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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"             "284284424" 
   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: 167742
'data.frame':	17568 obs. of  21 variables:
 $ Year      : atomic  2012 2012 2012 2012 2012 2012 2012 2012 2012 2012 ...
  ..- 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  NA NA NA NA NA NA NA NA NA NA ...
  ..- 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  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "H"
  ..- attr(*, "units")= chr "-"
 $ LE        : atomic  NA NA NA NA NA NA NA NA NA NA ...
  ..- attr(*, "varnames")= chr "LE"
  ..- attr(*, "units")= chr "-"
 $ Tair      : atomic  2.7 2.7 2.8 2.8 2.2 1.7 1.6 1.4 1.3 1.1 ...
  ..- 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  NA NA NA NA NA NA 99.2 NA NA NA ...
  ..- attr(*, "varnames")= chr "rH"
  ..- attr(*, "units")= chr "-"
 $ Press_MDS : atomic  96.2 96.1 96.1 96.1 96.1 ...
  ..- attr(*, "varnames")= chr "Press_MDS"
  ..- attr(*, "units")= chr "-"
 $ PAR_MDS   : atomic  1.68 1.68 1.68 1.47 1.47 1.68 1.68 1.68 2.52 2.52 ...
  ..- attr(*, "varnames")= chr "PAR_MDS"
  ..- attr(*, "units")= chr "-"
 $ Rg        : atomic  0.8 0.8 0.8 0.7 0.7 0.8 0.8 0.8 1.2 1.2 ...
  ..- 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 ...
  ..- 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."
Warning in fCheckOutsideRange(cbind(RelHumidity_Percent = RH.V.n), "RelHumidity_Percent",  :
  fCalcVPDfromRHandTair:::fCheckOutsideRange::: Variable outside (plausible) range in 3 cases! Invalid values with 'RelHumidity_Percent < 0 | > 100': 100, 100, 100 ...
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
Warning in fCheckOutsideRange(Data.F, VarName.V.s[v.i], c("<", 0), SubCallFunc.s) :
  sEddyProc.initialize:::fCheckColPlausibility:::fCheckOutsideRange::: Variable outside (plausible) range in 3 cases! Invalid values with 'VPD < 0': -0.0029, -0.0086, -0.0155 ...
New sEddyProc class for site 'Mendota'
[1] "------------- Gapfilling ---------------"
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 13823 and 17568 will not be filled!
Initialized variable 'NEE' with 13989 real gaps for gap filling of all 13822 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
............................................................
.............................................................
...................9424
Look up table with window size of 14 days with Rg VPD Tair
...........................................1137
Look up table with window size of 7 days with Rg
................................1788
Mean diurnal course with window size of 0 days: .
..............202
Mean diurnal course with window size of 1 days: .
............80
Mean diurnal course with window size of 2 days: .
...........48
Look up table with window size of 21 days with Rg VPD Tair
...........204
Look up table with window size of 28 days with Rg VPD Tair
.........464
Look up table with window size of 35 days with Rg VPD Tair
....134
Look up table with window size of 42 days with Rg VPD Tair
...72
Look up table with window size of 49 days with Rg VPD Tair
..14
Look up table with window size of 56 days with Rg VPD Tair
..6
Look up table with window size of 63 days with Rg VPD Tair
..4
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
..126
Look up table with window size of 21 days with Rg
.22
Look up table with window size of 28 days with Rg
23
Look up table with window size of 35 days with Rg
27
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: .
36
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
3
Mean diurnal course with window size of 28 days: .
3
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'NEE' in 18 seconds. Artificial gaps filled: 13822, real gaps filled: 13989, unfilled (long) gaps: 3746.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14340 and 17568 will not be filled!
Initialized variable 'LE' with 13880 real gaps for gap filling of all 14339 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
............................................................
.............................................................
........................9783
Look up table with window size of 14 days with Rg VPD Tair
.............................................1226
Look up table with window size of 7 days with Rg
.................................1838
Mean diurnal course with window size of 0 days: .
..............200
Mean diurnal course with window size of 1 days: .
............81
Mean diurnal course with window size of 2 days: .
............41
Look up table with window size of 21 days with Rg VPD Tair
...........223
Look up table with window size of 28 days with Rg VPD Tair
.........469
Look up table with window size of 35 days with Rg VPD Tair
....133
Look up table with window size of 42 days with Rg VPD Tair
...72
Look up table with window size of 49 days with Rg VPD Tair
..13
Look up table with window size of 56 days with Rg VPD Tair
..3
Look up table with window size of 63 days with Rg VPD Tair
..1
Look up table with window size of 70 days with Rg VPD Tair
..1
Look up table with window size of 14 days with Rg
..126
Look up table with window size of 21 days with Rg
.22
Look up table with window size of 28 days with Rg
.23
Look up table with window size of 35 days with Rg
27
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: .
46
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
3
Mean diurnal course with window size of 28 days: .
3
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'LE' in 19 seconds. Artificial gaps filled: 14339, real gaps filled: 13880, unfilled (long) gaps: 3229.
Initialized variable 'H' with 13264 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................12446
Look up table with window size of 14 days with Rg VPD Tair
...................................................1327
Look up table with window size of 7 days with Rg
.....................................2195
Mean diurnal course with window size of 0 days: .
................239
Mean diurnal course with window size of 1 days: .
.............112
Mean diurnal course with window size of 2 days: .
............48
Look up table with window size of 21 days with Rg VPD Tair
............203
Look up table with window size of 28 days with Rg VPD Tair
.........481
Look up table with window size of 35 days with Rg VPD Tair
.....145
Look up table with window size of 42 days with Rg VPD Tair
...88
Look up table with window size of 49 days with Rg VPD Tair
..15
Look up table with window size of 56 days with Rg VPD Tair
..3
Look up table with window size of 63 days with Rg VPD Tair
..4
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
..111
Look up table with window size of 21 days with Rg
.25
Look up table with window size of 28 days with Rg
.32
Look up table with window size of 35 days with Rg
26
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: .
57
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
3
Mean diurnal course with window size of 28 days: .
3
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'H' in 24 seconds. Artificial gaps filled: 17568, real gaps filled: 13264, unfilled (long) gaps: 0.
Initialized variable 'Rg' with 428 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: .
....341
Mean diurnal course with window size of 1 days: .
84
Mean diurnal course with window size of 2 days: .
3
Finished gap filling of 'Rg' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 428, unfilled (long) gaps: 0.
Initialized variable 'VPD' with 1155 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
...........1111
Mean diurnal course with window size of 0 days: .
19
Mean diurnal course with window size of 1 days: .
21
Mean diurnal course with window size of 2 days: .
3
Look up table with window size of 14 days with Rg
0
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: .
1
Finished gap filling of 'VPD' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 1155, unfilled (long) gaps: 0.
Initialized variable 'rH' with 502 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
.....483
Mean diurnal course with window size of 0 days: .
10
Mean diurnal course with window size of 1 days: .
9
Finished gap filling of 'rH' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 502, unfilled (long) gaps: 0.
Initialized variable 'Tair' with 677 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
......652
Mean diurnal course with window size of 0 days: .
9
Mean diurnal course with window size of 1 days: .
12
Mean diurnal course with window size of 2 days: .
3
Look up table with window size of 14 days with Rg
0
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: .
1
Finished gap filling of 'Tair' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 677, unfilled (long) gaps: 0.
Initialized variable 'Ustar_MDS' with 13857 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................12246
Look up table with window size of 14 days with Rg VPD Tair
.....................................................1433
Look up table with window size of 7 days with Rg
......................................2257
Mean diurnal course with window size of 0 days: .
................258
Mean diurnal course with window size of 1 days: .
.............105
Mean diurnal course with window size of 2 days: .
............17
Look up table with window size of 21 days with Rg VPD Tair
............200
Look up table with window size of 28 days with Rg VPD Tair
..........433
Look up table with window size of 35 days with Rg VPD Tair
......197
Look up table with window size of 42 days with Rg VPD Tair
....93
Look up table with window size of 49 days with Rg VPD Tair
...19
Look up table with window size of 56 days with Rg VPD Tair
...5
Look up table with window size of 63 days with Rg VPD Tair
...6
Look up table with window size of 70 days with Rg VPD Tair
..9
Look up table with window size of 14 days with Rg
..126
Look up table with window size of 21 days with Rg
.54
Look up table with window size of 28 days with Rg
.29
Look up table with window size of 35 days with Rg
28
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
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: .
41
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
3
Mean diurnal course with window size of 28 days: .
3
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'Ustar_MDS' in 23 seconds. Artificial gaps filled: 17568, real gaps filled: 13857, unfilled (long) gaps: 0.
Initialized variable 'Tau_MDS' with 13855 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................12246
Look up table with window size of 14 days with Rg VPD Tair
.....................................................1433
Look up table with window size of 7 days with Rg
......................................2257
Mean diurnal course with window size of 0 days: .
................258
Mean diurnal course with window size of 1 days: .
.............105
Mean diurnal course with window size of 2 days: .
............17
Look up table with window size of 21 days with Rg VPD Tair
............200
Look up table with window size of 28 days with Rg VPD Tair
..........433
Look up table with window size of 35 days with Rg VPD Tair
......197
Look up table with window size of 42 days with Rg VPD Tair
....93
Look up table with window size of 49 days with Rg VPD Tair
...19
Look up table with window size of 56 days with Rg VPD Tair
...5
Look up table with window size of 63 days with Rg VPD Tair
...6
Look up table with window size of 70 days with Rg VPD Tair
..9
Look up table with window size of 14 days with Rg
..126
Look up table with window size of 21 days with Rg
.54
Look up table with window size of 28 days with Rg
.29
Look up table with window size of 35 days with Rg
28
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
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: .
41
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
3
Mean diurnal course with window size of 28 days: .
3
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'Tau_MDS' in 23 seconds. Artificial gaps filled: 17568, real gaps filled: 13855, unfilled (long) gaps: 0.
Initialized variable 'ws_MDS' with 13865 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................12182
Look up table with window size of 14 days with Rg VPD Tair
.....................................................1466
Look up table with window size of 7 days with Rg
.......................................2296
Mean diurnal course with window size of 0 days: .
................264
Mean diurnal course with window size of 1 days: .
.............96
Mean diurnal course with window size of 2 days: .
............19
Look up table with window size of 21 days with Rg VPD Tair
............198
Look up table with window size of 28 days with Rg VPD Tair
..........438
Look up table with window size of 35 days with Rg VPD Tair
......191
Look up table with window size of 42 days with Rg VPD Tair
....88
Look up table with window size of 49 days with Rg VPD Tair
...18
Look up table with window size of 56 days with Rg VPD Tair
...3
Look up table with window size of 63 days with Rg VPD Tair
...8
Look up table with window size of 70 days with Rg VPD Tair
...7
Look up table with window size of 14 days with Rg
..136
Look up table with window size of 21 days with Rg
.50
Look up table with window size of 28 days with Rg
.27
Look up table with window size of 35 days with Rg
29
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: .
41
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
5
Mean diurnal course with window size of 28 days: .
1
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'ws_MDS' in 23 seconds. Artificial gaps filled: 17568, real gaps filled: 13865, unfilled (long) gaps: 0.
Initialized variable 'Press_MDS' with 1311 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................15948
Look up table with window size of 14 days with Rg VPD Tair
................62
Look up table with window size of 7 days with Rg
...............1130
Mean diurnal course with window size of 0 days: .
....402
Mean diurnal course with window size of 1 days: .
26
Finished gap filling of 'Press_MDS' in 20 seconds. Artificial gaps filled: 17568, real gaps filled: 1311, unfilled (long) gaps: 0.
Initialized variable 'PAR_MDS' with 428 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................15997
Look up table with window size of 14 days with Rg VPD Tair
...............23
Look up table with window size of 7 days with Rg
...............1120
Mean diurnal course with window size of 0 days: .
....341
Mean diurnal course with window size of 1 days: .
84
Mean diurnal course with window size of 2 days: .
3
Finished gap filling of 'PAR_MDS' in 20 seconds. Artificial gaps filled: 17568, real gaps filled: 428, unfilled (long) gaps: 0.
Initialized variable 'Precip_MDS' with 648 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................15977
Look up table with window size of 14 days with Rg VPD Tair
...............42
Look up table with window size of 7 days with Rg
...............1121
Mean diurnal course with window size of 0 days: .
....425
Mean diurnal course with window size of 1 days: .
3
Finished gap filling of 'Precip_MDS' in 18 seconds. Artificial gaps filled: 17568, real gaps filled: 648, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 4321 will not be filled!
Initialized variable 'TW_0_MDS' with 5887 real gaps for gap filling of all 13247 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
............................................................
.............................................................
.............10867
Look up table with window size of 14 days with Rg VPD Tair
.......................378
Look up table with window size of 7 days with Rg
....................844
Mean diurnal course with window size of 0 days: .
...........345
Mean diurnal course with window size of 1 days: .
........5
Mean diurnal course with window size of 2 days: .
........5
Look up table with window size of 21 days with Rg VPD Tair
........213
Look up table with window size of 28 days with Rg VPD Tair
.....198
Look up table with window size of 35 days with Rg VPD Tair
...275
Look up table with window size of 42 days with Rg VPD Tair
.7
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
.38
Look up table with window size of 21 days with Rg
10
Look up table with window size of 28 days with Rg
27
Look up table with window size of 35 days with Rg
6
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: .
5
Mean diurnal course with window size of 14 days: .
15
Mean diurnal course with window size of 21 days: .
6
Mean diurnal course with window size of 28 days: .
3
Finished gap filling of 'TW_0_MDS' in 9 seconds. Artificial gaps filled: 13247, real gaps filled: 5887, unfilled (long) gaps: 4321.
Initialized variable 'CO2c_MDS' with 13977 real gaps for gap filling of all 17568 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
............................................................
.............................................................
........................................................12098
Look up table with window size of 14 days with Rg VPD Tair
......................................................1533
Look up table with window size of 7 days with Rg
.......................................2310
Mean diurnal course with window size of 0 days: .
................242
Mean diurnal course with window size of 1 days: .
.............112
Mean diurnal course with window size of 2 days: .
............24
Look up table with window size of 21 days with Rg VPD Tair
............200
Look up table with window size of 28 days with Rg VPD Tair
..........441
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
....89
Look up table with window size of 49 days with Rg VPD Tair
...19
Look up table with window size of 56 days with Rg VPD Tair
...3
Look up table with window size of 63 days with Rg VPD Tair
...8
Look up table with window size of 70 days with Rg VPD Tair
...7
Look up table with window size of 14 days with Rg
..136
Look up table with window size of 21 days with Rg
.50
Look up table with window size of 28 days with Rg
.27
Look up table with window size of 35 days with Rg
29
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: .
42
Mean diurnal course with window size of 14 days: .
4
Mean diurnal course with window size of 21 days: .
5
Mean diurnal course with window size of 28 days: .
1
Mean diurnal course with window size of 35 days: .
1
Finished gap filling of 'CO2c_MDS' in 15 seconds. Artificial gaps filled: 17568, real gaps filled: 13977, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 5788 will not be filled!
Initialized variable 'TW1_MDS' with 8470 real gaps for gap filling of all 11780 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
............................................................
..........................................................9269
Look up table with window size of 14 days with Rg VPD Tair
.........................520
Look up table with window size of 7 days with Rg
...................770
Mean diurnal course with window size of 0 days: .
............302
Mean diurnal course with window size of 1 days: .
.........15
Mean diurnal course with window size of 2 days: .
.........2
Look up table with window size of 21 days with Rg VPD Tair
.........303
Look up table with window size of 28 days with Rg VPD Tair
.....198
Look up table with window size of 35 days with Rg VPD Tair
....275
Look up table with window size of 42 days with Rg VPD Tair
.7
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
.21
Look up table with window size of 21 days with Rg
17
Look up table with window size of 28 days with Rg
17
Look up table with window size of 35 days with Rg
26
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: .
12
Mean diurnal course with window size of 14 days: .
17
Mean diurnal course with window size of 21 days: .
3
Mean diurnal course with window size of 28 days: .
6
Finished gap filling of 'TW1_MDS' in 9 seconds. Artificial gaps filled: 11780, real gaps filled: 8470, unfilled (long) gaps: 5788.
Saved plot to: ./Mendota_2012_FP_NEE.pdf
Saved plot to: ./Mendota_2012_Flux_NEE.pdf
Saved plot to: ./Mendota_2012_FP_LE.pdf
Saved plot to: ./Mendota_2012_Flux_LE.pdf
Saved plot to: ./Mendota_2012_FP_H.pdf
Saved plot to: ./Mendota_2012_Flux_H.pdf
Saved plot to: ./Mendota_2012_FP_Rg.pdf
Saved plot to: ./Mendota_2012_Flux_Rg.pdf
Saved plot to: ./Mendota_2012_FP_VPD.pdf
Saved plot to: ./Mendota_2012_Flux_VPD.pdf
Saved plot to: ./Mendota_2012_FP_rH.pdf
Saved plot to: ./Mendota_2012_Flux_rH.pdf
Saved plot to: ./Mendota_2012_FP_Tair.pdf
Saved plot to: ./Mendota_2012_Flux_Tair.pdf
Saved plot to: ./Mendota_2012_FP_Ustar_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_Ustar_MDS.pdf
Saved plot to: ./Mendota_2012_FP_Tau_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_Tau_MDS.pdf
Saved plot to: ./Mendota_2012_FP_ws_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_ws_MDS.pdf
Saved plot to: ./Mendota_2012_FP_Press_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_Press_MDS.pdf
Saved plot to: ./Mendota_2012_FP_PAR_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_PAR_MDS.pdf
Saved plot to: ./Mendota_2012_FP_Precip_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_Precip_MDS.pdf
Saved plot to: ./Mendota_2012_FP_TW_0_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_TW_0_MDS.pdf
Saved plot to: ./Mendota_2012_FP_CO2c_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_CO2c_MDS.pdf
Saved plot to: ./Mendota_2012_FP_TW1_MDS.pdf
Saved plot to: ./Mendota_2012_Flux_TW1_MDS.pdf
Saved plot to: ./Mendota_2012_FP_NEE_f.pdf
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_2012_DC_NEE_f.pdf
Saved plot to: ./Mendota_2012_DSumU_NEE_f.pdf
Saved plot to: ./Mendota_2012_Flux_NEE_f.pdf
Saved plot to: ./Mendota_2012_FP_LE_f.pdf
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_2012_DC_LE_f.pdf
Saved plot to: ./Mendota_2012_DSumU_LE_f.pdf
Saved plot to: ./Mendota_2012_Flux_LE_f.pdf
Saved plot to: ./Mendota_2012_FP_H_f.pdf
Saved plot to: ./Mendota_2012_DC_H_f.pdf
Saved plot to: ./Mendota_2012_DSumU_H_f.pdf
Saved plot to: ./Mendota_2012_Flux_H_f.pdf
Saved plot to: ./Mendota_2012_FP_Rg_f.pdf
Saved plot to: ./Mendota_2012_DC_Rg_f.pdf
Saved plot to: ./Mendota_2012_DSum_Rg_f.pdf
Saved plot to: ./Mendota_2012_Flux_Rg_f.pdf
Saved plot to: ./Mendota_2012_FP_VPD_f.pdf
Saved plot to: ./Mendota_2012_DC_VPD_f.pdf
Saved plot to: ./Mendota_2012_DSum_VPD_f.pdf
Saved plot to: ./Mendota_2012_Flux_VPD_f.pdf
Saved plot to: ./Mendota_2012_FP_rH_f.pdf
Saved plot to: ./Mendota_2012_DC_rH_f.pdf
Saved plot to: ./Mendota_2012_DSum_rH_f.pdf
Saved plot to: ./Mendota_2012_Flux_rH_f.pdf
Saved plot to: ./Mendota_2012_FP_Tair_f.pdf
Saved plot to: ./Mendota_2012_DC_Tair_f.pdf
Saved plot to: ./Mendota_2012_DSum_Tair_f.pdf
Saved plot to: ./Mendota_2012_Flux_Tair_f.pdf
Saved plot to: ./Mendota_2012_FP_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2012_FP_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2012_FP_ws_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_ws_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_ws_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_ws_MDS_f.pdf
Saved plot to: ./Mendota_2012_FP_Press_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_Press_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_Press_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_Press_MDS_f.pdf
Saved plot to: ./Mendota_2012_FP_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2012_FP_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2012_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!
Saved plot to: ./Mendota_2012_DC_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2012_FP_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2012_DC_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2012_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$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: March!
Saved plot to: ./Mendota_2012_DC_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2012_DSumU_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2012_Flux_TW1_MDS_f.pdf
Number of NA convertered to '-9999': 758157
Wrote tab separated textfile: output.txt
> 
> print("converting generated output pdf files to png format for display on results page.") # done in shell script 
[1] "converting generated output pdf files to png format for display on results page."
> 
> # write logEntry that will be appended by to reddy_jobs_out.txt by reddy_bjobs.sh
> logEntry <- paste( time["user.self"], retval$mode, retval$inputSize, sep="," )
> cat( logEntry, file="logEntry.txt")
> 
> 
> 
> proc.time()
   user  system elapsed 
262.844   0.728 264.164 
