GDD = ((con ([tmean_1] <= 100, 100, [tmean_1]) - 100)  +  (con ([tmean_2] <= 100, 100, [tmean_2]) - 100) + (con ([tmean_3] <= 100, 100, [tmean_3]) - 100) + (con ([tmean_4] <= 100, 100, [tmean_4]) - 100) + (con ([tmean_5] <= 100, 100, [tmean_5]) - 100) + (con ([tmean_6] <= 100, 100, [tmean_6]) - 100) + (con ([tmean_7] <= 100, 100, [tmean_7]) - 100) + (con ([tmean_8] <= 100, 100, [tmean_8]) - 100) + (con ([tmean_9] <= 100, 100, [tmean_9]) - 100) + (con ([tmean_10] <= 100, 100, [tmean_10]) - 100) + (con ([tmean_11] <= 100, 100, [tmean_11]) - 100) + (con ([tmean_12] <= 100, 100, [tmean_12]) - 100)) / 10

##

##

##

rm(list=ls(all=TRUE))

setwd("C:\\Users\\Frank\\Documents\\Data\\Climate_data\\CRU_TS_3.0")

library(ncdf)

vrb<-c("pre","tmn","tmp","tmx")

for(v in 4:4){

  # open data file

  nc<-open.ncdf(paste("cru_ts_3_00.1901.2006.",vrb[v],".nc",sep=""))           # open datafile

  nodata<-nc$var$tas$missval                                   # nodata value

  time.dim<-nc$dim$time$len                                    # time dimension

  time.base<-as.numeric(substr(nc$dim$time$units,14,17))       # base year

  time.start<-round(nc$dim$time$vals[1]/12)+time.base         # year simulation started

  time.end<-floor(nc$dim$time$vals[time.dim]/12)+time.base    # year simulation ended

  # build flip matrix

  I<-matrix(0,360,360)

  y<-360

  for(x in 1:360){

    I[x,y]<-1

    y<-y-1

  }

  ## extract data for 1968 to 2006 and output as ESRI ASCII files

  for(i in 1:time.dim){

    # define year and month

    if(trunc(i/12)!=i/12){

      year<-floor(i/12)+time.start

      month<-round((i/12-trunc(i/12))*12)

    }else{

      year<-floor(i/12)+time.start-1

      month<-12

    }

    if(year<2005) next

   # read data

    ncd<-get.var.ncdf(nc,start=c(1,1,i),count=c(720,360,1))

    # flip matrix

    grd<-I%*%(t(ncd))

    # ouput to file in ESRI ASCII format

    esri<-c(paste("ncols",720),

            paste("nrows",360),

            paste("xllcorner",-180),

            paste("yllcorner",-90),

            paste("cellsize",0.5),

            paste("nodata_value",-99.9))

        path2<-paste("cru_ts_3.0_",vrb[v],"_",year,"_",month,".asc",sep="")

        write.table(esri,path2,row.names=F,col.names=F,quote=F,append=F)

        write.table(data.frame(grd),path2,row.names=F,col.names=F,quote=F,append=T)

  }

  close.ncdf(nc) # close datafile

}

# Calculates the daily average clear day coverage for the clear day

# MODIS layer extracted from the MODIS LST files

#

# Reads a directory of .img files and groups them by day to calculate

# a daily aveage. This script also applies the clear day scaling factor

# to the resulting average raster and writes one raster for each day

# of the 1-year 2000 to 2010 period (one file for each 10-year group)

#

# Developed by John Donoghue

# Created: 16 October 2010

# Last Updated:

#

# For NCEAS Working Group Environment and Organisms

#

#setwd("/data/project/organisms/R")

#source("Calc Clear Day Daily Avg.r", echo=TRUE, print.eval=TRUE)

setwd("/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL")

inFiles <- list.files(pattern="*.img$")

library(raster)

print("")

print("Processing h08v04 tiles")

print("")

# process h08v04 tiles

# Create day averages for each day in the year

for(i in 1:366){

if (i < 9) {f <- "00"}

if ((i > 9) & (i <99 )) {f <- "0"}

if (i > 99) {f <- ""}

fpart <- paste(toString(f), toString(i), sep="")

# get a list of all files for that day of the year

print("")

print(sprintf("Reading day: %s", toString(fpart)))

myFiles <- grep(fpart,substr(inFiles, 14,16))

nFiles <-  length(myFiles)

# for each file in the list

filestoStack <- list()

for (iCtr in 1 : nFiles)

{

mFile <- myFiles[iCtr]

if (substr(inFiles[mFile],18,23) == "h08v04") {

print(sprintf("..Reading file: %s",inFiles[mFile]))

inputRaster <- raster()

inputRaster <- raster(inFiles[mFile])

filestoStack <- c(filestoStack, inFiles[mFile])

}

}

# now calculate the mean cell values

myStack <- stack(filestoStack)

print(sprintf("....Averaging Daily Values"))

# Check if file exists

outFile <- paste("Day_",toString(i),"_Average_Scaled_h08v04",".img",sep="")

if (file.exists(outFile) == FALSE) {

meanRaster <- mean(myStack, na.rm=TRUE)

scaledRaster <- meanRaster * 0.0005 # apply scaling factor to raster

print(sprintf("......Writing file: %s",outFile))

writeRaster(scaledRaster,filename=outFile,format="HFA",overwrite=TRUE)

}

}

print("")

print("Processing h09v04 tiles")

print("")

# now reloop and process h09v04 tiles

# Create day averages for each day in the year

for(i in 1:366){

if (i < 9) {f <- "00"}

if ((i > 9) & (i <99 )) {f <- "0"}

if (i > 99) {f <- ""}

fpart <- paste(toString(f), toString(i), sep="")

# get a list of all files for that day of the year

print("")

print(sprintf("Reading day: %s", toString(fpart)))

myFiles <- grep(fpart,substr(inFiles, 14,16))

nFiles <-  length(myFiles)

# for each file in the list

filestoStack <- list()

for (iCtr in 1 : nFiles)

{

mFile <- myFiles[iCtr]

if (substr(inFiles[mFile],18,23) == "h09v04") {

print(sprintf("..Reading file: %s",inFiles[mFile]))

inputRaster <- raster()

inputRaster <- raster(inFiles[mFile])

filestoStack <- c(filestoStack, inFiles[mFile])

}

}

# now calculate the mean cell values

myStack <- stack(filestoStack)

print(sprintf("....Averaging Daily Values"))

# Check if file exists

outFile <- paste("Day_",toString(i),"_Average_Scaled_h09v04",".img",sep="")

if (file.exists(outFile) == FALSE) {

meanRaster <- mean(myStack, na.rm=TRUE)

scaledRaster <- meanRaster * 0.0005 # apply scaling factor to raster

print(sprintf("......Writing file: %s",outFile))

writeRaster(scaledRaster,filename=outFile,format="HFA",overwrite=TRUE)

}

}

# finished

print("Finished")

# Calculates the monthly average clear day coverage for the clear day

# MODIS layer extracted from the MODIS LST files

#

# Reads a directory of .img files and groups them by month to calculate

# a monthly aveage. This script also applies the clear day scaling factor

# to the resulting average raster and writes one raster for each month

# of the 1-year 2000 to 2010 period (one file for each month of the

# 10-year group)

#

# Developed by John Donoghue

# Created: 20 October 2010

# Last Updated:

#

# For NCEAS Working Group Environment and Organisms

#

#setwd("/data/project/organisms/R")

#source("Calc Clear Day Monthly Avg.r", echo=TRUE, print.eval=TRUE)

wkDir <- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate"

setwd(wkDir)

inFiles <- list.files(pattern="*h08v04.005.ClearDay.img$")

nFiles <- length(inFiles)

library(raster)

# build a list of the files for each month

janList <- list()

febList <- list()

marList <- list()

aprList <- list()

mayList <- list()

junList <- list()

julList <- list()

augList <- list()

sepList <- list()

octList <- list()

novList <- list()

decList <- list()

# for each file in the list

for (i in 1:nFiles) {

#print(inFiles[i])

# get month of file

theMonth <- substr(inFiles[i], 16,17)

if (substr(theMonth, 2,2) == ".") {theMonth <- substr(theMonth, 1, 1)}

# group by month

if (theMonth == "1") {

a <- length(janList)

janList[a+1] <- inFiles[i]

}

if (theMonth == "2") {

a <- length(febList)

febList[a+1] <- inFiles[i]

}

if (theMonth == "3") {

a <- length(marList)

marList[a+1] <- inFiles[i]

}

if (theMonth == "4") {

a <- length(aprList)

aprList[a+1] <- inFiles[i]

}

if (theMonth == "5") {

a <- length(mayList)

mayList[a+1] <- inFiles[i]

}

if (theMonth == "6") {

a <- length(junList)

junList[a+1] <- inFiles[i]

}

if (theMonth == "7") {

a <- length(julList)

julList[a+1] <- inFiles[i]

}

if (theMonth == "8") {

a <- length(augList)

augList[a+1] <- inFiles[i]

}

if (theMonth == "9") {

a <- length(sepList)

sepList[a+1] <- inFiles[i]

}

if (theMonth == "10") {

a <- length(octList)

octList[a+1] <- inFiles[i]

}

if (theMonth == "11") {

a <- length(novList)

novList[a+1] <- inFiles[i]

}

if (theMonth == "12") {

a <- length(decList)

decList[a+1] <- inFiles[i]

}

# end list files

}

print("")

print("PROCESSING h08v04 FILES")

print("")

# for each file in the list

for (f in 1:12) {

if (f == 1) {myList <- janList}

if (f == 2) {myList <- febList}

if (f == 3) {myList <- marList}

if (f == 4) {myList <- aprList}

if (f == 5) {myList <- mayList}

if (f == 6) {myList <- junList}

if (f == 7) {myList <- julList}

if (f == 8) {myList <- augList}

if (f == 9) {myList <- sepList}

if (f == 10) {myList <- octList}

if (f == 11) {myList <- novList}

if (f == 12) {myList <- decList}

print ("")

print ("")

filestoStack <- raster()

for (iCtr in 1 : length(myList))

{

mFile <- myList[iCtr]

print(sprintf("..Reading file: %s",mFile))

myFile <- paste(wkDir, "/", mFile, sep="")

inputRaster <- raster()

inputRaster <- mFile

filestoStack <- c(filestoStack, inputRaster)

}

# now calculate the mean cell values

print("....Stacking Grids")

myStack <- stack(filestoStack)

# Check if file exists

outFile <- paste("Month_", f ,"_ClearDay_Average",".img",sep="")

if (file.exists(outFile) == FALSE) {

print("....Averaging Monthly Values")

meanRaster <- mean(myStack, na.rm=TRUE)

print("....Applying Scale Factor")

scaledRaster <- meanRaster * 0.0005 # apply scaling factor to raster

print(sprintf("......Writing file: %s",outFile))

writeRaster(scaledRaster,filename=outFile,format="HFA",overwrite=TRUE)

}

}

# finished

print("Finished")

#This is a simple code to convert hdf file into img format

listfiles1=glob.glob('*.hdf')

infile=listfiles1[1]

outfile=infile[:-4]+'.img' #this select the name of file without its extension

# renames MODIS files from a year and day to year.month.day

# ---------------------------------------------------------------------------

# Developed by John Donoghue II

# 620 October, 2010

# Convert MODIS Day of Year to Date File Name.py

import sys

import string

import os

import shutil

sourceDir = "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts"

outputDir = "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate"

# Loop through the folder

for dirname, dirnames, filenames in os.walk(sourceDir):

    for filename in filenames:

        ext = os.path.splitext(filename)[1]

        if ext == ".img":

		print "processing " + filename

		# process the file

		inFile = sourceDir + "/" + filename

		# rename the file to the month and day

		theYear = filename[9:13]

		theDay = filename[13:16]

		prefix = filename[0:9]

		tile = filename[17:27]

		# convert day to month and year

		theYear = int(theYear)

		theDay = int(theDay)

		from datetime import date

		myDate = date.fromordinal(date(theYear, 1, 1).toordinal() + theDay - 1)

		myYear = myDate.year

		myMonth = myDate.month

		myDay = myDate.day

		outFile = prefix + "."  + str(myYear) + "." + str(myMonth) + "." + str(myDay) + "." + tile + ".ClearDay.img"

		print ".. Writing " + outFile

		#print theYear + ' ' + theDay

		outFile = outputDir + "/" + outFile

		# remove outfile if present

		if not os.path.exists(outFile) == True:

			#os.remove(outFile)

			shutil.copy2(inFile,outFile)

		# Process: Extract Subdataset

                #print "   saving " + filename[0:27] + "_ClearDay.img"

                #myCommand = "gdal_translate -of HFA HDF4_EOS:EOS_GRID:" + filename + ":MODIS_Grid_Daily_1km_LST:Clear_day_cov " + outFile

                #output = os.popen(myCommand).read() # shows the ouput data of the command

print "Finished"

import sys

import string

import os

import osgeo

from osgeo import gdal, gdalconst

import re

import subprocess

from osgeo.gdalconst import *

driver = gdal.GetDriverByName('Ehdr')

driver2=gdal.GetDriverByName('HFA')

driver.Register()

driver2.Register()

# Convert Monthly averages to .bil

sourceDir = "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics"

outputDir = "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics"

# Loop through the folder

for dirname, dirnames, filenames in os.walk(sourceDir):

  for filename in filenames:

     ext = os.path.splitext(filename)[1]

     if ext == ".img":

       infile= sourceDir + "/" + filename

       outfile= re.sub(".img",".bil",infile)

       subprocess.call(["gdalwarp","-s_srs", "+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs","-t_srs", "+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs", "-ot", "int16", "-srcnodata", "3.39999999999999996e+38", "-dstnodata", "3.39999999999999996e+38", "-of", "EHdr", "-overwrite", infile, outfile])

#subprocess.call(["gdal_translate", "-ot", "int16", "-of", "EHdr", infile, outfile])

# Convert Daily averages to .bil

sourceDir2 = "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics"

outputDir2 = "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics"

# Loop through the folder

for dirname, dirnames, filenames in os.walk(sourceDir2):

  for filename in filenames:

     ext = os.path.splitext(filename)[1]

     if ext == ".img":

       infile2= sourceDir2 + "/" + filename

       outfile2= re.sub(".img",".bil",infile2)

       subprocess.call(["gdalwarp","-ot", "int16", "-srcnodata", "3.39999999999999996e+38", "-dstnodata", "3.39999999999999996e+38", "-of", "EHdr", "-overwrite", infile2, outfile2])

#subprocess.call(["gdal_translate", "-ot", "int16", "-of", "EHdr", infile2, outfile2])

gdalwarp -ot int16 -srcnodata "3.39999999999999996e+38" -dstnodata "3.39999999999999996e+38" -of EHdr infile2 outfile2 

library (raster)

path<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles"

#Find daily means for h08v04 tiles:

h08v04_infiles <- list.files(path=path, pattern="*.h08v04.005.ClearDay_corrected.img$")

for (i in 1: length(h08v04_infiles)){

  h08v04_infiles[i]<- paste (path,"/",h08v04_infiles[i],sep="")

}

h08v04_infiles

#Creating empty vectors in the form of day_1- day_366

N<- c(1:366)*NA

val<- c(1:length(h08v04_infiles))*NA

for (i in 1:366){

   N[i]<- paste("day_",i,"_h08v04",sep="")

   assign (N[i],val)

}

#Avg. calcs days 1-59:

for (i in 1:length(h08v04_infiles)){

    if(length(grep("\\.1.1.h",h08v04_infiles[i])!=0)){

        day_1_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.1.2.h",h08v04_infiles[i])!=0)){

        day_2_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.3.h",h08v04_infiles[i])!=0)){

        day_3_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.4.h",h08v04_infiles[i])!=0)){

        day_4_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.5.h",h08v04_infiles[i])!=0)){

        day_5_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.6.h",h08v04_infiles[i])!=0)){

        day_6_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.7.h",h08v04_infiles[i])!=0)){

        day_7_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.8.h",h08v04_infiles[i])!=0)){

        day_8_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.9.h",h08v04_infiles[i])!=0)){

        day_9_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.10.h",h08v04_infiles[i])!=0)){

        day_10_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.1.11.h",h08v04_infiles[i])!=0)){

        day_11_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.1.12.h",h08v04_infiles[i])!=0)){

        day_12_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.13.h",h08v04_infiles[i])!=0)){

        day_13_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.14.h",h08v04_infiles[i])!=0)){

        day_14_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.15.h",h08v04_infiles[i])!=0)){

        day_15_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.16.h",h08v04_infiles[i])!=0)){

        day_16_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.17.h",h08v04_infiles[i])!=0)){

        day_17_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.18.h",h08v04_infiles[i])!=0)){

        day_18_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.19.h",h08v04_infiles[i])!=0)){

        day_19_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.20.h",h08v04_infiles[i])!=0)){

        day_20_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.1.21.h",h08v04_infiles[i])!=0)){

        day_21_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.1.22.h",h08v04_infiles[i])!=0)){

        day_22_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.23.h",h08v04_infiles[i])!=0)){

        day_23_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.24.h",h08v04_infiles[i])!=0)){

        day_24_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.25.h",h08v04_infiles[i])!=0)){

        day_25_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.26.h",h08v04_infiles[i])!=0)){

        day_26_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.27.h",h08v04_infiles[i])!=0)){

        day_27_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.28.h",h08v04_infiles[i])!=0)){

        day_28_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.29.h",h08v04_infiles[i])!=0)){

        day_29_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.30.h",h08v04_infiles[i])!=0)){

        day_30_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.1.31.h",h08v04_infiles[i])!=0)){

        day_31_h08v04[i]<- h08v04_infiles[i]

    }  else if(length(grep("\\.2.1.h",h08v04_infiles[i])!=0)){

        day_32_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.2.2.h",h08v04_infiles[i])!=0)){

        day_33_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.3.h",h08v04_infiles[i])!=0)){

        day_34_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.4.h",h08v04_infiles[i])!=0)){

        day_35_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.5.h",h08v04_infiles[i])!=0)){

        day_36_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.6.h",h08v04_infiles[i])!=0)){

        day_37_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.7.h",h08v04_infiles[i])!=0)){

        day_38_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.8.h",h08v04_infiles[i])!=0)){

        day_39_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.9.h",h08v04_infiles[i])!=0)){

        day_40_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.10.h",h08v04_infiles[i])!=0)){

        day_41_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.2.11.h",h08v04_infiles[i])!=0)){

        day_42_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.2.12.h",h08v04_infiles[i])!=0)){

        day_43_h08v04[i]<- h08v04_infiles[i]  

    } else if (length(grep("\\.2.13.h",h08v04_infiles[i])!=0)){

        day_44_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.14.h",h08v04_infiles[i])!=0)){

        day_45_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.15.h",h08v04_infiles[i])!=0)){

        day_46_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.16.h",h08v04_infiles[i])!=0)){

        day_47_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.17.h",h08v04_infiles[i])!=0)){

        day_48_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.18.h",h08v04_infiles[i])!=0)){

        day_49_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.19.h",h08v04_infiles[i])!=0)){

        day_50_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.20.h",h08v04_infiles[i])!=0)){

        day_51_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.2.21.h",h08v04_infiles[i])!=0)){

        day_52_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.2.22.h",h08v04_infiles[i])!=0)){

        day_53_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.23.h",h08v04_infiles[i])!=0)){

        day_54_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.24.h",h08v04_infiles[i])!=0)){

        day_55_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.25.h",h08v04_infiles[i])!=0)){

        day_56_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.26.h",h08v04_infiles[i])!=0)){

        day_57_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.27.h",h08v04_infiles[i])!=0)){

        day_58_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.2.28.h",h08v04_infiles[i])!=0)){

        day_59_h08v04[i]<- h08v04_infiles[i]

    }

}

day_1_h08v04<- day_1_h08v04[!is.na(day_1_h08v04)]

day_2_h08v04<- day_2_h08v04[!is.na(day_2_h08v04)]

day_3_h08v04<- day_3_h08v04[!is.na(day_3_h08v04)]

day_4_h08v04<- day_4_h08v04[!is.na(day_4_h08v04)]

day_5_h08v04<- day_5_h08v04[!is.na(day_5_h08v04)]

day_6_h08v04<- day_6_h08v04[!is.na(day_6_h08v04)]

day_7_h08v04<- day_7_h08v04[!is.na(day_7_h08v04)]

day_8_h08v04<- day_8_h08v04[!is.na(day_8_h08v04)]

day_9_h08v04<- day_9_h08v04[!is.na(day_9_h08v04)]

day_10_h08v04<- day_10_h08v04[!is.na(day_10_h08v04)]

day_11_h08v04<- day_11_h08v04[!is.na(day_11_h08v04)]

day_12_h08v04<- day_12_h08v04[!is.na(day_12_h08v04)]

day_13_h08v04<- day_13_h08v04[!is.na(day_13_h08v04)]

day_14_h08v04<- day_14_h08v04[!is.na(day_14_h08v04)]

day_15_h08v04<- day_15_h08v04[!is.na(day_15_h08v04)]

day_16_h08v04<- day_16_h08v04[!is.na(day_16_h08v04)]

day_17_h08v04<- day_17_h08v04[!is.na(day_17_h08v04)]

day_18_h08v04<- day_18_h08v04[!is.na(day_18_h08v04)]

day_19_h08v04<- day_19_h08v04[!is.na(day_19_h08v04)]

day_20_h08v04<- day_20_h08v04[!is.na(day_20_h08v04)]

day_21_h08v04<- day_21_h08v04[!is.na(day_21_h08v04)]

day_22_h08v04<- day_22_h08v04[!is.na(day_22_h08v04)]

day_23_h08v04<- day_23_h08v04[!is.na(day_23_h08v04)]

day_24_h08v04<- day_24_h08v04[!is.na(day_24_h08v04)]

day_25_h08v04<- day_25_h08v04[!is.na(day_25_h08v04)]

day_26_h08v04<- day_26_h08v04[!is.na(day_26_h08v04)]

day_27_h08v04<- day_27_h08v04[!is.na(day_27_h08v04)]

day_28_h08v04<- day_28_h08v04[!is.na(day_28_h08v04)]

day_29_h08v04<- day_29_h08v04[!is.na(day_29_h08v04)]

day_30_h08v04<- day_30_h08v04[!is.na(day_30_h08v04)]

day_31_h08v04<- day_31_h08v04[!is.na(day_31_h08v04)]

day_32_h08v04<- day_32_h08v04[!is.na(day_32_h08v04)]

day_33_h08v04<- day_33_h08v04[!is.na(day_33_h08v04)]

day_34_h08v04<- day_34_h08v04[!is.na(day_34_h08v04)]

day_35_h08v04<- day_35_h08v04[!is.na(day_35_h08v04)]

day_36_h08v04<- day_36_h08v04[!is.na(day_36_h08v04)]

day_37_h08v04<- day_37_h08v04[!is.na(day_37_h08v04)]

day_38_h08v04<- day_38_h08v04[!is.na(day_38_h08v04)]

day_39_h08v04<- day_39_h08v04[!is.na(day_39_h08v04)]

day_40_h08v04<- day_40_h08v04[!is.na(day_40_h08v04)]

day_41_h08v04<- day_41_h08v04[!is.na(day_41_h08v04)]

day_42_h08v04<- day_42_h08v04[!is.na(day_42_h08v04)]

day_43_h08v04<- day_43_h08v04[!is.na(day_43_h08v04)]

day_44_h08v04<- day_44_h08v04[!is.na(day_44_h08v04)]

day_45_h08v04<- day_45_h08v04[!is.na(day_45_h08v04)]

day_46_h08v04<- day_46_h08v04[!is.na(day_46_h08v04)]

day_47_h08v04<- day_47_h08v04[!is.na(day_47_h08v04)]

day_48_h08v04<- day_48_h08v04[!is.na(day_48_h08v04)]

day_49_h08v04<- day_49_h08v04[!is.na(day_49_h08v04)]

day_50_h08v04<- day_50_h08v04[!is.na(day_50_h08v04)]

day_51_h08v04<- day_51_h08v04[!is.na(day_51_h08v04)]

day_52_h08v04<- day_52_h08v04[!is.na(day_52_h08v04)]

day_53_h08v04<- day_53_h08v04[!is.na(day_53_h08v04)]

day_54_h08v04<- day_54_h08v04[!is.na(day_54_h08v04)]

day_55_h08v04<- day_55_h08v04[!is.na(day_55_h08v04)]

day_56_h08v04<- day_56_h08v04[!is.na(day_56_h08v04)]

day_57_h08v04<- day_57_h08v04[!is.na(day_57_h08v04)]

day_58_h08v04<- day_58_h08v04[!is.na(day_58_h08v04)]

day_59_h08v04<- day_59_h08v04[!is.na(day_59_h08v04)]

day_1_h08v04_stack<- stack(day_1_h08v04)

nlayers(day_1_h08v04_stack) 

day_1_h08v04_mn<- mean(day_1_h08v04_stack, na.rm=TRUE)

day_1_h08v04_mnScaled<- day_1_h08v04_mn*0.0005

Out_day_1<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_1_h08v04_AVG_Scaled.img"

writeRaster (day_1_h08v04_mnScaled, filename=Out_day_1,format="HFA",overwrite=TRUE)

day_2_h08v04_stack<- stack(day_2_h08v04)

nlayers(day_2_h08v04_stack) 

day_2_h08v04_mn<- mean(day_2_h08v04_stack, na.rm=TRUE)

day_2_h08v04_mnScaled<- day_2_h08v04_mn*0.0005

Out_day_2<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_2_h08v04_AVG_Scaled.img"

writeRaster (day_2_h08v04_mnScaled, filename=Out_day_2,format="HFA",overwrite=TRUE)

day_3_h08v04_stack<- stack(day_3_h08v04)

nlayers(day_3_h08v04_stack) 

day_3_h08v04_mn<- mean(day_3_h08v04_stack, na.rm=TRUE)

day_3_h08v04_mnScaled<- day_3_h08v04_mn*0.0005

Out_day_3<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_3_h08v04_AVG_Scaled.img"

writeRaster (day_3_h08v04_mnScaled, filename=Out_day_3,format="HFA",overwrite=TRUE)

day_4_h08v04_stack<- stack(day_4_h08v04)

nlayers(day_4_h08v04_stack) 

day_4_h08v04_mn<- mean(day_4_h08v04_stack, na.rm=TRUE)

day_4_h08v04_mnScaled<- day_4_h08v04_mn*0.0005

Out_day_4<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_4_h08v04_AVG_Scaled.img"

writeRaster (day_4_h08v04_mnScaled, filename=Out_day_4,format="HFA",overwrite=TRUE)

day_5_h08v04_stack<- stack(day_5_h08v04)

nlayers(day_5_h08v04_stack) 

day_5_h08v04_mn<- mean(day_5_h08v04_stack, na.rm=TRUE)

day_5_h08v04_mnScaled<- day_5_h08v04_mn*0.0005

Out_day_5<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_5_h08v04_AVG_Scaled.img"

writeRaster (day_5_h08v04_mnScaled, filename=Out_day_5,format="HFA",overwrite=TRUE)

day_6_h08v04_stack<- stack(day_6_h08v04)

nlayers(day_6_h08v04_stack) 

day_6_h08v04_mn<- mean(day_6_h08v04_stack, na.rm=TRUE)

day_6_h08v04_mnScaled<- day_6_h08v04_mn*0.0005

Out_day_6<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_6_h08v04_AVG_Scaled.img"

writeRaster (day_6_h08v04_mnScaled, filename=Out_day_6,format="HFA",overwrite=TRUE)

day_7_h08v04_stack<- stack(day_7_h08v04)

nlayers(day_7_h08v04_stack) 

day_7_h08v04_mn<- mean(day_7_h08v04_stack, na.rm=TRUE)

day_7_h08v04_mnScaled<- day_7_h08v04_mn*0.0005

Out_day_7<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_7_h08v04_AVG_Scaled.img"

writeRaster (day_7_h08v04_mnScaled, filename=Out_day_7,format="HFA",overwrite=TRUE)

day_8_h08v04_stack<- stack(day_8_h08v04)

nlayers(day_8_h08v04_stack) 

day_8_h08v04_mn<- mean(day_8_h08v04_stack, na.rm=TRUE)

day_8_h08v04_mnScaled<- day_8_h08v04_mn*0.0005

Out_day_8<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_8_h08v04_AVG_Scaled.img"

writeRaster (day_8_h08v04_mnScaled, filename=Out_day_8,format="HFA",overwrite=TRUE)

day_9_h08v04_stack<- stack(day_9_h08v04)

nlayers(day_9_h08v04_stack) 

day_9_h08v04_mn<- mean(day_9_h08v04_stack, na.rm=TRUE)

day_9_h08v04_mnScaled<- day_9_h08v04_mn*0.0005

Out_day_9<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_9_h08v04_AVG_Scaled.img"

writeRaster (day_9_h08v04_mnScaled, filename=Out_day_9,format="HFA",overwrite=TRUE)

day_10_h08v04_stack<- stack(day_10_h08v04)

nlayers(day_10_h08v04_stack) 

day_10_h08v04_mn<- mean(day_10_h08v04_stack, na.rm=TRUE)

day_10_h08v04_mnScaled<- day_10_h08v04_mn*0.0005

Out_day_10<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_10_h08v04_AVG_Scaled.img"

writeRaster (day_10_h08v04_mnScaled, filename=Out_day_10,format="HFA",overwrite=TRUE)

day_11_h08v04_stack<- stack(day_11_h08v04)

nlayers(day_11_h08v04_stack) 

day_11_h08v04_mn<- mean(day_11_h08v04_stack, na.rm=TRUE)

day_11_h08v04_mnScaled<- day_11_h08v04_mn*0.0005

Out_day_11<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_11_h08v04_AVG_Scaled.img"

writeRaster (day_11_h08v04_mnScaled, filename=Out_day_11,format="HFA",overwrite=TRUE)

day_12_h08v04_stack<- stack(day_12_h08v04)

nlayers(day_12_h08v04_stack) 

day_12_h08v04_mn<- mean(day_12_h08v04_stack, na.rm=TRUE)

day_12_h08v04_mnScaled<- day_12_h08v04_mn*0.0005

Out_day_12<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_12_h08v04_AVG_Scaled.img"

writeRaster (day_12_h08v04_mnScaled, filename=Out_day_12,format="HFA",overwrite=TRUE)

day_13_h08v04_stack<- stack(day_13_h08v04)

nlayers(day_13_h08v04_stack) 

day_13_h08v04_mn<- mean(day_13_h08v04_stack, na.rm=TRUE)

day_13_h08v04_mnScaled<- day_13_h08v04_mn*0.0005

Out_day_13<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_13_h08v04_AVG_Scaled.img"

writeRaster (day_13_h08v04_mnScaled, filename=Out_day_13,format="HFA",overwrite=TRUE)

day_14_h08v04_stack<- stack(day_14_h08v04)

nlayers(day_14_h08v04_stack) 

day_14_h08v04_mn<- mean(day_14_h08v04_stack, na.rm=TRUE)

day_14_h08v04_mnScaled<- day_14_h08v04_mn*0.0005

Out_day_14<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_14_h08v04_AVG_Scaled.img"

writeRaster (day_14_h08v04_mnScaled, filename=Out_day_14,format="HFA",overwrite=TRUE)

day_15_h08v04_stack<- stack(day_15_h08v04)

nlayers(day_15_h08v04_stack) 

day_15_h08v04_mn<- mean(day_15_h08v04_stack, na.rm=TRUE)

day_15_h08v04_mnScaled<- day_15_h08v04_mn*0.0005

Out_day_15<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_15_h08v04_AVG_Scaled.img"

writeRaster (day_15_h08v04_mnScaled, filename=Out_day_15,format="HFA",overwrite=TRUE)

day_16_h08v04_stack<- stack(day_16_h08v04)

nlayers(day_16_h08v04_stack) 

day_16_h08v04_mn<- mean(day_16_h08v04_stack, na.rm=TRUE)

day_16_h08v04_mnScaled<- day_16_h08v04_mn*0.0005

Out_day_16<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_16_h08v04_AVG_Scaled.img"

writeRaster (day_16_h08v04_mnScaled, filename=Out_day_16,format="HFA",overwrite=TRUE)

day_17_h08v04_stack<- stack(day_17_h08v04)

nlayers(day_17_h08v04_stack) 

day_17_h08v04_mn<- mean(day_17_h08v04_stack, na.rm=TRUE)

day_17_h08v04_mnScaled<- day_17_h08v04_mn*0.0005

Out_day_17<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_17_h08v04_AVG_Scaled.img"

writeRaster (day_17_h08v04_mnScaled, filename=Out_day_17,format="HFA",overwrite=TRUE)

day_18_h08v04_stack<- stack(day_18_h08v04)

nlayers(day_18_h08v04_stack) 

day_18_h08v04_mn<- mean(day_18_h08v04_stack, na.rm=TRUE)

day_18_h08v04_mnScaled<- day_18_h08v04_mn*0.0005

Out_day_18<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_18_h08v04_AVG_Scaled.img"

writeRaster (day_18_h08v04_mnScaled, filename=Out_day_18,format="HFA",overwrite=TRUE)

day_19_h08v04_stack<- stack(day_19_h08v04)

nlayers(day_19_h08v04_stack) 

day_19_h08v04_mn<- mean(day_19_h08v04_stack, na.rm=TRUE)

day_19_h08v04_mnScaled<- day_19_h08v04_mn*0.0005

Out_day_19<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_19_h08v04_AVG_Scaled.img"

writeRaster (day_19_h08v04_mnScaled, filename=Out_day_19,format="HFA",overwrite=TRUE)

day_20_h08v04_stack<- stack(day_20_h08v04)

nlayers(day_20_h08v04_stack) 

day_20_h08v04_mn<- mean(day_20_h08v04_stack, na.rm=TRUE)

day_20_h08v04_mnScaled<- day_20_h08v04_mn*0.0005

Out_day_20<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_20_h08v04_AVG_Scaled.img"

writeRaster (day_20_h08v04_mnScaled, filename=Out_day_20,format="HFA",overwrite=TRUE)

day_21_h08v04_stack<- stack(day_21_h08v04)

nlayers(day_21_h08v04_stack) 

day_21_h08v04_mn<- mean(day_21_h08v04_stack, na.rm=TRUE)

day_21_h08v04_mnScaled<- day_21_h08v04_mn*0.0005

Out_day_21<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_21_h08v04_AVG_Scaled.img"

writeRaster (day_21_h08v04_mnScaled, filename=Out_day_21,format="HFA",overwrite=TRUE)

day_22_h08v04_stack<- stack(day_22_h08v04)

nlayers(day_22_h08v04_stack) 

day_22_h08v04_mn<- mean(day_22_h08v04_stack, na.rm=TRUE)

day_22_h08v04_mnScaled<- day_22_h08v04_mn*0.0005

Out_day_22<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_22_h08v04_AVG_Scaled.img"

writeRaster (day_22_h08v04_mnScaled, filename=Out_day_22,format="HFA",overwrite=TRUE)

day_23_h08v04_stack<- stack(day_23_h08v04)

nlayers(day_23_h08v04_stack) 

day_23_h08v04_mn<- mean(day_23_h08v04_stack, na.rm=TRUE)

day_23_h08v04_mnScaled<- day_23_h08v04_mn*0.0005

Out_day_23<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_23_h08v04_AVG_Scaled.img"

writeRaster (day_23_h08v04_mnScaled, filename=Out_day_23,format="HFA",overwrite=TRUE)

day_24_h08v04_stack<- stack(day_24_h08v04)

nlayers(day_24_h08v04_stack) 

day_24_h08v04_mn<- mean(day_24_h08v04_stack, na.rm=TRUE)

day_24_h08v04_mnScaled<- day_24_h08v04_mn*0.0005

Out_day_24<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_24_h08v04_AVG_Scaled.img"

writeRaster (day_24_h08v04_mnScaled, filename=Out_day_24,format="HFA",overwrite=TRUE)

day_25_h08v04_stack<- stack(day_25_h08v04)

nlayers(day_25_h08v04_stack) 

day_25_h08v04_mn<- mean(day_25_h08v04_stack, na.rm=TRUE)

day_25_h08v04_mnScaled<- day_25_h08v04_mn*0.0005

Out_day_25<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_25_h08v04_AVG_Scaled.img"

writeRaster (day_25_h08v04_mnScaled, filename=Out_day_25,format="HFA",overwrite=TRUE)

day_26_h08v04_stack<- stack(day_26_h08v04)

nlayers(day_26_h08v04_stack) 

day_26_h08v04_mn<- mean(day_26_h08v04_stack, na.rm=TRUE)

day_26_h08v04_mnScaled<- day_26_h08v04_mn*0.0005

Out_day_26<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_26_h08v04_AVG_Scaled.img"

writeRaster (day_26_h08v04_mnScaled, filename=Out_day_26,format="HFA",overwrite=TRUE)

day_27_h08v04_stack<- stack(day_27_h08v04)

nlayers(day_27_h08v04_stack) 

day_27_h08v04_mn<- mean(day_27_h08v04_stack, na.rm=TRUE)

day_27_h08v04_mnScaled<- day_27_h08v04_mn*0.0005

Out_day_27<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_27_h08v04_AVG_Scaled.img"

writeRaster (day_27_h08v04_mnScaled, filename=Out_day_27,format="HFA",overwrite=TRUE)

day_28_h08v04_stack<- stack(day_28_h08v04)

nlayers(day_28_h08v04_stack) 

day_28_h08v04_mn<- mean(day_28_h08v04_stack, na.rm=TRUE)

day_28_h08v04_mnScaled<- day_28_h08v04_mn*0.0005

Out_day_28<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_28_h08v04_AVG_Scaled.img"

writeRaster (day_28_h08v04_mnScaled, filename=Out_day_28,format="HFA",overwrite=TRUE)

day_29_h08v04_stack<- stack(day_29_h08v04)

nlayers(day_29_h08v04_stack) 

day_29_h08v04_mn<- mean(day_29_h08v04_stack, na.rm=TRUE)

day_29_h08v04_mnScaled<- day_29_h08v04_mn*0.0005

Out_day_29<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_29_h08v04_AVG_Scaled.img"

writeRaster (day_29_h08v04_mnScaled, filename=Out_day_29,format="HFA",overwrite=TRUE)

day_30_h08v04_stack<- stack(day_30_h08v04)

nlayers(day_30_h08v04_stack) 

day_30_h08v04_mn<- mean(day_30_h08v04_stack, na.rm=TRUE)

day_30_h08v04_mnScaled<- day_30_h08v04_mn*0.0005

Out_day_30<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_30_h08v04_AVG_Scaled.img"

writeRaster (day_30_h08v04_mnScaled, filename=Out_day_30,format="HFA",overwrite=TRUE)

day_31_h08v04_stack<- stack(day_31_h08v04)

nlayers(day_31_h08v04_stack) 

day_31_h08v04_mn<- mean(day_31_h08v04_stack, na.rm=TRUE)

day_31_h08v04_mnScaled<- day_31_h08v04_mn*0.0005

Out_day_31<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_31_h08v04_AVG_Scaled.img"

writeRaster (day_31_h08v04_mnScaled, filename=Out_day_31,format="HFA",overwrite=TRUE)

day_32_h08v04_stack<- stack(day_32_h08v04)

nlayers(day_32_h08v04_stack) 

day_32_h08v04_mn<- mean(day_32_h08v04_stack, na.rm=TRUE)

day_32_h08v04_mnScaled<- day_32_h08v04_mn*0.0005

Out_day_32<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_32_h08v04_AVG_Scaled.img"

writeRaster (day_32_h08v04_mnScaled, filename=Out_day_32,format="HFA",overwrite=TRUE)

day_33_h08v04_stack<- stack(day_33_h08v04)

nlayers(day_33_h08v04_stack) 

day_33_h08v04_mn<- mean(day_33_h08v04_stack, na.rm=TRUE)

day_33_h08v04_mnScaled<- day_33_h08v04_mn*0.0005

Out_day_33<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_33_h08v04_AVG_Scaled.img"

writeRaster (day_33_h08v04_mnScaled, filename=Out_day_33,format="HFA",overwrite=TRUE)

day_34_h08v04_stack<- stack(day_34_h08v04)

nlayers(day_34_h08v04_stack) 

day_34_h08v04_mn<- mean(day_34_h08v04_stack, na.rm=TRUE)

day_34_h08v04_mnScaled<- day_34_h08v04_mn*0.0005

Out_day_34<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_34_h08v04_AVG_Scaled.img"

writeRaster (day_34_h08v04_mnScaled, filename=Out_day_34,format="HFA",overwrite=TRUE)

day_35_h08v04_stack<- stack(day_35_h08v04)

nlayers(day_35_h08v04_stack) 

day_35_h08v04_mn<- mean(day_35_h08v04_stack, na.rm=TRUE)

day_35_h08v04_mnScaled<- day_35_h08v04_mn*0.0005

Out_day_35<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_35_h08v04_AVG_Scaled.img"

writeRaster (day_35_h08v04_mnScaled, filename=Out_day_35,format="HFA",overwrite=TRUE)

day_36_h08v04_stack<- stack(day_36_h08v04)

nlayers(day_36_h08v04_stack) 

day_36_h08v04_mn<- mean(day_36_h08v04_stack, na.rm=TRUE)

day_36_h08v04_mnScaled<- day_36_h08v04_mn*0.0005

Out_day_36<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_36_h08v04_AVG_Scaled.img"

writeRaster (day_36_h08v04_mnScaled, filename=Out_day_36,format="HFA",overwrite=TRUE)

day_37_h08v04_stack<- stack(day_37_h08v04)

nlayers(day_37_h08v04_stack) 

day_37_h08v04_mn<- mean(day_37_h08v04_stack, na.rm=TRUE)

day_37_h08v04_mnScaled<- day_37_h08v04_mn*0.0005

Out_day_37<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_37_h08v04_AVG_Scaled.img"

writeRaster (day_37_h08v04_mnScaled, filename=Out_day_37,format="HFA",overwrite=TRUE)

day_38_h08v04_stack<- stack(day_38_h08v04)

nlayers(day_38_h08v04_stack) 

day_38_h08v04_mn<- mean(day_38_h08v04_stack, na.rm=TRUE)

day_38_h08v04_mnScaled<- day_38_h08v04_mn*0.0005

Out_day_38<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_38_h08v04_AVG_Scaled.img"

writeRaster (day_38_h08v04_mnScaled, filename=Out_day_38,format="HFA",overwrite=TRUE)

day_39_h08v04_stack<- stack(day_39_h08v04)

nlayers(day_39_h08v04_stack) 

day_39_h08v04_mn<- mean(day_39_h08v04_stack, na.rm=TRUE)

day_39_h08v04_mnScaled<- day_39_h08v04_mn*0.0005

Out_day_39<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_39_h08v04_AVG_Scaled.img"

writeRaster (day_39_h08v04_mnScaled, filename=Out_day_39,format="HFA",overwrite=TRUE)

day_40_h08v04_stack<- stack(day_40_h08v04)

nlayers(day_40_h08v04_stack) 

day_40_h08v04_mn<- mean(day_40_h08v04_stack, na.rm=TRUE)

day_40_h08v04_mnScaled<- day_40_h08v04_mn*0.0005

Out_day_40<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_40_h08v04_AVG_Scaled.img"

writeRaster (day_40_h08v04_mnScaled, filename=Out_day_40,format="HFA",overwrite=TRUE)

day_41_h08v04_stack<- stack(day_41_h08v04)

nlayers(day_41_h08v04_stack) 

day_41_h08v04_mn<- mean(day_41_h08v04_stack, na.rm=TRUE)

day_41_h08v04_mnScaled<- day_41_h08v04_mn*0.0005

Out_day_41<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_41_h08v04_AVG_Scaled.img"

writeRaster (day_41_h08v04_mnScaled, filename=Out_day_41,format="HFA",overwrite=TRUE)

day_42_h08v04_stack<- stack(day_42_h08v04)

nlayers(day_42_h08v04_stack) 

day_42_h08v04_mn<- mean(day_42_h08v04_stack, na.rm=TRUE)

day_42_h08v04_mnScaled<- day_42_h08v04_mn*0.0005

Out_day_42<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_42_h08v04_AVG_Scaled.img"

writeRaster (day_42_h08v04_mnScaled, filename=Out_day_42,format="HFA",overwrite=TRUE)

day_43_h08v04_stack<- stack(day_43_h08v04)

nlayers(day_43_h08v04_stack) 

day_43_h08v04_mn<- mean(day_43_h08v04_stack, na.rm=TRUE)

day_43_h08v04_mnScaled<- day_43_h08v04_mn*0.0005

Out_day_43<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_43_h08v04_AVG_Scaled.img"

writeRaster (day_43_h08v04_mnScaled, filename=Out_day_43,format="HFA",overwrite=TRUE)

day_44_h08v04_stack<- stack(day_44_h08v04)

nlayers(day_44_h08v04_stack) 

day_44_h08v04_mn<- mean(day_44_h08v04_stack, na.rm=TRUE)

day_44_h08v04_mnScaled<- day_44_h08v04_mn*0.0005

Out_day_44<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_44_h08v04_AVG_Scaled.img"

writeRaster (day_44_h08v04_mnScaled, filename=Out_day_44,format="HFA",overwrite=TRUE)

day_45_h08v04_stack<- stack(day_45_h08v04)

nlayers(day_45_h08v04_stack) 

day_45_h08v04_mn<- mean(day_45_h08v04_stack, na.rm=TRUE)

day_45_h08v04_mnScaled<- day_45_h08v04_mn*0.0005

Out_day_45<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_45_h08v04_AVG_Scaled.img"

writeRaster (day_45_h08v04_mnScaled, filename=Out_day_45,format="HFA",overwrite=TRUE)

day_46_h08v04_stack<- stack(day_46_h08v04)

nlayers(day_46_h08v04_stack) 

day_46_h08v04_mn<- mean(day_46_h08v04_stack, na.rm=TRUE)

day_46_h08v04_mnScaled<- day_46_h08v04_mn*0.0005

Out_day_46<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_46_h08v04_AVG_Scaled.img"

writeRaster (day_46_h08v04_mnScaled, filename=Out_day_46,format="HFA",overwrite=TRUE)

day_47_h08v04_stack<- stack(day_47_h08v04)

nlayers(day_47_h08v04_stack) 

day_47_h08v04_mn<- mean(day_47_h08v04_stack, na.rm=TRUE)

day_47_h08v04_mnScaled<- day_47_h08v04_mn*0.0005

Out_day_47<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_47_h08v04_AVG_Scaled.img"

writeRaster (day_47_h08v04_mnScaled, filename=Out_day_47,format="HFA",overwrite=TRUE)

day_48_h08v04_stack<- stack(day_48_h08v04)

nlayers(day_48_h08v04_stack) 

day_48_h08v04_mn<- mean(day_48_h08v04_stack, na.rm=TRUE)

day_48_h08v04_mnScaled<- day_48_h08v04_mn*0.0005

Out_day_48<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_48_h08v04_AVG_Scaled.img"

writeRaster (day_48_h08v04_mnScaled, filename=Out_day_48,format="HFA",overwrite=TRUE)

day_49_h08v04_stack<- stack(day_49_h08v04)

nlayers(day_49_h08v04_stack) 

day_49_h08v04_mn<- mean(day_49_h08v04_stack, na.rm=TRUE)

day_49_h08v04_mnScaled<- day_49_h08v04_mn*0.0005

Out_day_49<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_49_h08v04_AVG_Scaled.img"

writeRaster (day_49_h08v04_mnScaled, filename=Out_day_49,format="HFA",overwrite=TRUE)

day_50_h08v04_stack<- stack(day_50_h08v04)

nlayers(day_50_h08v04_stack) 

day_50_h08v04_mn<- mean(day_50_h08v04_stack, na.rm=TRUE)

day_50_h08v04_mnScaled<- day_50_h08v04_mn*0.0005

Out_day_50<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_50_h08v04_AVG_Scaled.img"

writeRaster (day_50_h08v04_mnScaled, filename=Out_day_50,format="HFA",overwrite=TRUE)

day_51_h08v04_stack<- stack(day_51_h08v04)

nlayers(day_51_h08v04_stack) 

day_51_h08v04_mn<- mean(day_51_h08v04_stack, na.rm=TRUE)

day_51_h08v04_mnScaled<- day_51_h08v04_mn*0.0005

Out_day_51<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_51_h08v04_AVG_Scaled.img"

writeRaster (day_51_h08v04_mnScaled, filename=Out_day_51,format="HFA",overwrite=TRUE)

day_52_h08v04_stack<- stack(day_52_h08v04)

nlayers(day_52_h08v04_stack) 

day_52_h08v04_mn<- mean(day_52_h08v04_stack, na.rm=TRUE)

day_52_h08v04_mnScaled<- day_52_h08v04_mn*0.0005

Out_day_52<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_52_h08v04_AVG_Scaled.img"

writeRaster (day_52_h08v04_mnScaled, filename=Out_day_52,format="HFA",overwrite=TRUE)

day_53_h08v04_stack<- stack(day_53_h08v04)

nlayers(day_53_h08v04_stack) 

day_53_h08v04_mn<- mean(day_53_h08v04_stack, na.rm=TRUE)

day_53_h08v04_mnScaled<- day_53_h08v04_mn*0.0005

Out_day_53<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_53_h08v04_AVG_Scaled.img"

writeRaster (day_53_h08v04_mnScaled, filename=Out_day_53,format="HFA",overwrite=TRUE)

day_54_h08v04_stack<- stack(day_54_h08v04)

nlayers(day_54_h08v04_stack) 

day_54_h08v04_mn<- mean(day_54_h08v04_stack, na.rm=TRUE)

day_54_h08v04_mnScaled<- day_54_h08v04_mn*0.0005

Out_day_54<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_54_h08v04_AVG_Scaled.img"

writeRaster (day_54_h08v04_mnScaled, filename=Out_day_54,format="HFA",overwrite=TRUE)

day_55_h08v04_stack<- stack(day_55_h08v04)

nlayers(day_55_h08v04_stack) 

day_55_h08v04_mn<- mean(day_55_h08v04_stack, na.rm=TRUE)

day_55_h08v04_mnScaled<- day_55_h08v04_mn*0.0005

Out_day_55<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_55_h08v04_AVG_Scaled.img"

writeRaster (day_55_h08v04_mnScaled, filename=Out_day_55,format="HFA",overwrite=TRUE)

day_56_h08v04_stack<- stack(day_56_h08v04)

nlayers(day_56_h08v04_stack) 

day_56_h08v04_mn<- mean(day_56_h08v04_stack, na.rm=TRUE)

day_56_h08v04_mnScaled<- day_56_h08v04_mn*0.0005

Out_day_56<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_56_h08v04_AVG_Scaled.img"

writeRaster (day_56_h08v04_mnScaled, filename=Out_day_56,format="HFA",overwrite=TRUE)

day_57_h08v04_stack<- stack(day_57_h08v04)

nlayers(day_57_h08v04_stack) 

day_57_h08v04_mn<- mean(day_57_h08v04_stack, na.rm=TRUE)

day_57_h08v04_mnScaled<- day_57_h08v04_mn*0.0005

Out_day_57<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_57_h08v04_AVG_Scaled.img"

writeRaster (day_57_h08v04_mnScaled, filename=Out_day_57,format="HFA",overwrite=TRUE)

day_58_h08v04_stack<- stack(day_58_h08v04)

nlayers(day_58_h08v04_stack) 

day_58_h08v04_mn<- mean(day_58_h08v04_stack, na.rm=TRUE)

day_58_h08v04_mnScaled<- day_58_h08v04_mn*0.0005

Out_day_58<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_58_h08v04_AVG_Scaled.img"

writeRaster (day_58_h08v04_mnScaled, filename=Out_day_58,format="HFA",overwrite=TRUE)

day_59_h08v04_stack<- stack(day_59_h08v04)

nlayers(day_59_h08v04_stack) 

day_59_h08v04_mn<- mean(day_59_h08v04_stack, na.rm=TRUE)

day_59_h08v04_mnScaled<- day_59_h08v04_mn*0.0005

Out_day_59<- "/data/project/organisms/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day_59_h08v04_AVG_Scaled.img"

writeRaster (day_59_h08v04_mnScaled, filename=Out_day_59,format="HFA",overwrite=TRUE)

# Days 60-365 or 366-----------------------------------------------------------------------------

for (i in 1:length(h08v04_infiles)){

  if (length(grep("\\.2004\\.",h08v04_infiles[i])!=0)|| length(grep("\\.2008\\.",h08v04_infiles[i])!=0)){

    if(length(grep("\\.2.29.h",h08v04_infiles[i])!=0)){

        day_60_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.3.1.h",h08v04_infiles[i])!=0)){

        day_61_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.3.2.h",h08v04_infiles[i])!=0)){

        day_62_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.3.h",h08v04_infiles[i])!=0)){

        day_63_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.4.h",h08v04_infiles[i])!=0)){

        day_64_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.5.h",h08v04_infiles[i])!=0)){

        day_65_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.6.h",h08v04_infiles[i])!=0)){

        day_66_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.7.h",h08v04_infiles[i])!=0)){

        day_67_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.8.h",h08v04_infiles[i])!=0)){

        day_68_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.9.h",h08v04_infiles[i])!=0)){

        day_69_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.10.h",h08v04_infiles[i])!=0)){

        day_70_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.3.11.h",h08v04_infiles[i])!=0)){

        day_71_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.3.12.h",h08v04_infiles[i])!=0)){

        day_72_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.13.h",h08v04_infiles[i])!=0)){

        day_73_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.14.h",h08v04_infiles[i])!=0)){

        day_74_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.15.h",h08v04_infiles[i])!=0)){

        day_75_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.16.h",h08v04_infiles[i])!=0)){

        day_76_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.17.h",h08v04_infiles[i])!=0)){

        day_77_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.18.h",h08v04_infiles[i])!=0)){

        day_78_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.19.h",h08v04_infiles[i])!=0)){

        day_79_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.20.h",h08v04_infiles[i])!=0)){

        day_80_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.3.21.h",h08v04_infiles[i])!=0)){

        day_81_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.3.22.h",h08v04_infiles[i])!=0)){

        day_82_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.23.h",h08v04_infiles[i])!=0)){

        day_83_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.24.h",h08v04_infiles[i])!=0)){

        day_84_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.25.h",h08v04_infiles[i])!=0)){

        day_85_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.26.h",h08v04_infiles[i])!=0)){

        day_86_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.27.h",h08v04_infiles[i])!=0)){

        day_87_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.28.h",h08v04_infiles[i])!=0)){

        day_88_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.29.h",h08v04_infiles[i])!=0)){

        day_89_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.30.h",h08v04_infiles[i])!=0)){

        day_90_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.3.31.h",h08v04_infiles[i])!=0)){

        day_91_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.4.1.h",h08v04_infiles[i])!=0)){

        day_92_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.4.2.h",h08v04_infiles[i])!=0)){

        day_93_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.3.h",h08v04_infiles[i])!=0)){

        day_94_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.4.h",h08v04_infiles[i])!=0)){

        day_95_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.5.h",h08v04_infiles[i])!=0)){

        day_96_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.6.h",h08v04_infiles[i])!=0)){

        day_97_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.7.h",h08v04_infiles[i])!=0)){

        day_98_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.8.h",h08v04_infiles[i])!=0)){

        day_99_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.9.h",h08v04_infiles[i])!=0)){

        day_100_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.10.h",h08v04_infiles[i])!=0)){

        day_101_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.4.11.h",h08v04_infiles[i])!=0)){

        day_102_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.4.12.h",h08v04_infiles[i])!=0)){

        day_103_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.13.h",h08v04_infiles[i])!=0)){

        day_104_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.14.h",h08v04_infiles[i])!=0)){

        day_105_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.15.h",h08v04_infiles[i])!=0)){

        day_106_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.16.h",h08v04_infiles[i])!=0)){

        day_107_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.17.h",h08v04_infiles[i])!=0)){

        day_108_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.18.h",h08v04_infiles[i])!=0)){

        day_109_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.19.h",h08v04_infiles[i])!=0)){

        day_110_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.20.h",h08v04_infiles[i])!=0)){

        day_111_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.4.21.h",h08v04_infiles[i])!=0)){

        day_112_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.4.22.h",h08v04_infiles[i])!=0)){

        day_113_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.23.h",h08v04_infiles[i])!=0)){

        day_114_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.24.h",h08v04_infiles[i])!=0)){

        day_115_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.25.h",h08v04_infiles[i])!=0)){

        day_116_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.26.h",h08v04_infiles[i])!=0)){

        day_117_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.27.h",h08v04_infiles[i])!=0)){

        day_118_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.28.h",h08v04_infiles[i])!=0)){

        day_119_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.29.h",h08v04_infiles[i])!=0)){

        day_120_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.4.30.h",h08v04_infiles[i])!=0)){

        day_121_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.5.1.h",h08v04_infiles[i])!=0)){

        day_122_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.5.2.h",h08v04_infiles[i])!=0)){

        day_123_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.3.h",h08v04_infiles[i])!=0)){

        day_124_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.4.h",h08v04_infiles[i])!=0)){

        day_125_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.5.h",h08v04_infiles[i])!=0)){

        day_126_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.6.h",h08v04_infiles[i])!=0)){

        day_127_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.7.h",h08v04_infiles[i])!=0)){

        day_128_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.8.h",h08v04_infiles[i])!=0)){

        day_129_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.9.h",h08v04_infiles[i])!=0)){

        day_130_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.10.h",h08v04_infiles[i])!=0)){

        day_131_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.5.11.h",h08v04_infiles[i])!=0)){

        day_132_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.5.12.h",h08v04_infiles[i])!=0)){

        day_133_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.13.h",h08v04_infiles[i])!=0)){

        day_134_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.14.h",h08v04_infiles[i])!=0)){

        day_135_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.15.h",h08v04_infiles[i])!=0)){

        day_136_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.16.h",h08v04_infiles[i])!=0)){

        day_137_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.17.h",h08v04_infiles[i])!=0)){

        day_138_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.18.h",h08v04_infiles[i])!=0)){

        day_139_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.19.h",h08v04_infiles[i])!=0)){

        day_140_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.20.h",h08v04_infiles[i])!=0)){

        day_141_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.5.21.h",h08v04_infiles[i])!=0)){

        day_142_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.5.22.h",h08v04_infiles[i])!=0)){

        day_143_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.23.h",h08v04_infiles[i])!=0)){

        day_144_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.24.h",h08v04_infiles[i])!=0)){

        day_145_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.25.h",h08v04_infiles[i])!=0)){

        day_146_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.26.h",h08v04_infiles[i])!=0)){

        day_147_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.27.h",h08v04_infiles[i])!=0)){

        day_148_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.28.h",h08v04_infiles[i])!=0)){

        day_149_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.29.h",h08v04_infiles[i])!=0)){

        day_150_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.30.h",h08v04_infiles[i])!=0)){

        day_151_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.5.31.h",h08v04_infiles[i])!=0)){

        day_152_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.6.1.h",h08v04_infiles[i])!=0)){

        day_153_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.6.2.h",h08v04_infiles[i])!=0)){

        day_154_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.3.h",h08v04_infiles[i])!=0)){

        day_155_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.4.h",h08v04_infiles[i])!=0)){

        day_156_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.5.h",h08v04_infiles[i])!=0)){

        day_157_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.6.h",h08v04_infiles[i])!=0)){

        day_158_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.7.h",h08v04_infiles[i])!=0)){

        day_159_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.8.h",h08v04_infiles[i])!=0)){

        day_160_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.9.h",h08v04_infiles[i])!=0)){

        day_161_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.10.h",h08v04_infiles[i])!=0)){

        day_162_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.6.11.h",h08v04_infiles[i])!=0)){

        day_163_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.6.12.h",h08v04_infiles[i])!=0)){

        day_164_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.13.h",h08v04_infiles[i])!=0)){

        day_165_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.14.h",h08v04_infiles[i])!=0)){

        day_166_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.15.h",h08v04_infiles[i])!=0)){

        day_167_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.16.h",h08v04_infiles[i])!=0)){

        day_168_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.17.h",h08v04_infiles[i])!=0)){

        day_169_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.18.h",h08v04_infiles[i])!=0)){

        day_170_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.19.h",h08v04_infiles[i])!=0)){

        day_171_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.20.h",h08v04_infiles[i])!=0)){

        day_172_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.6.21.h",h08v04_infiles[i])!=0)){

        day_173_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.6.22.h",h08v04_infiles[i])!=0)){

        day_174_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.23.h",h08v04_infiles[i])!=0)){

        day_175_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.24.h",h08v04_infiles[i])!=0)){

        day_176_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.25.h",h08v04_infiles[i])!=0)){

        day_177_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.26.h",h08v04_infiles[i])!=0)){

        day_178_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.27.h",h08v04_infiles[i])!=0)){

        day_179_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.28.h",h08v04_infiles[i])!=0)){

        day_180_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.29.h",h08v04_infiles[i])!=0)){

        day_181_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.6.30.h",h08v04_infiles[i])!=0)){

        day_182_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.7.1.h",h08v04_infiles[i])!=0)){

        day_183_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.7.2.h",h08v04_infiles[i])!=0)){

        day_184_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.3.h",h08v04_infiles[i])!=0)){

        day_185_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.4.h",h08v04_infiles[i])!=0)){

        day_186_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.5.h",h08v04_infiles[i])!=0)){

        day_187_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.6.h",h08v04_infiles[i])!=0)){

        day_188_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.7.h",h08v04_infiles[i])!=0)){

        day_189_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.8.h",h08v04_infiles[i])!=0)){

        day_190_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.9.h",h08v04_infiles[i])!=0)){

        day_191_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.10.h",h08v04_infiles[i])!=0)){

        day_192_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.7.11.h",h08v04_infiles[i])!=0)){

        day_193_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.7.12.h",h08v04_infiles[i])!=0)){

        day_194_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.13.h",h08v04_infiles[i])!=0)){

        day_195_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.14.h",h08v04_infiles[i])!=0)){

        day_196_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.15.h",h08v04_infiles[i])!=0)){

        day_197_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.16.h",h08v04_infiles[i])!=0)){

        day_198_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.17.h",h08v04_infiles[i])!=0)){

        day_199_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.18.h",h08v04_infiles[i])!=0)){

        day_200_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.19.h",h08v04_infiles[i])!=0)){

        day_201_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.20.h",h08v04_infiles[i])!=0)){

        day_202_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.7.21.h",h08v04_infiles[i])!=0)){

        day_203_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.7.22.h",h08v04_infiles[i])!=0)){

        day_204_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.23.h",h08v04_infiles[i])!=0)){

        day_205_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.24.h",h08v04_infiles[i])!=0)){

        day_206_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.25.h",h08v04_infiles[i])!=0)){

        day_207_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.26.h",h08v04_infiles[i])!=0)){

        day_208_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.27.h",h08v04_infiles[i])!=0)){

        day_209_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.28.h",h08v04_infiles[i])!=0)){

        day_210_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.29.h",h08v04_infiles[i])!=0)){

        day_211_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.30.h",h08v04_infiles[i])!=0)){

        day_212_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.7.31.h",h08v04_infiles[i])!=0)){

        day_213_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.8.1.h",h08v04_infiles[i])!=0)){

        day_214_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.8.2.h",h08v04_infiles[i])!=0)){

        day_215_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.3.h",h08v04_infiles[i])!=0)){

        day_216_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.4.h",h08v04_infiles[i])!=0)){

        day_217_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.5.h",h08v04_infiles[i])!=0)){

        day_218_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.6.h",h08v04_infiles[i])!=0)){

        day_219_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.7.h",h08v04_infiles[i])!=0)){

        day_220_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.8.h",h08v04_infiles[i])!=0)){

        day_221_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.9.h",h08v04_infiles[i])!=0)){

        day_222_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.10.h",h08v04_infiles[i])!=0)){

        day_223_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.8.11.h",h08v04_infiles[i])!=0)){

        day_224_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.8.12.h",h08v04_infiles[i])!=0)){

        day_225_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.13.h",h08v04_infiles[i])!=0)){

        day_226_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.14.h",h08v04_infiles[i])!=0)){

        day_227_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.15.h",h08v04_infiles[i])!=0)){

        day_228_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.16.h",h08v04_infiles[i])!=0)){

        day_229_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.17.h",h08v04_infiles[i])!=0)){

        day_230_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.18.h",h08v04_infiles[i])!=0)){

        day_231_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.19.h",h08v04_infiles[i])!=0)){

        day_232_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.20.h",h08v04_infiles[i])!=0)){

        day_233_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.8.21.h",h08v04_infiles[i])!=0)){

        day_234_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.8.22.h",h08v04_infiles[i])!=0)){

        day_235_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.23.h",h08v04_infiles[i])!=0)){

        day_236_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.24.h",h08v04_infiles[i])!=0)){

        day_237_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.25.h",h08v04_infiles[i])!=0)){

        day_238_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.26.h",h08v04_infiles[i])!=0)){

        day_239_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.27.h",h08v04_infiles[i])!=0)){

        day_240_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.28.h",h08v04_infiles[i])!=0)){

        day_241_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.29.h",h08v04_infiles[i])!=0)){

        day_242_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.30.h",h08v04_infiles[i])!=0)){

        day_243_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.8.31.h",h08v04_infiles[i])!=0)){

        day_244_h08v04[i]<- h08v04_infiles[i]

    }else if(length(grep("\\.9.1.h",h08v04_infiles[i])!=0)){

        day_245_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.9.2.h",h08v04_infiles[i])!=0)){

        day_246_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.3.h",h08v04_infiles[i])!=0)){

        day_247_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.4.h",h08v04_infiles[i])!=0)){

        day_248_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.5.h",h08v04_infiles[i])!=0)){

        day_249_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.6.h",h08v04_infiles[i])!=0)){

        day_250_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.7.h",h08v04_infiles[i])!=0)){

        day_251_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.8.h",h08v04_infiles[i])!=0)){

        day_252_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.9.h",h08v04_infiles[i])!=0)){

        day_253_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.10.h",h08v04_infiles[i])!=0)){

        day_254_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.9.11.h",h08v04_infiles[i])!=0)){

        day_255_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.9.12.h",h08v04_infiles[i])!=0)){

        day_256_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.13.h",h08v04_infiles[i])!=0)){

        day_257_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.14.h",h08v04_infiles[i])!=0)){

        day_258_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.15.h",h08v04_infiles[i])!=0)){

        day_259_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.16.h",h08v04_infiles[i])!=0)){

        day_260_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.17.h",h08v04_infiles[i])!=0)){

        day_261_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.18.h",h08v04_infiles[i])!=0)){

        day_262_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.19.h",h08v04_infiles[i])!=0)){

        day_263_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.20.h",h08v04_infiles[i])!=0)){

        day_264_h08v04[i]<- h08v04_infiles[i]

    } else if(length(grep("\\.9.21.h",h08v04_infiles[i])!=0)){

        day_265_h08v04[i]<- h08v04_infiles[i]         

    } else if (length(grep("\\.9.22.h",h08v04_infiles[i])!=0)){

        day_266_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.23.h",h08v04_infiles[i])!=0)){

        day_267_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.24.h",h08v04_infiles[i])!=0)){

        day_268_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.25.h",h08v04_infiles[i])!=0)){

        day_269_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.26.h",h08v04_infiles[i])!=0)){

        day_270_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.27.h",h08v04_infiles[i])!=0)){

        day_271_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.28.h",h08v04_infiles[i])!=0)){

        day_272_h08v04[i]<- h08v04_infiles[i]

    } else if (length(grep("\\.9.29.h",h08v04_infiles[i])!=0)){

        day_273_h08v04[i]<- h08v04_infiles[i]