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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"             "330457870" 
   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: 168729
'data.frame':	17520 obs. of  21 variables:
 $ Year      : atomic  2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
  ..- 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  -8.8 -9 -9.2 -9.4 -9.5 -9.6 -9.8 -9.9 -10 -10 ...
  ..- 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  61.4 61.3 61.9 63.4 64 64.7 66.4 68 69.5 71 ...
  ..- attr(*, "varnames")= chr "rH"
  ..- attr(*, "units")= chr "-"
 $ Press_MDS : atomic  97.6 97.6 97.6 97.6 97.6 ...
  ..- 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,TW1_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,CO20_MDS 
No additional columns picked to keep in processing
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 14514 and 17520 will not be filled!
Initialized variable 'NEE' with 13038 real gaps for gap filling of all 14513 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
............................................................
.............................................................
..........................10986
Look up table with window size of 14 days with Rg VPD Tair
...................................899
Look up table with window size of 7 days with Rg
..........................2229
Mean diurnal course with window size of 0 days: .
...292
Mean diurnal course with window size of 1 days: .
.89
Mean diurnal course with window size of 2 days: .
17
Look up table with window size of 21 days with Rg VPD Tair
0
Look up table with window size of 28 days with Rg VPD Tair
0
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
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 'NEE' in 16 seconds. Artificial gaps filled: 14513, real gaps filled: 13038, unfilled (long) gaps: 3007.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14521 and 17520 will not be filled!
Initialized variable 'LE' with 13147 real gaps for gap filling of all 14520 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
............................................................
.............................................................
..........................10571
Look up table with window size of 14 days with Rg VPD Tair
.......................................828
Look up table with window size of 7 days with Rg
...............................2406
Mean diurnal course with window size of 0 days: .
.......280
Mean diurnal course with window size of 1 days: .
....117
Mean diurnal course with window size of 2 days: .
...31
Look up table with window size of 21 days with Rg VPD Tair
..85
Look up table with window size of 28 days with Rg VPD Tair
..29
Look up table with window size of 35 days with Rg VPD Tair
.7
Look up table with window size of 42 days with Rg VPD Tair
.28
Look up table with window size of 49 days with Rg VPD Tair
.44
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
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
85
Look up table with window size of 21 days with Rg
4
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: .
2
Finished gap filling of 'LE' in 17 seconds. Artificial gaps filled: 14520, real gaps filled: 13147, unfilled (long) gaps: 3000.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14521 and 17520 will not be filled!
Initialized variable 'H' with 12875 real gaps for gap filling of all 14520 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
............................................................
.............................................................
..........................11136
Look up table with window size of 14 days with Rg VPD Tair
.................................873
Look up table with window size of 7 days with Rg
.........................2112
Mean diurnal course with window size of 0 days: .
...293
Mean diurnal course with window size of 1 days: .
.92
Mean diurnal course with window size of 2 days: .
11
Look up table with window size of 21 days with Rg VPD Tair
0
Look up table with window size of 28 days with Rg VPD Tair
0
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
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: .
3
Finished gap filling of 'H' in 15 seconds. Artificial gaps filled: 14520, real gaps filled: 12875, unfilled (long) gaps: 3000.
Initialized variable 'Rg' with 447 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: .
....279
Mean diurnal course with window size of 1 days: .
.158
Mean diurnal course with window size of 2 days: .
10
Finished gap filling of 'Rg' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 447, unfilled (long) gaps: 0.
Initialized variable 'VPD' with 1587 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
...............1526
Mean diurnal course with window size of 0 days: .
18
Mean diurnal course with window size of 1 days: .
41
Mean diurnal course with window size of 2 days: .
2
Finished gap filling of 'VPD' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 1587, unfilled (long) gaps: 0.
Initialized variable 'rH' with 797 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
.......751
Mean diurnal course with window size of 0 days: .
14
Mean diurnal course with window size of 1 days: .
30
Mean diurnal course with window size of 2 days: .
2
Finished gap filling of 'rH' in 1 seconds. Artificial gaps filled: 17520, real gaps filled: 797, unfilled (long) gaps: 0.
Initialized variable 'Tair' with 823 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
........807
Mean diurnal course with window size of 0 days: .
5
Mean diurnal course with window size of 1 days: .
11
Finished gap filling of 'Tair' in 0 seconds. Artificial gaps filled: 17520, real gaps filled: 823, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14523 and 17520 will not be filled!
Initialized variable 'Ustar_MDS' with 13995 real gaps for gap filling of all 14522 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
............................................................
.............................................................
..........................10901
Look up table with window size of 14 days with Rg VPD Tair
....................................1030
Look up table with window size of 7 days with Rg
.........................2192
Mean diurnal course with window size of 0 days: .
...258
Mean diurnal course with window size of 1 days: .
.117
Mean diurnal course with window size of 2 days: .
21
Look up table with window size of 21 days with Rg VPD Tair
0
Look up table with window size of 28 days with Rg VPD Tair
0
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
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: .
3
Finished gap filling of 'Ustar_MDS' in 15 seconds. Artificial gaps filled: 14522, real gaps filled: 13995, unfilled (long) gaps: 2998.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14523 and 17520 will not be filled!
Initialized variable 'Tau_MDS' with 13998 real gaps for gap filling of all 14522 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
............................................................
.............................................................
..........................10901
Look up table with window size of 14 days with Rg VPD Tair
....................................1030
Look up table with window size of 7 days with Rg
.........................2192
Mean diurnal course with window size of 0 days: .
...257
Mean diurnal course with window size of 1 days: .
.118
Mean diurnal course with window size of 2 days: .
21
Look up table with window size of 21 days with Rg VPD Tair
0
Look up table with window size of 28 days with Rg VPD Tair
0
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
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: .
3
Finished gap filling of 'Tau_MDS' in 13 seconds. Artificial gaps filled: 14522, real gaps filled: 13998, unfilled (long) gaps: 2998.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14523 and 17520 will not be filled!
Initialized variable 'ws_MDS' with 14016 real gaps for gap filling of all 14522 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
............................................................
.............................................................
..........................10843
Look up table with window size of 14 days with Rg VPD Tair
....................................1086
Look up table with window size of 7 days with Rg
.........................2193
Mean diurnal course with window size of 0 days: .
....259
Mean diurnal course with window size of 1 days: .
.118
Mean diurnal course with window size of 2 days: .
21
Look up table with window size of 21 days with Rg VPD Tair
0
Look up table with window size of 28 days with Rg VPD Tair
0
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
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: .
2
Finished gap filling of 'ws_MDS' in 14 seconds. Artificial gaps filled: 14522, real gaps filled: 14016, unfilled (long) gaps: 2998.
Initialized variable 'Press_MDS' with 1029 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
............................................................
.............................................................
........................................................15459
Look up table with window size of 14 days with Rg VPD Tair
....................58
Look up table with window size of 7 days with Rg
....................1556
Mean diurnal course with window size of 0 days: .
....412
Mean diurnal course with window size of 1 days: .
35
Finished gap filling of 'Press_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 1029, unfilled (long) gaps: 0.
Initialized variable 'PAR_MDS' with 447 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
............................................................
.............................................................
........................................................15500
Look up table with window size of 14 days with Rg VPD Tair
....................32
Look up table with window size of 7 days with Rg
...................1541
Mean diurnal course with window size of 0 days: .
....279
Mean diurnal course with window size of 1 days: .
.158
Mean diurnal course with window size of 2 days: .
10
Finished gap filling of 'PAR_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 447, unfilled (long) gaps: 0.
Initialized variable 'Precip_MDS' with 272 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
............................................................
.............................................................
........................................................15494
Look up table with window size of 14 days with Rg VPD Tair
....................38
Look up table with window size of 7 days with Rg
...................1541
Mean diurnal course with window size of 0 days: .
....446
Mean diurnal course with window size of 1 days: .
1
Finished gap filling of 'Precip_MDS' in 20 seconds. Artificial gaps filled: 17520, real gaps filled: 272, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 4897 will not be filled!
Initialized variable 'TW_0_MDS' with 6517 real gaps for gap filling of all 12623 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
............................................................
.............................................................
.......10479
Look up table with window size of 14 days with Rg VPD Tair
.....................437
Look up table with window size of 7 days with Rg
.................1068
Mean diurnal course with window size of 0 days: .
......383
Mean diurnal course with window size of 1 days: .
..6
Mean diurnal course with window size of 2 days: .
..9
Look up table with window size of 21 days with Rg VPD Tair
..13
Look up table with window size of 28 days with Rg VPD Tair
..3
Look up table with window size of 35 days with Rg VPD Tair
..9
Look up table with window size of 42 days with Rg VPD Tair
..186
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
12
Look up table with window size of 21 days with Rg
4
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: .
14
Finished gap filling of 'TW_0_MDS' in 12 seconds. Artificial gaps filled: 12623, real gaps filled: 6517, unfilled (long) gaps: 4897.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 14523 and 17520 will not be filled!
Initialized variable 'CO2c_MDS' with 13937 real gaps for gap filling of all 14522 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
............................................................
.............................................................
..........................10971
Look up table with window size of 14 days with Rg VPD Tair
...................................993
Look up table with window size of 7 days with Rg
.........................2159
Mean diurnal course with window size of 0 days: .
...268
Mean diurnal course with window size of 1 days: .
.112
Mean diurnal course with window size of 2 days: .
17
Look up table with window size of 21 days with Rg VPD Tair
0
Look up table with window size of 28 days with Rg VPD Tair
0
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
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: .
2
Finished gap filling of 'CO2c_MDS' in 13 seconds. Artificial gaps filled: 14522, real gaps filled: 13937, unfilled (long) gaps: 2998.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 8014 will not be filled!
Initialized variable 'CO20_MDS' with 10831 real gaps for gap filling of all 9506 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'CO20_MDS' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
....................................6388
Look up table with window size of 14 days with Rg VPD Tair
...............................263
Look up table with window size of 7 days with Rg
............................590
Mean diurnal course with window size of 0 days: .
......................185
Mean diurnal course with window size of 1 days: .
....................13
Mean diurnal course with window size of 2 days: .
....................3
Look up table with window size of 21 days with Rg VPD Tair
....................158
Look up table with window size of 28 days with Rg VPD Tair
...................140
Look up table with window size of 35 days with Rg VPD Tair
.................291
Look up table with window size of 42 days with Rg VPD Tair
..............224
Look up table with window size of 49 days with Rg VPD Tair
............202
Look up table with window size of 56 days with Rg VPD Tair
..........81
Look up table with window size of 63 days with Rg VPD Tair
.........22
Look up table with window size of 70 days with Rg VPD Tair
.........19
Look up table with window size of 14 days with Rg
.........96
Look up table with window size of 21 days with Rg
........174
Look up table with window size of 28 days with Rg
......106
Look up table with window size of 35 days with Rg
.....13
Look up table with window size of 42 days with Rg
.....152
Look up table with window size of 49 days with Rg
...116
Look up table with window size of 56 days with Rg
..237
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: .
3
Mean diurnal course with window size of 14 days: .
2
Mean diurnal course with window size of 21 days: .
7
Mean diurnal course with window size of 28 days: .
10
Mean diurnal course with window size of 35 days: .
2
Mean diurnal course with window size of 42 days: .
9
Finished gap filling of 'CO20_MDS' in 17 seconds. Artificial gaps filled: 9506, real gaps filled: 10831, unfilled (long) gaps: 8014.
Saved plot to: ./Mendota_2015_FP_NEE.pdf
Saved plot to: ./Mendota_2015_Flux_NEE.pdf
Saved plot to: ./Mendota_2015_FP_LE.pdf
Saved plot to: ./Mendota_2015_Flux_LE.pdf
Saved plot to: ./Mendota_2015_FP_H.pdf
Saved plot to: ./Mendota_2015_Flux_H.pdf
Saved plot to: ./Mendota_2015_FP_Rg.pdf
Saved plot to: ./Mendota_2015_Flux_Rg.pdf
Saved plot to: ./Mendota_2015_FP_VPD.pdf
Saved plot to: ./Mendota_2015_Flux_VPD.pdf
Saved plot to: ./Mendota_2015_FP_rH.pdf
Saved plot to: ./Mendota_2015_Flux_rH.pdf
Saved plot to: ./Mendota_2015_FP_Tair.pdf
Saved plot to: ./Mendota_2015_Flux_Tair.pdf
Saved plot to: ./Mendota_2015_FP_Ustar_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_Ustar_MDS.pdf
Saved plot to: ./Mendota_2015_FP_Tau_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_Tau_MDS.pdf
Saved plot to: ./Mendota_2015_FP_ws_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_ws_MDS.pdf
Saved plot to: ./Mendota_2015_FP_Press_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_Press_MDS.pdf
Saved plot to: ./Mendota_2015_FP_PAR_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_PAR_MDS.pdf
Saved plot to: ./Mendota_2015_FP_Precip_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_Precip_MDS.pdf
Saved plot to: ./Mendota_2015_FP_TW_0_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_TW_0_MDS.pdf
Saved plot to: ./Mendota_2015_FP_CO2c_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_CO2c_MDS.pdf
Saved plot to: ./Mendota_2015_FP_CO20_MDS.pdf
Saved plot to: ./Mendota_2015_Flux_CO20_MDS.pdf
Saved plot to: ./Mendota_2015_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_2015_DC_NEE_f.pdf
Saved plot to: ./Mendota_2015_DSumU_NEE_f.pdf
Saved plot to: ./Mendota_2015_Flux_NEE_f.pdf
Saved plot to: ./Mendota_2015_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_2015_DC_LE_f.pdf
Saved plot to: ./Mendota_2015_DSumU_LE_f.pdf
Saved plot to: ./Mendota_2015_Flux_LE_f.pdf
Saved plot to: ./Mendota_2015_FP_H_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_2015_DC_H_f.pdf
Saved plot to: ./Mendota_2015_DSumU_H_f.pdf
Saved plot to: ./Mendota_2015_Flux_H_f.pdf
Saved plot to: ./Mendota_2015_FP_Rg_f.pdf
Saved plot to: ./Mendota_2015_DC_Rg_f.pdf
Saved plot to: ./Mendota_2015_DSum_Rg_f.pdf
Saved plot to: ./Mendota_2015_Flux_Rg_f.pdf
Saved plot to: ./Mendota_2015_FP_VPD_f.pdf
Saved plot to: ./Mendota_2015_DC_VPD_f.pdf
Saved plot to: ./Mendota_2015_DSum_VPD_f.pdf
Saved plot to: ./Mendota_2015_Flux_VPD_f.pdf
Saved plot to: ./Mendota_2015_FP_rH_f.pdf
Saved plot to: ./Mendota_2015_DC_rH_f.pdf
Saved plot to: ./Mendota_2015_DSum_rH_f.pdf
Saved plot to: ./Mendota_2015_Flux_rH_f.pdf
Saved plot to: ./Mendota_2015_FP_Tair_f.pdf
Saved plot to: ./Mendota_2015_DC_Tair_f.pdf
Saved plot to: ./Mendota_2015_DSum_Tair_f.pdf
Saved plot to: ./Mendota_2015_Flux_Tair_f.pdf
Saved plot to: ./Mendota_2015_FP_Ustar_MDS_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_2015_DC_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_Tau_MDS_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_2015_DC_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_ws_MDS_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_2015_DC_ws_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_ws_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_ws_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_Press_MDS_f.pdf
Saved plot to: ./Mendota_2015_DC_Press_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_Press_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_Press_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2015_DC_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2015_DC_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2015_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$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: March!
Saved plot to: ./Mendota_2015_DC_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_CO2c_MDS_f.pdf
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: November!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i) :
  .sPlotDiurnalCycleM::: No data available for month: December!
Saved plot to: ./Mendota_2015_DC_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2015_FP_CO20_MDS_f.pdf
Warning in .self$.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$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: April!
Warning in .self$.sPlotDiurnalCycleM(Var.s, QFVar.s, QFValue.n, Month.i,  :
  .sPlotDiurnalCycleM::: No data available for month: May!
Saved plot to: ./Mendota_2015_DC_CO20_MDS_f.pdf
Saved plot to: ./Mendota_2015_DSumU_CO20_MDS_f.pdf
Saved plot to: ./Mendota_2015_Flux_CO20_MDS_f.pdf
Number of NA convertered to '-9999': 889895
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 
237.342   0.780 238.615 
