Error in re-building vignettes:
  ...
New sEddyProc class for site 'DE-Geb'
Converted time format 'YDH' to POSIX with column name 'DateTime'.
Estimated UStar threshold of:  0.16 by using controls:
                       taClasses                    UstarClasses 
                              7                              20 
                          swThr            minRecordsWithinTemp 
                             10                             100 
         minRecordsWithinSeason            minRecordsWithinYear 
                            160                            3000 
isUsingOneBigSeasonOnFewRecords 
                              1 
Ustar filtering (u * Th_1 = 0.137666666666667), marked 29% of the data as gap
Initialized variable 'NEE' with 25111 real gaps for gap filling.
Full MDS algorithm for gap filling of 'NEE.Ustar_WithUstar_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Finished gap filling of 'NEE' in 45 seconds. Artificial gaps filled: 52608, real gaps filled: 25111, unfilled (long) gaps: 0.

Estimated UStar distribution of:
       uStar       10%       90%
1 0.1578889 0.1432771 0.1924472 
by using  30 bootstrap samples and controls:
                       taClasses                    UstarClasses 
                              7                              20 
                          swThr            minRecordsWithinTemp 
                             10                             100 
         minRecordsWithinSeason            minRecordsWithinYear 
                            160                            3000 
isUsingOneBigSeasonOnFewRecords 
                              1 
Ustar filtering (u * Th_1 = 0.137666666666667), marked 29% of the data as gap
Initialized variable 'NEE' with 25111 real gaps for gap filling.
Full MDS algorithm for gap filling of 'NEE.Ustar_uStar_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
.............................................................
.............................................................
............22442
Look up table with window size of 14 days with Rg VPD Tair
..........................1555
Look up table with window size of 7 days with Rg
...........1075
Mean diurnal course with window size of 0 days: .
9
Mean diurnal course with window size of 1 days: .
9
Mean diurnal course with window size of 2 days: .
4
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
1
Look up table with window size of 42 days with Rg VPD Tair
10
Look up table with window size of 49 days with Rg VPD Tair
1
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
5
Finished gap filling of 'NEE' in 47 seconds. Artificial gaps filled: 52608, real gaps filled: 25111, unfilled (long) gaps: 0.
Ustar filtering (u * Th_1 = 0.0942154545454545), marked 25% of the data as gap
Initialized variable 'NEE' with 23764 real gaps for gap filling.
Full MDS algorithm for gap filling of 'NEE.Ustar_U10_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
.............................................................
..........................................................21378
Look up table with window size of 14 days with Rg VPD Tair
.......................1425
Look up table with window size of 7 days with Rg
.........922
Mean diurnal course with window size of 0 days: .
9
Mean diurnal course with window size of 1 days: .
9
Mean diurnal course with window size of 2 days: .
4
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
1
Look up table with window size of 42 days with Rg VPD Tair
10
Look up table with window size of 49 days with Rg VPD Tair
1
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
5
Finished gap filling of 'NEE' in 44 seconds. Artificial gaps filled: 52608, real gaps filled: 23764, unfilled (long) gaps: 0.
Ustar filtering (u * Th_1 = 0.189253333333333), marked 34% of the data as gap
Initialized variable 'NEE' with 26477 real gaps for gap filling.
Full MDS algorithm for gap filling of 'NEE.Ustar_U90_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
.............................................................
.............................................................
.........................23474
Look up table with window size of 14 days with Rg VPD Tair
..............................1599
Look up table with window size of 7 days with Rg
..............1364
Mean diurnal course with window size of 0 days: .
9
Mean diurnal course with window size of 1 days: .
10
Mean diurnal course with window size of 2 days: .
4
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
1
Look up table with window size of 42 days with Rg VPD Tair
10
Look up table with window size of 49 days with Rg VPD Tair
1
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
5
Finished gap filling of 'NEE' in 54 seconds. Artificial gaps filled: 52608, real gaps filled: 26477, unfilled (long) gaps: 0.
Initialized variable 'Tair' with 0 real gaps for gap filling.
Limited MDS algorithm for gap filling of 'Tair' with LUT(Rg only) and MDC.
Finished gap filling of 'Tair' in 0 seconds. Artificial gaps filled: 52608, real gaps filled: 0, unfilled (long) gaps: 0.
Start flux partitioning for variable NEE_U10_f with temperature Tair_f.
Estimate of the temperature sensitivity E_0 from short term data: 186.24.
Regression of reference temperature R_ref for 269 periods.
Start flux partitioning for variable NEE_U90_f with temperature Tair_f.
Estimate of the temperature sensitivity E_0 from short term data: 180.46.
Regression of reference temperature R_ref for 260 periods.
New sEddyProc class for site 'DE-Geb'
Estimated UStar threshold of:  0.34 by using controls:
                       taClasses                    UstarClasses 
                              7                              20 
                          swThr            minRecordsWithinTemp 
                             10                             100 
         minRecordsWithinSeason            minRecordsWithinYear 
                            160                            3000 
isUsingOneBigSeasonOnFewRecords 
                              1 

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Converted time format 'YDH' to POSIX with column name 'DateTime'.
New sEddyProc class for site 'DE-Tha'
Initialized variable 'LE' with 6998 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'LE.QF_0' with LUT(Rg, Tsoil, Step) and MDC.
Look up table with window size of 7 days with Rg Tsoil Step
............................................................
.............................................................
........................................................16806
Look up table with window size of 14 days with Rg Tsoil Step
.......352
Look up table with window size of 7 days with Rg
...84
Mean diurnal course with window size of 0 days: .
..167
Mean diurnal course with window size of 1 days: .
.9
Mean diurnal course with window size of 2 days: .
.9
Look up table with window size of 21 days with Rg Tsoil Step
80
Look up table with window size of 28 days with Rg Tsoil Step
4
Look up table with window size of 35 days with Rg Tsoil Step
0
Look up table with window size of 42 days with Rg Tsoil Step
0
Look up table with window size of 49 days with Rg Tsoil Step
0
Look up table with window size of 56 days with Rg Tsoil Step
0
Look up table with window size of 63 days with Rg Tsoil Step
0
Look up table with window size of 70 days with Rg Tsoil Step
0
Look up table with window size of 14 days with Rg
8
Look up table with window size of 21 days with Rg
1
Finished gap filling of 'LE' in 34 seconds. Artificial gaps filled: 17520, real gaps filled: 6998, unfilled (long) gaps: 0.
Initialized variable 'NEE' with 6257 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Look up table with window size of 3 days with Rg rH Tair Tsoil Step
............................................................
.............................................................
........................................................15756
Look up table with window size of 6 days with Tair VPD Step
.................1164
Mean diurnal course with window size of 3 days: .
......149
New sEddyProc class for site 'DE-Tha'
Initialized variable 'NEE' with 6257 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................16587
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
.....184
Mean diurnal course with window size of 0 days: .
...133
Mean diurnal course with window size of 1 days: .
..43
Mean diurnal course with window size of 2 days: .
.1
Look up table with window size of 21 days with Rg VPD Tair
.100
Look up table with window size of 28 days with Rg VPD Tair
27
Look up table with window size of 35 days with Rg VPD Tair
10
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
3
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
3
Look up table with window size of 70 days with Rg VPD Tair
20
Look up table with window size of 14 days with Rg
28
Converted time format 'YDH' to POSIX with column name 'DateTime'.
New sEddyProc class for site 'DE-Tha'
Initialized variable 'NEE' with 6257 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................16587
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
.....184
Mean diurnal course with window size of 0 days: .
...133
Mean diurnal course with window size of 1 days: .
..43
Mean diurnal course with window size of 2 days: .
.1
Look up table with window size of 21 days with Rg VPD Tair
.100
Look up table with window size of 28 days with Rg VPD Tair
27
Look up table with window size of 35 days with Rg VPD Tair
10
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
3
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
3
Look up table with window size of 70 days with Rg VPD Tair
20
Look up table with window size of 14 days with Rg
28
Finished gap filling of 'NEE' in 28 seconds. Artificial gaps filled: 17520, real gaps filled: 6257, unfilled (long) gaps: 0.
New sEddyProc class for site 'DE-Tha'
Ustar filtering (u * Th_1 = 0.46), marked 27% of the data as gap
Initialized variable 'NEE' with 8220 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE.Ustar_WithUstar_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................16394
Look up table with window size of 14 days with Rg VPD Tair
...........408
Look up table with window size of 7 days with Rg
.......301
Mean diurnal course with window size of 0 days: .
....101
Mean diurnal course with window size of 1 days: .
...64
Mean diurnal course with window size of 2 days: .
..12
Look up table with window size of 21 days with Rg VPD Tair
..95
Look up table with window size of 28 days with Rg VPD Tair
.31
Look up table with window size of 35 days with Rg VPD Tair
.53
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
3
Look up table with window size of 56 days with Rg VPD Tair
2
Look up table with window size of 63 days with Rg VPD Tair
5
Look up table with window size of 70 days with Rg VPD Tair
23
Look up table with window size of 14 days with Rg
28
Finished gap filling of 'NEE' in 26 seconds. Artificial gaps filled: 17520, real gaps filled: 8220, unfilled (long) gaps: 0.
New sEddyProc class for site 'DE-Tha'
Estimated UStar threshold of:  0.42 by using controls:
                       taClasses                    UstarClasses 
                              7                              20 
                          swThr            minRecordsWithinTemp 
                             10                             100 
         minRecordsWithinSeason            minRecordsWithinYear 
                            160                            3000 
isUsingOneBigSeasonOnFewRecords 
                              1 
Saved plot to: /tmp/Rtmpbyn36K/DE-Tha_1998_NEEvsUStar_1998006_none.pdf
Ustar filtering (u * Th_1 = 0.41625), marked 24% of the data as gap
Initialized variable 'NEE' with 7798 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE.Ustar_WithUstar_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................16493
Look up table with window size of 14 days with Rg VPD Tair
..........394
Look up table with window size of 7 days with Rg
......224
Mean diurnal course with window size of 0 days: .
....104
Mean diurnal course with window size of 1 days: .
...63
Mean diurnal course with window size of 2 days: .
..10
Look up table with window size of 21 days with Rg VPD Tair
..89
Look up table with window size of 28 days with Rg VPD Tair
.31
Look up table with window size of 35 days with Rg VPD Tair
.51
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
3
Look up table with window size of 56 days with Rg VPD Tair
2
Look up table with window size of 63 days with Rg VPD Tair
5
Look up table with window size of 70 days with Rg VPD Tair
23
Look up table with window size of 14 days with Rg
28
Finished gap filling of 'NEE' in 27 seconds. Artificial gaps filled: 17520, real gaps filled: 7798, unfilled (long) gaps: 0.
Loaded file /tmp/Rtmpbyn36K/REddyProcExamples/Example_DETha98.txt with the following variables (units):
 *** Year(-) DoY(-) Hour(-) NEE(umolm-2s-1) LE(Wm-2) H(Wm-2) Rg(Wm-2) Tair(degC) Tsoil(degC) rH(%) VPD(hPa) Ustar(ms-1)
Number of '-9999' convertered to NA: 11657
Converted time format 'YDH' to POSIX with column name 'DateTime'.
New sEddyProc class for site 'DE-Tha'

Estimated UStar distribution of:
     uStar        5%       50%       95%
1 0.41625 0.3762929 0.4496429 0.6290729 
by using  100 bootstrap samples and controls:
                       taClasses                    UstarClasses 
                              7                              20 
                          swThr            minRecordsWithinTemp 
                             10                             100 
         minRecordsWithinSeason            minRecordsWithinYear 
                            160                            3000 
isUsingOneBigSeasonOnFewRecords 
                              1 
Ustar filtering (u * Th_1 = 0.376292857142857), marked 21% of the data as gap
Initialized variable 'NEE' with 7384 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE.Ustar_U05_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................16531
Look up table with window size of 14 days with Rg VPD Tair
.........362
Look up table with window size of 7 days with Rg
......218
Mean diurnal course with window size of 0 days: .
....111
Mean diurnal course with window size of 1 days: .
..65
Mean diurnal course with window size of 2 days: .
..1
Look up table with window size of 21 days with Rg VPD Tair
..89
Look up table with window size of 28 days with Rg VPD Tair
.34
Look up table with window size of 35 days with Rg VPD Tair
.48
Look up table with window size of 42 days with Rg VPD Tair
0
Look up table with window size of 49 days with Rg VPD Tair
3
Look up table with window size of 56 days with Rg VPD Tair
2
Look up table with window size of 63 days with Rg VPD Tair
5
Look up table with window size of 70 days with Rg VPD Tair
23
Look up table with window size of 14 days with Rg
28
Finished gap filling of 'NEE' in 25 seconds. Artificial gaps filled: 17520, real gaps filled: 7384, unfilled (long) gaps: 0.
Ustar filtering (u * Th_1 = 0.449642857142857), marked 26% of the data as gap
Initialized variable 'NEE' with 8127 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE.Ustar_U50_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............................................................
........................................................16399
Look up table with window size of 14 days with Rg VPD Tair
...........406
Look up table with window size of 7 days with Rg
.......298
Mean diurnal course with window size of 0 days: .
....101
Mean diurnal course with window size of 1 days: .
...64
Mean diurnal course with window size of 2 days: .
..12
Look up table with window size of 21 days with Rg VPD Tair
..95
Look up table with window size of 28 days with Rg VPD Tair
.31
Look up table with window size of 35 days with Rg VPD Tair
.53
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
3
Look up table with window size of 56 days with Rg VPD Tair
2
Look up table with window size of 63 days with Rg VPD Tair
5
Look up table with window size of 70 days with Rg VPD Tair
23
Look up table with window size of 14 days with Rg
28
Finished gap filling of 'NEE' in 28 seconds. Artificial gaps filled: 17520, real gaps filled: 8127, unfilled (long) gaps: 0.
Ustar filtering (u * Th_1 = 0.629072916666667), marked 38% of the data as gap
Initialized variable 'NEE' with 9570 real gaps for gap filling of all 17520 values (to estimate uncertainties).
Full MDS algorithm for gap filling of 'NEE.Ustar_U95_fqc_0' with LUT(Rg, VPD, Tair) and MDC.
Look up table with window size of 7 days with Rg VPD Tair
............................................................
.............Killed