[1] "2025-04-29 17:13:30 MDT"
[1] "1212"   "121106" "d311"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/121106a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 38294    63
[1] 38294
[1] 38294
[1] "testing skipping spike filter"
[1] 38294
[1] 38294
[1] "recalculating jog averages"
[1] "recalculating jog sds"
[1] "recalculating jog slopes"
[1] "Parsing MR flags"
[1] "Calculating derived concentration values"
[1] "2025-04-29 17:13:32 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.766, ave o2scale2 = 0.777"
[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] "2 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.766, ave o2scale2 = 0.777"
[1] "Removing 0 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 1 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 1 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "4 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 17:13:32 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 17:13:32 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 17:13:35 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 17:13:36 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 4 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 339 row(s) with low FLSP"
[1] "TEMP: 294 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 17:13:38 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -449.4"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.96 O2 = -543.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.1"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2"
[1] "position 5 cylinder CB09982 description: WT1 CO2 = 479.38 O2 = -1131.8"
[1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.412  co2off = 382.91 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.02 minutes"
[1] "Average Cal: 9.02 minutes"
[1] "Shortest Cal: 9.01 minutes"
[1] "Longest Cal: 9.02 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
3    2  112  121 0.07961241 0.08587234 0.08343811   3 -11.68699 200.50077
4    4  122  131 0.08656768 0.09283032 0.09039630   3  63.78069  39.60966
5    3  132  141 0.09352824 0.09979239 0.09874646   3  38.01838 115.54755
     jfcv1    jfcv2       co2slp     o2slp       co2sd     o2sd
3 1.308878 1.291517 -0.006838484  1.612710 0.019569685 9.511844
4 1.308523 1.291276 -0.002993975 -2.772579 0.009240765 7.271542
5 1.308422 1.291200 -0.022715700  0.800742 0.058604488 2.122167
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 379.171  co2l1 = 0.412 co2l0 = 0.074"
[1] "co2l0 = -121.61  co2l1 = 0.222"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "7 out of 35 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "28 out of 250 1-min values rejected as stack air"
[1] "0 out of 222 Line 1 1-min values rejected as stack air"
[1] "28 out of 28 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"