[1] "2025-04-30 02:13:59 MDT"
[1] "1701"   "170111" "d011"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170111a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 33895    63
[1] 33895
[1] 33895
[1] "testing skipping spike filter"
[1] 33895
[1] 33895
[1] "recalculating jog averages"
[1] "recalculating jog sds"
[1] "recalculating jog slopes"
[1] "Parsing MR flags"
[1] "Calculating derived concentration values"
[1] "2025-04-30 02:14:00 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 1.049, ave o2scale2 = 0.855"
[1] "Removing 0 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 3 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "128 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 1.049, ave o2scale2 = 0.855"
[1] "Removing 0 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 3 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "128 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 02:14:00 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 02:14:00 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 02:14:03 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 02:14:04 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 128 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 23 row(s) with variable TFCELL"
[1] "TEMP: 412 380 TRUE"
[1] "Removed 380 row(s) with -999.99 for a Licor jog SD"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 02:14:06 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 384.67 O2 = -523"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 406.17 O2 = -648"
[1] "position 4 cylinder CB08905 description: LT CO2 = 404.34 O2 = -653.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07556 description: WT2 CO2 = 398.16 O2 = -1524.9"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.965  co2off = 408.52 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 7.81 minutes"
[1] "Average Cal: 7.81 minutes"
[1] "Shortest Cal: 7.23 minutes"
[1] "Longest Cal: 8.39 minutes"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      2
[1] "calperiods"
  type posi pose     timei     timee     timea grp    co2sig    o2sig     jfcv1
2    4    5   13 0.9107677 0.9165956 0.9144074   2 -13.52299 107.9774 0.9545554
3    2   14   21 0.9173293 0.9223472 0.9205507   2 -35.82620 232.6294 0.9545771
     jfcv2        co2slp       o2slp      co2sd     o2sd
2 1.171345 -0.0003576354 -2.67747144 0.00187063 9.888962
3 1.171282 -0.0017787315 -0.03234329 0.00494934 3.509418
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 419.209  co2l1 = 0.964 co2l0 = 0"
[1] "co2l0 = -138.07  co2l1 = 0.202"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "0 out of 1 5-value periods OK w SD < 0.1 ppm"
[1] "0 out of 8 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "8 out of 8 1-min values rejected as stack air"
[1] "8 out of 8 Line 1 1-min values rejected as stack air"
[1] "0 out of 0 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"