[1] "2025-04-30 00:34:59 MDT"
[1] "1509"   "151107" "d311"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/151107a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 46680    63
[1] 46680
[1] 46680
[1] "testing skipping spike filter"
[1] 46680
[1] 46680
[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 00:35:01 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.883, ave o2scale2 = 0.785"
[1] "Removing 0 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] "21 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.883, ave o2scale2 = 0.785"
[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] "21 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 00:35:01 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 00:35:01 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 00:35:05 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 00:35:06 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 21 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 684 row(s) with low FLSP"
[1] "TEMP: 72 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 00:35:07 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 384.68 O2 = -522.3"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.4"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.11 O2 = -572.1"
[1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.946  co2off = 399.28 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.02 minutes"
[1] "Average Cal: 103.51 minutes"
[1] "Shortest Cal: 6.01 minutes"
[1] "Longest Cal: 299.54 minutes"
[1] "Removed 1 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      2
[2,]        3      5
[1] "calperiods"
  type posi pose     timei     timee     timea grp     co2sig    o2sig    jfcv1
2    2    8   17 0.4734062 0.4796690 0.4772348   2 -15.181148 486.0243 1.141339
3    4   18   35 0.4803646 0.6814016 0.5934037   2   7.493699 371.3755 1.136993
4    2   36   53 0.6820971 0.8901111 0.7990627   3 -15.402551 485.0332 1.131830
5    4   54   63 0.8908065 0.8970655 0.8946314   3   7.370484 372.9425 1.130801
6    3   64   72 0.8977611 0.9033249 0.9026295   3  -6.250964 467.2639 1.131263
     jfcv2        co2slp        o2slp       co2sd     o2sd
2 1.285068 -0.0004658925  0.457436817 0.003020196 6.928066
3 1.279849 -0.0005802404  0.009540484 0.084582280 5.544316
4 1.273548 -0.0001962742 -0.008475250 0.030202340 5.161696
5 1.272205  0.0036358864 -0.370861860 0.010069333 4.037732
6 1.272525  0.0029754607 -4.075883360 0.007807820 4.179892
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 399.15  co2l1 = 0.945 co2l0 = -0.007"
[1] "co2l0 = -200.62  co2l1 = 0.227"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "NO SAMPLE PERIODS"
[1] "JGOFS data found"
[1] "making html"