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> # R file to be executed by run runEddyProc.sh or reddy_runLocal.sh
> 
> # stop("under construction, come back on 27th of June")
> # setwd("m:/services/REddyProcWeb/work/001")
> 
> dumpfileBasename <- "RBatch_dump"
> options(error=quote({dump.frames(dumpfileBasename,TRUE); stop(paste("dump in ",dumpfileBasename))}))
> options(warn=1)		# print all warnings (instead of a summary at the end)
> 
> .libPaths( c("../../Library", .libPaths()) )	# add REddyProc/Library as first library path, see readme in Library folder
> library(REddyProc)
Warning: replacing previous import by ‘tibble::as_tibble’ when loading ‘REddyProc’
Warning: replacing previous import by ‘tibble::tibble’ when loading ‘REddyProc’
> 
> cat('Using REddyProc version ', paste(unlist(packageVersion("REddyProc")),collapse="."),"\n")
Using REddyProc version  1.1 
> Sys.time()
[1] "2018-01-27 20:01:09 CET"
> 
> source("../../R/readConfig.R")
> configurationFileName="post.dcf"
> eddyProcConfiguration <- compileAndValidateEddyProcConfiguration(configurationFileName)
Entries supplied by the web form:
                 SiteID             ustarFilter       ustarFilterMethod 
              "Mendota"                    "NO"                   "RTw" 
   ustarFilterSeasoning  ustarFilterUncertainty            isGapfilling 
           "Continuous"                   "YES"                   "YES" 
     temperatureVarName                   email          fileIdentifier 
                 "Tair" "golub.gosia@gmail.com"             "906921885" 
   REddyProcWebRevision 
                   "71" 
> sourceFunctions(eddyProcConfiguration)
> 
> time <- system.time(
+ 		retval <- processEddyData(eddyProcConfiguration=eddyProcConfiguration) 	# call as function for easier debugging with dump
+ )		
Loaded file input.txt with the following variables (units):
 *** Year(-) DoY(-) Hour(-) NEE(-) CH4_MDS(-) H(-) LE(-) Tair(-) Ustar_MDS(-) Tau_MDS(-) ws_MDS(-) rH(-) Press_MDS(-) PAR_MDS(-) Rg(-) Rnet_MDS(-) Precip_MDS(-) TW_0_MDS(-) CO2c_MDS(-) TW1_MDS(-) CO20_MDS(-)
Number of '-9999' convertered to NA: 166313
'data.frame':	17520 obs. of  21 variables:
 $ Year      : atomic  2014 2014 2014 2014 2014 2014 2014 2014 2014 2014 ...
  ..- attr(*, "varnames")= chr "Year"
  ..- attr(*, "units")= chr "-"
 $ DoY       : atomic  1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, "varnames")= chr "DoY"
  ..- attr(*, "units")= chr "-"
 $ Hour      : atomic  0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 ...
  ..- attr(*, "varnames")= chr "Hour"
  ..- attr(*, "units")= chr "-"
 $ NEE       : atomic  0.8 0.7 -3 2.2 -3.3 0.9 1.2 0.7 -0.1 -4.7 ...
  ..- attr(*, "varnames")= chr "NEE"
  ..- attr(*, "units")= chr "-"
 $ CH4_MDS   : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "CH4_MDS"
  ..- attr(*, "units")= chr "-"
 $ H         : atomic  19.4 20.9 50.7 19.3 46.5 23.1 21.5 30.5 24.3 24.6 ...
  ..- attr(*, "varnames")= chr "H"
  ..- attr(*, "units")= chr "-"
 $ LE        : atomic  15.1 11.9 13.2 13.7 11.3 13.5 11.3 12.3 12.7 1.3 ...
  ..- attr(*, "varnames")= chr "LE"
  ..- attr(*, "units")= chr "-"
 $ Tair      : atomic  -16 -16.5 -16.9 -17.2 -17.2 -17.3 -17.4 -17.5 -17.6 -17.6 ...
  ..- attr(*, "varnames")= chr "Tair"
  ..- attr(*, "units")= chr "-"
 $ Ustar_MDS : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "Ustar_MDS"
  ..- attr(*, "units")= chr "-"
 $ Tau_MDS   : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "Tau_MDS"
  ..- attr(*, "units")= chr "-"
 $ ws_MDS    : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "ws_MDS"
  ..- attr(*, "units")= chr "-"
 $ rH        : atomic  60.8 58.8 58.4 57.1 56.5 55.6 56.5 56.3 56.6 56.8 ...
  ..- attr(*, "varnames")= chr "rH"
  ..- attr(*, "units")= chr "-"
 $ Press_MDS : atomic  98.6 98.6 98.5 98.5 98.6 ...
  ..- attr(*, "varnames")= chr "Press_MDS"
  ..- attr(*, "units")= chr "-"
 $ PAR_MDS   : atomic  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "varnames")= chr "PAR_MDS"
  ..- attr(*, "units")= chr "-"
 $ Rg        : atomic  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "varnames")= chr "Rg"
  ..- attr(*, "units")= chr "-"
 $ Rnet_MDS  : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "Rnet_MDS"
  ..- attr(*, "units")= chr "-"
 $ Precip_MDS: atomic  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "varnames")= chr "Precip_MDS"
  ..- attr(*, "units")= chr "-"
 $ TW_0_MDS  : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "TW_0_MDS"
  ..- attr(*, "units")= chr "-"
 $ CO2c_MDS  : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "CO2c_MDS"
  ..- attr(*, "units")= chr "-"
 $ TW1_MDS   : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "TW1_MDS"
  ..- attr(*, "units")= chr "-"
 $ CO20_MDS  : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "CO20_MDS"
  ..- attr(*, "units")= chr "-"
Warning in validateInputData(inputData) :
  Columns CH4_MDS,Rnet_MDS,CO20_MDS have no data. They are not included in processing.
[1] "Calculating VPD from rH and Tair."
Converted time format 'YDH' to POSIX with column name 'DateTime'.
Data variables picked for gap filling (dataVariablesToFill):  NEE,LE,H,Rg,VPD,rH,Tair,Ustar_MDS,Tau_MDS,ws_MDS,Press_MDS,PAR_MDS,Precip_MDS,TW_0_MDS,CO2c_MDS,TW1_MDS 
No additional columns picked to keep in processing
New sEddyProc class for site 'Mendota'
[1] "------------- Gapfilling ---------------"
Initialized variable 'NEE' with 11709 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................13393
Look up table with window size of 14 days with Rg VPD Tair
.........................................946
Look up table with window size of 7 days with Rg
...............................2190
Mean diurnal course with window size of 0 days: .
.........237
Mean diurnal course with window size of 1 days: .
.......82
Mean diurnal course with window size of 2 days: .
......22
Look up table with window size of 21 days with Rg VPD Tair
......246
Look up table with window size of 28 days with Rg VPD Tair
....157
Look up table with window size of 35 days with Rg VPD Tair
..48
Look up table with window size of 42 days with Rg VPD Tair
.50
Look up table with window size of 49 days with Rg VPD Tair
.51
Look up table with window size of 56 days with Rg VPD Tair
0
Look up table with window size of 63 days with Rg VPD Tair
0
Look up table with window size of 70 days with Rg VPD Tair
0
Look up table with window size of 14 days with Rg
54
Look up table with window size of 21 days with Rg
18
Look up table with window size of 28 days with Rg
1
Look up table with window size of 35 days with Rg
0
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
11
Mean diurnal course with window size of 14 days: .
11
Mean diurnal course with window size of 21 days: .
3
Finished gap filling of 'NEE' in 15 seconds. Artificial gaps filled: 17520, real gaps filled: 11709, unfilled (long) gaps: 0.
Initialized variable 'LE' with 11642 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'LE' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................13451
Look up table with window size of 14 days with Rg VPD Tair
........................................878
Look up table with window size of 7 days with Rg
...............................2129
Mean diurnal course with window size of 0 days: .
..........233
Mean diurnal course with window size of 1 days: .
........83
Mean diurnal course with window size of 2 days: .
.......26
Look up table with window size of 21 days with Rg VPD Tair
.......258
Look up table with window size of 28 days with Rg VPD Tair
....204
Look up table with window size of 35 days with Rg VPD Tair
..60
Look up table with window size of 42 days with Rg VPD Tair
.48
Look up table with window size of 49 days with Rg VPD Tair
.48
Look up table with window size of 56 days with Rg VPD Tair
.0
Look up table with window size of 63 days with Rg VPD Tair
.0
Look up table with window size of 70 days with Rg VPD Tair
.0
Look up table with window size of 14 days with Rg
.47
Look up table with window size of 21 days with Rg
30
Look up table with window size of 28 days with Rg
1
Look up table with window size of 35 days with Rg
0
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
10
Mean diurnal course with window size of 14 days: .
11
Mean diurnal course with window size of 21 days: .
3
Finished gap filling of 'LE' in 15 seconds. Artificial gaps filled: 17520, real gaps filled: 11642, unfilled (long) gaps: 0.
Initialized variable 'H' with 11461 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'H' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................13532
Look up table with window size of 14 days with Rg VPD Tair
.......................................835
Look up table with window size of 7 days with Rg
...............................2153
Mean diurnal course with window size of 0 days: .
..........226
Mean diurnal course with window size of 1 days: .
.......96
Mean diurnal course with window size of 2 days: .
......20
Look up table with window size of 21 days with Rg VPD Tair
......251
Look up table with window size of 28 days with Rg VPD Tair
....160
Look up table with window size of 35 days with Rg VPD Tair
..49
Look up table with window size of 42 days with Rg VPD Tair
.48
Look up table with window size of 49 days with Rg VPD Tair
.48
Look up table with window size of 56 days with Rg VPD Tair
.0
Look up table with window size of 63 days with Rg VPD Tair
.0
Look up table with window size of 70 days with Rg VPD Tair
.0
Look up table with window size of 14 days with Rg
.56
Look up table with window size of 21 days with Rg
21
Look up table with window size of 28 days with Rg
1
Look up table with window size of 35 days with Rg
0
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
10
Mean diurnal course with window size of 14 days: .
11
Mean diurnal course with window size of 21 days: .
3
Finished gap filling of 'H' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 11461, unfilled (long) gaps: 0.
Initialized variable 'Rg' with 366 real gaps for gap filling.
Restriced MDS algorithm for gap filling of 'Rg' with no meteo conditions and hence only MDC.
Mean diurnal course with window size of 0 days: .
...267
Mean diurnal course with window size of 1 days: .
99
Finished gap filling of 'Rg' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 366, unfilled (long) gaps: 0.
Initialized variable 'VPD' with 1484 real gaps for gap filling.
Limited MDS algorithm for gap filling of 'VPD' with LUT(Rg only) and MDC.
Look up table with window size of 7 days with Rg
..............1459
Mean diurnal course with window size of 0 days: .
9
Mean diurnal course with window size of 1 days: .
16
Finished gap filling of 'VPD' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 1484, unfilled (long) gaps: 0.
Initialized variable 'rH' with 608 real gaps for gap filling.
Full MDS algorithm for gap filling of 'rH' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
......0
Look up table with window size of 14 days with Rg VPD Tair
......0
Look up table with window size of 7 days with Rg
......589
Mean diurnal course with window size of 0 days: .
8
Mean diurnal course with window size of 1 days: .
11
Finished gap filling of 'rH' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 608, unfilled (long) gaps: 0.
Initialized variable 'Tair' with 896 real gaps for gap filling.
Limited MDS algorithm for gap filling of 'Tair' with LUT(Rg only) and MDC.
Look up table with window size of 7 days with Rg
........890
Mean diurnal course with window size of 0 days: .
1
Mean diurnal course with window size of 1 days: .
5
Finished gap filling of 'Tair' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 896, unfilled (long) gaps: 0.
Initialized variable 'Ustar_MDS' with 13892 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'Ustar_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................11762
Look up table with window size of 14 days with Rg VPD Tair
.........................................................1364
Look up table with window size of 7 days with Rg
...........................................2284
Mean diurnal course with window size of 0 days: .
.....................198
Mean diurnal course with window size of 1 days: .
...................100
Mean diurnal course with window size of 2 days: .
..................21
Look up table with window size of 21 days with Rg VPD Tair
.................373
Look up table with window size of 28 days with Rg VPD Tair
..............355
Look up table with window size of 35 days with Rg VPD Tair
..........292
Look up table with window size of 42 days with Rg VPD Tair
.......248
Look up table with window size of 49 days with Rg VPD Tair
.....78
Look up table with window size of 56 days with Rg VPD Tair
....28
Look up table with window size of 63 days with Rg VPD Tair
....27
Look up table with window size of 70 days with Rg VPD Tair
...18
Look up table with window size of 14 days with Rg
...135
Look up table with window size of 21 days with Rg
..33
Look up table with window size of 28 days with Rg
..123
Look up table with window size of 35 days with Rg
34
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
20
Mean diurnal course with window size of 14 days: .
10
Mean diurnal course with window size of 21 days: .
9
Mean diurnal course with window size of 28 days: .
8
Finished gap filling of 'Ustar_MDS' in 26 seconds. Artificial gaps filled: 17520, real gaps filled: 13892, unfilled (long) gaps: 0.
Initialized variable 'Tau_MDS' with 13892 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'Tau_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................11762
Look up table with window size of 14 days with Rg VPD Tair
.........................................................1364
Look up table with window size of 7 days with Rg
...........................................2284
Mean diurnal course with window size of 0 days: .
.....................198
Mean diurnal course with window size of 1 days: .
...................100
Mean diurnal course with window size of 2 days: .
..................21
Look up table with window size of 21 days with Rg VPD Tair
.................373
Look up table with window size of 28 days with Rg VPD Tair
..............355
Look up table with window size of 35 days with Rg VPD Tair
..........292
Look up table with window size of 42 days with Rg VPD Tair
.......248
Look up table with window size of 49 days with Rg VPD Tair
.....78
Look up table with window size of 56 days with Rg VPD Tair
....28
Look up table with window size of 63 days with Rg VPD Tair
....27
Look up table with window size of 70 days with Rg VPD Tair
...18
Look up table with window size of 14 days with Rg
...135
Look up table with window size of 21 days with Rg
..33
Look up table with window size of 28 days with Rg
..123
Look up table with window size of 35 days with Rg
34
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
20
Mean diurnal course with window size of 14 days: .
10
Mean diurnal course with window size of 21 days: .
9
Mean diurnal course with window size of 28 days: .
8
Finished gap filling of 'Tau_MDS' in 26 seconds. Artificial gaps filled: 17520, real gaps filled: 13892, unfilled (long) gaps: 0.
Initialized variable 'ws_MDS' with 13898 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'ws_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................11823
Look up table with window size of 14 days with Rg VPD Tair
........................................................1394
Look up table with window size of 7 days with Rg
...........................................2213
Mean diurnal course with window size of 0 days: .
....................210
Mean diurnal course with window size of 1 days: .
..................89
Mean diurnal course with window size of 2 days: .
.................21
Look up table with window size of 21 days with Rg VPD Tair
.................371
Look up table with window size of 28 days with Rg VPD Tair
.............337
Look up table with window size of 35 days with Rg VPD Tair
..........299
Look up table with window size of 42 days with Rg VPD Tair
.......246
Look up table with window size of 49 days with Rg VPD Tair
.....77
Look up table with window size of 56 days with Rg VPD Tair
....28
Look up table with window size of 63 days with Rg VPD Tair
....29
Look up table with window size of 70 days with Rg VPD Tair
...18
Look up table with window size of 14 days with Rg
...134
Look up table with window size of 21 days with Rg
..31
Look up table with window size of 28 days with Rg
..123
Look up table with window size of 35 days with Rg
31
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
19
Mean diurnal course with window size of 14 days: .
10
Mean diurnal course with window size of 21 days: .
9
Mean diurnal course with window size of 28 days: .
8
Finished gap filling of 'ws_MDS' in 26 seconds. Artificial gaps filled: 17520, real gaps filled: 13898, unfilled (long) gaps: 0.
Initialized variable 'Press_MDS' with 911 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'Press_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................15583
Look up table with window size of 14 days with Rg VPD Tair
...................49
Look up table with window size of 7 days with Rg
..................1522
Mean diurnal course with window size of 0 days: .
...341
Mean diurnal course with window size of 1 days: .
25
Finished gap filling of 'Press_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 911, unfilled (long) gaps: 0.
Initialized variable 'PAR_MDS' with 366 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'PAR_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................15652
Look up table with window size of 14 days with Rg VPD Tair
..................29
Look up table with window size of 7 days with Rg
..................1473
Mean diurnal course with window size of 0 days: .
...267
Mean diurnal course with window size of 1 days: .
99
Finished gap filling of 'PAR_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 366, unfilled (long) gaps: 0.
Initialized variable 'Precip_MDS' with 356 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'Precip_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................15644
Look up table with window size of 14 days with Rg VPD Tair
..................35
Look up table with window size of 7 days with Rg
..................1475
Mean diurnal course with window size of 0 days: .
...359
Mean diurnal course with window size of 1 days: .
7
Finished gap filling of 'Precip_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 356, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 4849 will not be filled!
Initialized variable 'TW_0_MDS' with 7587 real gaps for gap filling of all 12671 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'TW_0_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
.......9487
Look up table with window size of 14 days with Rg VPD Tair
...............................341
Look up table with window size of 7 days with Rg
............................1123
Mean diurnal course with window size of 0 days: .
.................275
Mean diurnal course with window size of 1 days: .
..............23
Mean diurnal course with window size of 2 days: .
..............15
Look up table with window size of 21 days with Rg VPD Tair
..............310
Look up table with window size of 28 days with Rg VPD Tair
..........235
Look up table with window size of 35 days with Rg VPD Tair
........187
Look up table with window size of 42 days with Rg VPD Tair
......84
Look up table with window size of 49 days with Rg VPD Tair
.....6
Look up table with window size of 56 days with Rg VPD Tair
.....4
Look up table with window size of 63 days with Rg VPD Tair
.....0
Look up table with window size of 70 days with Rg VPD Tair
.....0
Look up table with window size of 14 days with Rg
.....255
Look up table with window size of 21 days with Rg
...125
Look up table with window size of 28 days with Rg
..123
Look up table with window size of 35 days with Rg
13
Look up table with window size of 42 days with Rg
1
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
36
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
2
Mean diurnal course with window size of 14 days: .
10
Mean diurnal course with window size of 21 days: .
8
Mean diurnal course with window size of 28 days: .
7
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'TW_0_MDS' in 19 seconds. Artificial gaps filled: 12671, real gaps filled: 7587, unfilled (long) gaps: 4849.
Initialized variable 'CO2c_MDS' with 13819 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'CO2c_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................11928
Look up table with window size of 14 days with Rg VPD Tair
.......................................................1353
Look up table with window size of 7 days with Rg
..........................................2141
Mean diurnal course with window size of 0 days: .
....................207
Mean diurnal course with window size of 1 days: .
..................90
Mean diurnal course with window size of 2 days: .
..................23
Look up table with window size of 21 days with Rg VPD Tair
.................370
Look up table with window size of 28 days with Rg VPD Tair
..............343
Look up table with window size of 35 days with Rg VPD Tair
..........311
Look up table with window size of 42 days with Rg VPD Tair
.......237
Look up table with window size of 49 days with Rg VPD Tair
.....68
Look up table with window size of 56 days with Rg VPD Tair
....29
Look up table with window size of 63 days with Rg VPD Tair
....29
Look up table with window size of 70 days with Rg VPD Tair
...18
Look up table with window size of 14 days with Rg
...140
Look up table with window size of 21 days with Rg
..29
Look up table with window size of 28 days with Rg
..120
Look up table with window size of 35 days with Rg
38
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
17
Mean diurnal course with window size of 14 days: .
12
Mean diurnal course with window size of 21 days: .
9
Mean diurnal course with window size of 28 days: .
8
Finished gap filling of 'CO2c_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 13819, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 5508 will not be filled!
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 12820 and 17520 will not be filled!
Initialized variable 'TW1_MDS' with 12350 real gaps for gap filling of all 7311 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'TW1_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
..............5859
Look up table with window size of 14 days with Rg VPD Tair
..............636
Look up table with window size of 7 days with Rg
........474
Mean diurnal course with window size of 0 days: .
...143
Mean diurnal course with window size of 1 days: .
.21
Mean diurnal course with window size of 2 days: .
.9
Look up table with window size of 21 days with Rg VPD Tair
.46
Look up table with window size of 28 days with Rg VPD Tair
.19
Look up table with window size of 35 days with Rg VPD Tair
.0
Look up table with window size of 42 days with Rg VPD Tair
.0
Look up table with window size of 49 days with Rg VPD Tair
.0
Look up table with window size of 56 days with Rg VPD Tair
.0
Look up table with window size of 63 days with Rg VPD Tair
.0
Look up table with window size of 70 days with Rg VPD Tair
.0
Look up table with window size of 14 days with Rg
.48
Look up table with window size of 21 days with Rg
0
Look up table with window size of 28 days with Rg
0
Look up table with window size of 35 days with Rg
0
Look up table with window size of 42 days with Rg
0
Look up table with window size of 49 days with Rg
0
Look up table with window size of 56 days with Rg
0
Look up table with window size of 63 days with Rg
0
Look up table with window size of 70 days with Rg
0
Mean diurnal course with window size of 7 days: .
28
Mean diurnal course with window size of 14 days: .
28
Finished gap filling of 'TW1_MDS' in 4 seconds. Artificial gaps filled: 7311, real gaps filled: 12350, unfilled (long) gaps: 10209.
Saved plot to: ./Mendota_2014_FP_NEE.pdf
Saved plot to: ./Mendota_2014_Flux_NEE.pdf
Saved plot to: ./Mendota_2014_FP_LE.pdf
Saved plot to: ./Mendota_2014_Flux_LE.pdf
Saved plot to: ./Mendota_2014_FP_H.pdf
Saved plot to: ./Mendota_2014_Flux_H.pdf
Saved plot to: ./Mendota_2014_FP_Rg.pdf
Saved plot to: ./Mendota_2014_Flux_Rg.pdf
Saved plot to: ./Mendota_2014_FP_VPD.pdf
Saved plot to: ./Mendota_2014_Flux_VPD.pdf
Saved plot to: ./Mendota_2014_FP_rH.pdf
Saved plot to: ./Mendota_2014_Flux_rH.pdf
Saved plot to: ./Mendota_2014_FP_Tair.pdf
Saved plot to: ./Mendota_2014_Flux_Tair.pdf
Saved plot to: ./Mendota_2014_FP_Ustar_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_Ustar_MDS.pdf
Saved plot to: ./Mendota_2014_FP_Tau_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_Tau_MDS.pdf
Saved plot to: ./Mendota_2014_FP_ws_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_ws_MDS.pdf
Saved plot to: ./Mendota_2014_FP_Press_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_Press_MDS.pdf
Saved plot to: ./Mendota_2014_FP_PAR_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_PAR_MDS.pdf
Saved plot to: ./Mendota_2014_FP_Precip_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_Precip_MDS.pdf
Saved plot to: ./Mendota_2014_FP_TW_0_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_TW_0_MDS.pdf
Saved plot to: ./Mendota_2014_FP_CO2c_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_CO2c_MDS.pdf
Saved plot to: ./Mendota_2014_FP_TW1_MDS.pdf
Saved plot to: ./Mendota_2014_Flux_TW1_MDS.pdf
Saved plot to: ./Mendota_2014_FP_NEE_f.pdf
Saved plot to: ./Mendota_2014_DC_NEE_f.pdf
Saved plot to: ./Mendota_2014_DSumU_NEE_f.pdf
Saved plot to: ./Mendota_2014_Flux_NEE_f.pdf
Saved plot to: ./Mendota_2014_FP_LE_f.pdf
Saved plot to: ./Mendota_2014_DC_LE_f.pdf
Saved plot to: ./Mendota_2014_DSumU_LE_f.pdf
Saved plot to: ./Mendota_2014_Flux_LE_f.pdf
Saved plot to: ./Mendota_2014_FP_H_f.pdf
Saved plot to: ./Mendota_2014_DC_H_f.pdf
Saved plot to: ./Mendota_2014_DSumU_H_f.pdf
Saved plot to: ./Mendota_2014_Flux_H_f.pdf
Saved plot to: ./Mendota_2014_FP_Rg_f.pdf
Saved plot to: ./Mendota_2014_DC_Rg_f.pdf
Saved plot to: ./Mendota_2014_DSum_Rg_f.pdf
Saved plot to: ./Mendota_2014_Flux_Rg_f.pdf
Saved plot to: ./Mendota_2014_FP_VPD_f.pdf
Saved plot to: ./Mendota_2014_DC_VPD_f.pdf
Saved plot to: ./Mendota_2014_DSum_VPD_f.pdf
Saved plot to: ./Mendota_2014_Flux_VPD_f.pdf
Saved plot to: ./Mendota_2014_FP_rH_f.pdf
Saved plot to: ./Mendota_2014_DC_rH_f.pdf
Saved plot to: ./Mendota_2014_DSum_rH_f.pdf
Saved plot to: ./Mendota_2014_Flux_rH_f.pdf
Saved plot to: ./Mendota_2014_FP_Tair_f.pdf
Saved plot to: ./Mendota_2014_DC_Tair_f.pdf
Saved plot to: ./Mendota_2014_DSum_Tair_f.pdf
Saved plot to: ./Mendota_2014_Flux_Tair_f.pdf
Saved plot to: ./Mendota_2014_FP_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_ws_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_ws_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_ws_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_ws_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_Press_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_Press_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_Press_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_Press_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_TW_0_MDS_f.pdf
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: January!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: February!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: March!
Saved plot to: ./Mendota_2014_DC_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2014_DC_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2014_FP_TW1_MDS_f.pdf
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: January!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: February!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: March!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: October!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: November!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i) :
  .sPlotDiurnalCycleM::: No data available for month: December!
Saved plot to: ./Mendota_2014_DC_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2014_DSumU_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2014_Flux_TW1_MDS_f.pdf
Number of NA convertered to '-9999': 735644
Wrote tab separated textfile: output.txt
> 
> print("converting generated output pdf files to png format for display on results page.") # done in shell script 
[1] "converting generated output pdf files to png format for display on results page."
> 
> # write logEntry that will be appended by to reddy_jobs_out.txt by reddy_bjobs.sh
> logEntry <- paste( time["user.self"], retval$mode, retval$inputSize, sep="," )
> cat( logEntry, file="logEntry.txt")
> 
> 
> 
> proc.time()
   user  system elapsed 
269.428   0.792 270.901 
