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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"             "600166231" 
   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: 152046
'data.frame':	17568 obs. of  21 variables:
 $ Year      : atomic  2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 ...
  ..- 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  -7.5 -7.6 -7.6 -7.6 NA -7.6 -7.4 -6.9 -6.7 -6.3 ...
  ..- 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  75.4 75 75 75.5 76.5 78.1 79 78.1 78 78 ...
  ..- attr(*, "varnames")= chr "rH"
  ..- attr(*, "units")= chr "-"
 $ Press_MDS : atomic  98.1 98.1 98.1 98.1 98.1 ...
  ..- 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 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,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 1 and 2986 will not be filled!
Initialized variable 'NEE' with 13277 real gaps for gap filling of all 14582 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
............................................................
.............................................................
..........................11834
Look up table with window size of 14 days with Rg VPD Tair
...........................673
Look up table with window size of 7 days with Rg
....................1605
Mean diurnal course with window size of 0 days: .
....263
Mean diurnal course with window size of 1 days: .
..133
Mean diurnal course with window size of 2 days: .
49
Look up table with window size of 21 days with Rg VPD Tair
3
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: .
22
Finished gap filling of 'NEE' in 11 seconds. Artificial gaps filled: 14582, real gaps filled: 13277, unfilled (long) gaps: 2986.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 2986 will not be filled!
Initialized variable 'LE' with 13104 real gaps for gap filling of all 14582 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
............................................................
.............................................................
..........................11922
Look up table with window size of 14 days with Rg VPD Tair
..........................664
Look up table with window size of 7 days with Rg
...................1528
Mean diurnal course with window size of 0 days: .
....264
Mean diurnal course with window size of 1 days: .
..133
Mean diurnal course with window size of 2 days: .
51
Look up table with window size of 21 days with Rg VPD Tair
2
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: .
18
Finished gap filling of 'LE' in 16 seconds. Artificial gaps filled: 14582, real gaps filled: 13104, unfilled (long) gaps: 2986.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 2986 will not be filled!
Initialized variable 'H' with 12865 real gaps for gap filling of all 14582 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
............................................................
.............................................................
..........................12050
Look up table with window size of 14 days with Rg VPD Tair
.........................611
Look up table with window size of 7 days with Rg
...................1452
Mean diurnal course with window size of 0 days: .
....271
Mean diurnal course with window size of 1 days: .
.131
Mean diurnal course with window size of 2 days: .
50
Look up table with window size of 21 days with Rg VPD Tair
2
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
1
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: .
14
Finished gap filling of 'H' in 12 seconds. Artificial gaps filled: 14582, real gaps filled: 12865, unfilled (long) gaps: 2986.
Initialized variable 'Rg' with 497 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: .
....320
Mean diurnal course with window size of 1 days: .
.166
Mean diurnal course with window size of 2 days: .
9
Mean diurnal course with window size of 7 days: .
2
Finished gap filling of 'Rg' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 497, unfilled (long) gaps: 0.
Initialized variable 'VPD' with 1161 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
...........1110
Mean diurnal course with window size of 0 days: .
21
Mean diurnal course with window size of 1 days: .
30
Finished gap filling of 'VPD' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 1161, unfilled (long) gaps: 0.
Initialized variable 'rH' with 486 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
....465
Mean diurnal course with window size of 0 days: .
12
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: 486, unfilled (long) gaps: 0.
Initialized variable 'Tair' with 712 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
.......682
Mean diurnal course with window size of 0 days: .
10
Mean diurnal course with window size of 1 days: .
20
Finished gap filling of 'Tair' in 0 seconds. Artificial gaps filled: 17568, real gaps filled: 712, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 3082 will not be filled!
Initialized variable 'Ustar_MDS' with 14239 real gaps for gap filling of all 14486 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
............................................................
.............................................................
.........................11443
Look up table with window size of 14 days with Rg VPD Tair
..............................866
Look up table with window size of 7 days with Rg
.....................1704
Mean diurnal course with window size of 0 days: .
....246
Mean diurnal course with window size of 1 days: .
..178
Mean diurnal course with window size of 2 days: .
39
Look up table with window size of 21 days with Rg VPD Tair
2
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
1
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: .
7
Finished gap filling of 'Ustar_MDS' in 10 seconds. Artificial gaps filled: 14486, real gaps filled: 14239, unfilled (long) gaps: 3082.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 3082 will not be filled!
Initialized variable 'Tau_MDS' with 14239 real gaps for gap filling of all 14486 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
............................................................
.............................................................
.........................11443
Look up table with window size of 14 days with Rg VPD Tair
..............................866
Look up table with window size of 7 days with Rg
.....................1704
Mean diurnal course with window size of 0 days: .
....246
Mean diurnal course with window size of 1 days: .
..178
Mean diurnal course with window size of 2 days: .
39
Look up table with window size of 21 days with Rg VPD Tair
2
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
1
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: .
7
Finished gap filling of 'Tau_MDS' in 10 seconds. Artificial gaps filled: 14486, real gaps filled: 14239, unfilled (long) gaps: 3082.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 3082 will not be filled!
Initialized variable 'ws_MDS' with 14256 real gaps for gap filling of all 14486 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
............................................................
.............................................................
.........................11393
Look up table with window size of 14 days with Rg VPD Tair
..............................918
Look up table with window size of 7 days with Rg
.....................1703
Mean diurnal course with window size of 0 days: .
....249
Mean diurnal course with window size of 1 days: .
..169
Mean diurnal course with window size of 2 days: .
37
Look up table with window size of 21 days with Rg VPD Tair
3
Look up table with window size of 28 days with Rg VPD Tair
1
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
2
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: .
11
Finished gap filling of 'ws_MDS' in 11 seconds. Artificial gaps filled: 14486, real gaps filled: 14256, unfilled (long) gaps: 3082.
Initialized variable 'Press_MDS' with 1310 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
............................................................
.............................................................
........................................................15834
Look up table with window size of 14 days with Rg VPD Tair
.................87
Look up table with window size of 7 days with Rg
................1150
Mean diurnal course with window size of 0 days: .
....460
Mean diurnal course with window size of 1 days: .
36
Mean diurnal course with window size of 2 days: .
0
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 'Press_MDS' in 14 seconds. Artificial gaps filled: 17568, real gaps filled: 1310, unfilled (long) gaps: 0.
Initialized variable 'PAR_MDS' with 497 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
............................................................
.............................................................
........................................................15919
Look up table with window size of 14 days with Rg VPD Tair
................21
Look up table with window size of 7 days with Rg
................1131
Mean diurnal course with window size of 0 days: .
....320
Mean diurnal course with window size of 1 days: .
.166
Mean diurnal course with window size of 2 days: .
9
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 'PAR_MDS' in 13 seconds. Artificial gaps filled: 17568, real gaps filled: 497, unfilled (long) gaps: 0.
Initialized variable 'Precip_MDS' with 773 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
............................................................
.............................................................
........................................................15874
Look up table with window size of 14 days with Rg VPD Tair
................63
Look up table with window size of 7 days with Rg
................1134
Mean diurnal course with window size of 0 days: .
....484
Mean diurnal course with window size of 1 days: .
12
Mean diurnal course with window size of 2 days: .
0
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 'Precip_MDS' in 13 seconds. Artificial gaps filled: 17568, real gaps filled: 773, unfilled (long) gaps: 0.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 3457 will not be filled!
Initialized variable 'TW_0_MDS' with 5029 real gaps for gap filling of all 14111 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
............................................................
.............................................................
......................11953
Look up table with window size of 14 days with Rg VPD Tair
.....................102
Look up table with window size of 7 days with Rg
....................996
Mean diurnal course with window size of 0 days: .
..........428
Mean diurnal course with window size of 1 days: .
......5
Mean diurnal course with window size of 2 days: .
......7
Look up table with window size of 21 days with Rg VPD Tair
......291
Look up table with window size of 28 days with Rg VPD Tair
...173
Look up table with window size of 35 days with Rg VPD Tair
.22
Look up table with window size of 42 days with Rg VPD Tair
.19
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
39
Look up table with window size of 28 days with Rg
5
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
Mean diurnal course with window size of 14 days: .
12
Mean diurnal course with window size of 21 days: .
8
Finished gap filling of 'TW_0_MDS' in 10 seconds. Artificial gaps filled: 14111, real gaps filled: 5029, unfilled (long) gaps: 3457.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 3082 will not be filled!
Initialized variable 'CO2c_MDS' with 14173 real gaps for gap filling of all 14486 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
............................................................
.............................................................
.........................11481
Look up table with window size of 14 days with Rg VPD Tair
..............................869
Look up table with window size of 7 days with Rg
.....................1668
Mean diurnal course with window size of 0 days: .
....254
Mean diurnal course with window size of 1 days: .
..165
Mean diurnal course with window size of 2 days: .
40
Look up table with window size of 21 days with Rg VPD Tair
2
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
1
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: .
6
Finished gap filling of 'CO2c_MDS' in 10 seconds. Artificial gaps filled: 14486, real gaps filled: 14173, unfilled (long) gaps: 3082.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 4244 will not be filled!
Initialized variable 'TW1_MDS' with 6041 real gaps for gap filling of all 13324 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
............................................................
.............................................................
..............11099
Look up table with window size of 14 days with Rg VPD Tair
......................110
Look up table with window size of 7 days with Rg
.....................902
Mean diurnal course with window size of 0 days: .
............424
Mean diurnal course with window size of 1 days: .
.......4
Mean diurnal course with window size of 2 days: .
.......0
Look up table with window size of 21 days with Rg VPD Tair
.......248
Look up table with window size of 28 days with Rg VPD Tair
.....248
Look up table with window size of 35 days with Rg VPD Tair
..29
Look up table with window size of 42 days with Rg VPD Tair
..15
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
..207
Look up table with window size of 21 days with Rg
16
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: .
5
Mean diurnal course with window size of 14 days: .
11
Mean diurnal course with window size of 21 days: .
5
Finished gap filling of 'TW1_MDS' in 10 seconds. Artificial gaps filled: 13324, real gaps filled: 6041, unfilled (long) gaps: 4244.
Warning in sFillInit(Var.s, QFVar.s, QFValue.n, FillAll.b) :
  sMDSGapFill::: The long gap between position 1 and 3878 will not be filled!
Initialized variable 'CO20_MDS' with 5412 real gaps for gap filling of all 13690 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
............................................................
.............................................................
.................11610
Look up table with window size of 14 days with Rg VPD Tair
....................86
Look up table with window size of 7 days with Rg
...................942
Mean diurnal course with window size of 0 days: .
..........420
Mean diurnal course with window size of 1 days: .
......10
Mean diurnal course with window size of 2 days: .
......7
Look up table with window size of 21 days with Rg VPD Tair
......291
Look up table with window size of 28 days with Rg VPD Tair
...173
Look up table with window size of 35 days with Rg VPD Tair
.21
Look up table with window size of 42 days with Rg VPD Tair
.19
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
.44
Look up table with window size of 21 days with Rg
39
Look up table with window size of 28 days with Rg
6
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
Mean diurnal course with window size of 14 days: .
12
Mean diurnal course with window size of 21 days: .
8
Finished gap filling of 'CO20_MDS' in 9 seconds. Artificial gaps filled: 13690, real gaps filled: 5412, unfilled (long) gaps: 3878.
Saved plot to: ./Mendota_2016_FP_NEE.pdf
Saved plot to: ./Mendota_2016_Flux_NEE.pdf
Saved plot to: ./Mendota_2016_FP_LE.pdf
Saved plot to: ./Mendota_2016_Flux_LE.pdf
Saved plot to: ./Mendota_2016_FP_H.pdf
Saved plot to: ./Mendota_2016_Flux_H.pdf
Saved plot to: ./Mendota_2016_FP_Rg.pdf
Saved plot to: ./Mendota_2016_Flux_Rg.pdf
Saved plot to: ./Mendota_2016_FP_VPD.pdf
Saved plot to: ./Mendota_2016_Flux_VPD.pdf
Saved plot to: ./Mendota_2016_FP_rH.pdf
Saved plot to: ./Mendota_2016_Flux_rH.pdf
Saved plot to: ./Mendota_2016_FP_Tair.pdf
Saved plot to: ./Mendota_2016_Flux_Tair.pdf
Saved plot to: ./Mendota_2016_FP_Ustar_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_Ustar_MDS.pdf
Saved plot to: ./Mendota_2016_FP_Tau_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_Tau_MDS.pdf
Saved plot to: ./Mendota_2016_FP_ws_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_ws_MDS.pdf
Saved plot to: ./Mendota_2016_FP_Press_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_Press_MDS.pdf
Saved plot to: ./Mendota_2016_FP_PAR_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_PAR_MDS.pdf
Saved plot to: ./Mendota_2016_FP_Precip_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_Precip_MDS.pdf
Saved plot to: ./Mendota_2016_FP_TW_0_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_TW_0_MDS.pdf
Saved plot to: ./Mendota_2016_FP_CO2c_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_CO2c_MDS.pdf
Saved plot to: ./Mendota_2016_FP_TW1_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_TW1_MDS.pdf
Saved plot to: ./Mendota_2016_FP_CO20_MDS.pdf
Saved plot to: ./Mendota_2016_Flux_CO20_MDS.pdf
Saved plot to: ./Mendota_2016_FP_NEE_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_2016_DC_NEE_f.pdf
Saved plot to: ./Mendota_2016_DSumU_NEE_f.pdf
Saved plot to: ./Mendota_2016_Flux_NEE_f.pdf
Saved plot to: ./Mendota_2016_FP_LE_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_2016_DC_LE_f.pdf
Saved plot to: ./Mendota_2016_DSumU_LE_f.pdf
Saved plot to: ./Mendota_2016_Flux_LE_f.pdf
Saved plot to: ./Mendota_2016_FP_H_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_2016_DC_H_f.pdf
Saved plot to: ./Mendota_2016_DSumU_H_f.pdf
Saved plot to: ./Mendota_2016_Flux_H_f.pdf
Saved plot to: ./Mendota_2016_FP_Rg_f.pdf
Saved plot to: ./Mendota_2016_DC_Rg_f.pdf
Saved plot to: ./Mendota_2016_DSum_Rg_f.pdf
Saved plot to: ./Mendota_2016_Flux_Rg_f.pdf
Saved plot to: ./Mendota_2016_FP_VPD_f.pdf
Saved plot to: ./Mendota_2016_DC_VPD_f.pdf
Saved plot to: ./Mendota_2016_DSum_VPD_f.pdf
Saved plot to: ./Mendota_2016_Flux_VPD_f.pdf
Saved plot to: ./Mendota_2016_FP_rH_f.pdf
Saved plot to: ./Mendota_2016_DC_rH_f.pdf
Saved plot to: ./Mendota_2016_DSum_rH_f.pdf
Saved plot to: ./Mendota_2016_Flux_rH_f.pdf
Saved plot to: ./Mendota_2016_FP_Tair_f.pdf
Saved plot to: ./Mendota_2016_DC_Tair_f.pdf
Saved plot to: ./Mendota_2016_DSum_Tair_f.pdf
Saved plot to: ./Mendota_2016_Flux_Tair_f.pdf
Saved plot to: ./Mendota_2016_FP_Ustar_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_2016_DC_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_Ustar_MDS_f.pdf
Saved plot to: ./Mendota_2016_FP_Tau_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_2016_DC_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_Tau_MDS_f.pdf
Saved plot to: ./Mendota_2016_FP_ws_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_2016_DC_ws_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_ws_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_ws_MDS_f.pdf
Saved plot to: ./Mendota_2016_FP_Press_MDS_f.pdf
Saved plot to: ./Mendota_2016_DC_Press_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_Press_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_Press_MDS_f.pdf
Saved plot to: ./Mendota_2016_FP_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2016_DC_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_PAR_MDS_f.pdf
Saved plot to: ./Mendota_2016_FP_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2016_DC_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_Precip_MDS_f.pdf
Saved plot to: ./Mendota_2016_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_2016_DC_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_TW_0_MDS_f.pdf
Saved plot to: ./Mendota_2016_FP_CO2c_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_2016_DC_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_CO2c_MDS_f.pdf
Saved plot to: ./Mendota_2016_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!
Saved plot to: ./Mendota_2016_DC_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_TW1_MDS_f.pdf
Saved plot to: ./Mendota_2016_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!
Saved plot to: ./Mendota_2016_DC_CO20_MDS_f.pdf
Saved plot to: ./Mendota_2016_DSumU_CO20_MDS_f.pdf
Saved plot to: ./Mendota_2016_Flux_CO20_MDS_f.pdf
Number of NA convertered to '-9999': 870117
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 
191.523   0.680 192.566 
