[1] "2025-04-29 17:13:10 MDT"
[1] "1212"   "121105" "d310"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/121105a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 65760    63
[1] 65760
[1] 65760
[1] "testing skipping spike filter"
[1] 65760
[1] 65760
[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 17:13:13 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.763, ave o2scale2 = 0.773"
[1] "Removing 2 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 1 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 1 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "91 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.763, ave o2scale2 = 0.773"
[1] "Removing 2 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 2 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] "91 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 17:13:14 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 17:13:14 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 17:13:22 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 17:13:24 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 91 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 664 row(s) with low FLWTA"
[1] "TEMP: 340 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 17:13:26 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 = 0.408  co2off = 363.72 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.01 minutes"
[1] "Average Cal: 7.68 minutes"
[1] "Shortest Cal: 5.01 minutes"
[1] "Longest Cal: 9.02 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
3    4  159  168 0.8708451 0.8771053 0.8746708   2  64.16973  47.20957 1.309423
4    2  169  174 0.8778009 0.8812785 0.8802350   2 -11.86312 204.07635 1.309464
5    5  175  184 0.8847625 0.8910270 0.8899823  NA  27.41288  94.57431 1.309277
     jfcv2      co2slp      o2slp      co2sd     o2sd
3 1.293143 -0.01997096  1.1814690 0.05725071 4.889951
4 1.293153 -0.03830005 -0.3157700 0.05194280 6.154142
5 1.292979  0.10480023  0.2620066 0.07442299 2.210400
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 379.151  co2l1 = 0.408 co2l0 = 0"
[1] "co2l0 = -123.22  co2l1 = 0.228"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "25 out of 55 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "30 out of 290 1-min values rejected as stack air"
[1] "2 out of 262 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"