ReadEKRaw_updated:

# SubsetData: function to subset data based on user specified start and end time or by GPS lat/longs; 
# intended to subset data files into the individual transects from each lake  
# that can then be plotted or further analyzed. Remember, that plotting function 
# only works if the first ping in the data set is the start of the transect. 

# input is a data object from ReadEraw, ConvertPower or FindBottom 
# 		start 				time as character in format:"YYYY-MM-DD HH:MM:SS GMT"
# 		end				  	or decimal degrees as a number with the form c(lat,long)				
#
#		method 				specified by user as either "time" or "latlong", must match units in start and end
  
SubsetData = function(data, start, end, method){
  
  	idx.select = c() # empty vector to store the index values in.  
  	
  	# assess method time, then find appropriate index values accordingly
    	# TIME  
    	if(method == "time"){
        	# turn start and end times into as.POSIXct and then as.numeric
            	s.time.num  = as.numeric(as.POSIXct(strptime(start, "%Y-%m-%d %H:%M:%S"), tz = "GMT"))
            	e.time.num  = as.numeric(as.POSIXct(strptime(end, "%Y-%m-%d %H:%M:%S"), tz = "GMT"))
            # for loop to check if [i] is between start and end times
                for (i in 1:(length(data$GPS))){
                  # pull out time from data$GPS
                  		t = as.numeric(data$GPS[[i]]$time)
                  # compare t to start and end time (must be between)
                  		if((t >= s.time.num & t <= e.time.num) == TRUE ){ 
                    			idx = i
                  		} else { 
                  		  idx = NA
                  		  }
                  # add idx to vector
						idx.select = c(idx.select, idx)
                }
        }
    	
    	# LATLONG
    	if(method == "latlong"){
    		# re-write the start and end lat/longs into lats and longs
				lats = c(start[1], end[1])
				longs = c(start[2], end [2])
  			# for loop to seach for inclusion in subset based on lat, long 
  				for (i in 1:(length(data$GPS))){
    				# pull out time from data$GPS
    					lat = as.numeric(data$GPS[[i]]$lat) # needs to be as numeric to keep all of the decimal places
    					long = as.numeric(data$GPS[[i]]$long)
    
    				# check if each i fall within the range of lat/longs specified by user
    					if((lat >= min(lats) & lat <= max(lats) & long >= min(longs) & long <= max(longs)) == TRUE ){ 
      						idx = i
    					} else { 
    					  idx = NA
    					}
    			# add idx to vector
						idx.select = c(idx.select, idx)
  				}	
    	}
  
  ## generate new data object that is only the subset specified by user  
  		# idx values
    		idx.min  = min(idx.select, na.rm = TRUE) #  start index value 
    		idx.max  = max(idx.select, na.rm = TRUE) #  stop index value 
  	
  	# check if FindBottom has been run already - this makes it so data is subset regardless of whether user has run FindBottom on data yet 
    	
  			if(is.null(data$bottom.line) == TRUE) { 
                      			  data.new  = list(header = data$header # this keeps the entire header with the data
                      			                   , pings = data$pings[idx.min:idx.max]
                      			                   , GPS = data$GPS[idx.min:idx.max]
                      			                   #, bottom.line = data$bottom.line[idx.min: idx.max]
                     									        )
                      			  
  			} else { 
  			  										data.new  = list(header = data$header # this keeps the entire header with the data
                     									        , pings = data$pings[idx.min:idx.max]
                     									        , GPS = data$GPS[idx.min:idx.max]
                     									        , bottom.line = data$bottom.line[idx.min:idx.max]
                     									        )
  			}
  
  data.new # return the subset of the data 
}

# test using Rock Pond
#start = "2015-06-03 18:42:11 GMT" # idx 3
#end = "2015-06-03 18:44:38 GMT" # idx 150

#start = c(43.6504, -74.97595 ) # idx 3 (lat, long) in decimal degrees
#end = c(43.65122, -74.9746) # idx 150 

# Example
#testsub = SubsetData(data, start =  c(43.6504, -74.97595 ), end = c(43.65122, -74.9746), method = "latlong" )
#testsub = SubsetData(data, start = "2015-06-03 18:42:11 GMT", end = "2015-06-03 18:44:38 GMT", method = "time" )
#start.test = "2015-06-17 20:07:30 GMT"
#end.test = "2015-06-17 20:19:35 GMT"

#start = "2015-06-17 20:07:30 GMT"
#end = "2015-06-17 20:19:35 GMT"
#method = "time"
#testGIL = SubsetData(data, start = start.test , end = end.test , method = "time")