[1] "2025-04-30 03:06:10 MDT"
[1] "1706"   "170719" "d200"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170719a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 15420    63
[1] 15420
[1] 15420
[1] "testing skipping spike filter"
[1] 15420
[1] 15420
[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 03:06:11 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.863, ave o2scale2 = 0.957"
[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 0 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "15 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.863, ave o2scale2 = 0.957"
[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 0 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "15 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 03:06:11 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 03:06:11 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 03:06:13 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 03:06:14 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 15 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 241 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 03:06:15 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CC339495 description: HS CO2 = 396.87 O2 = -495.4"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CC339490 description: LS CO2 = 409.04 O2 = -699.1"
[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 CB10100 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 4.514  co2off = 426.33 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 10.23 minutes"
[1] "Average Cal: 10.22 minutes"
[1] "Shortest Cal: 10.21 minutes"
[1] "Longest Cal: 10.24 minutes"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      3
[1] "calperiods"
  type posi pose     timei     timee     timea grp    co2sig    o2sig    jfcv1
2    3   10   19 0.8058906 0.8129888 0.8118073   3 -7.008812 332.5231 1.155373
3    2   20   29 0.8137765 0.8208830 0.8181136   3 -6.230148 353.2108 1.155834
4    4   30   39 0.8216707 0.8287594 0.8260027   3 -3.531906 188.1273 1.156352
5    5   40   49 0.8295487 0.8366573 0.8354726  NA -4.664469 224.7500 1.156874
     jfcv2        co2slp     o2slp       co2sd      o2sd
2 1.044930 -0.0006375756 -8.443124 0.002163001 13.802943
3 1.045070 -0.0025777560 -1.358001 0.007321304  8.494456
4 1.045252 -0.0031842826 -1.397399 0.008883673  8.794722
5 1.045360 -0.0035624246 -1.862042 0.002872621  6.146464
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 425.014  co2l1 = 4.522 co2l0 = -0.453"
[1] "co2l0 = -166.73  co2l1 = 0.22"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "12 out of 89 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "77 out of 179 1-min values rejected as stack air"
[1] "77 out of 179 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"