitTime2=.POSIXct(NA),
                                      visitTypeID=0,
                                      wmForkLength=0, 
                                      nForkLength=0,
                                      StartTime=.POSIXct(NA),
                                      EndTime=.POSIXct(NA),
                                      JasonSampleMinutes=difftime(.POSIXct(NA),.POSIXct(NA)),
                                      uniqueDate=0,
                                      sunMinutes=0,
                                      sunProp=0,
                                      moonMinutes=0,
                                      moonProp=0,
                                      nightMinutes=0,
                                      nightProp=0,
                                      halfConeAdj=0,    
                                      oldRecaps=0,
                                      allNightMins=0,
                                      allMoonMins=0,
                                      allSampleMins=0,
                                      allfl=0,
                                      allNfl=0,        
                                      HrsToFirstVisitAfter=0,
                                      HrsToLastVisitAfter=0,
                                      meanRecapTime=.POSIXct(NA),
                                      meanTimeAtLargeHrs=0,
                                      meanNightProp=0,
                                      meanMoonProp=0,       
                                      meanForkLength=0,
                                      thisIsFake=1)
        release.df <- rbind(release.df,release.df.trap)
        
        #   ---- Clean up workspace.  
        rm(splineDays,reMap2list,strt.dt,end.dt,min.max.dates,strt.end.dates,AintB,release.df.trap)
      } else {
        cat(paste0("No intersection between min.date and max.date and enh.eff spline strt.dt and end.dt.\n"))
        cat(paste0("To estimate passage, choose a min.date and max.date that spans at least one day in \n"))
        cat(paste0("the enh.eff spline strt.dt and end.dt range for trap ",trap,".\n"))
      }
    }
  }  
  return(release.df)
}