[1] "2025-04-29 16:32:20 MDT"
[1] "1206"   "120609" "d161"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120609y.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 85168    63
[1] 85168
[1] 85168
[1] "testing skipping spike filter"
[1] 85168
[1] 85168
[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 16:32:24 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.788, ave o2scale2 = 0.795"
[1] "Removing 46 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 41 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 43 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 44 MR FC 2 jog(s) with SP SD > 1000"
[1] "574 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.788, ave o2scale2 = 0.795"
[1] "Removing 47 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 42 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 43 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 45 RC FC 2 jog(s) with SP SD > 1000"
[1] "576 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 16:32:24 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 16:32:24 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 16:32:36 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 16:32:37 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 576 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 840 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 16:32:50 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 = -450.5"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.95 O2 = -543.5"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.9"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2"
[1] "position 5 cylinder CC339495 description: WT1 CO2 = 394.28 O2 = -550.6"
[1] "position 6 cylinder CC339490 description: WT2 CO2 = 396.41 O2 = -582.4"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.982  co2off = 374.7 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 7.01 minutes"
[1] "Average Cal: 6.67 minutes"
[1] "Shortest Cal: 2.01 minutes"
[1] "Longest Cal: 9.02 minutes"
[1] "Removed 4 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      1
[2,]        2      3
[1] "calperiods"
  type posi pose     timei     timee     timea grp    co2sig     o2sig    jfcv1
4    4  600  607 0.7046895 0.7095625 0.7078214   1  18.33309 -70.53809 1.269842
7    4  698  704 0.8174576 0.8237190 0.8214928   2  18.41471 -99.30633 1.271959
8    2  705  713 0.8244150 0.8306775 0.8284901   2 -13.19145  49.04403 1.271794
     jfcv2       co2slp     o2slp       co2sd     o2sd
4 1.259160  0.003991540 -3.511739 0.008146582 18.94609
7 1.261457 -0.003425824 -1.853712 0.011079048  7.01365
8 1.261247  0.010635038  8.438524 0.025966235 24.41512
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 387.294  co2l1 = 0.981 co2l0 = 0"
[1] "co2l0 = -88.69  co2l1 = 0.241"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "3 out of 20 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "17 out of 745 1-min values rejected as stack air"
[1] "17 out of 745 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"