[1] "2025-04-29 18:17:24 MDT"
[1] "1303"   "130318" "d077"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130318a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 19049    63
[1] 19049
[1] 19049
[1] "testing skipping spike filter"
[1] 19049
[1] 19049
[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 18:17:25 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.77, ave o2scale2 = 0.776"
[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] "3 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.77, ave o2scale2 = 0.776"
[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] "3 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 18:17:25 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 18:17:25 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 18:17:30 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 18:17:31 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 4 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 313 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 18:17:35 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 = -448.4"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.97 O2 = -542.8"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.33 O2 = -625.5"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.397  co2off = 390.77 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 8.02 minutes"
[1] "Average Cal: 8.27 minutes"
[1] "Shortest Cal: 8.01 minutes"
[1] "Longest Cal: 9.01 minutes"
[1] "Removed 1 calibration row(s) with high SD"
[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
2    2   24   33 0.01670778 0.02296759 0.02053346   3 -8.125664 206.88410
3    4   34   42 0.02366314 0.02922685 0.02714034   3 70.196393  43.80684
5    3   52   60 0.03828704 0.04385460 0.04315657   3 43.302804 117.45410
     jfcv1    jfcv2       co2slp      o2slp      co2sd     o2sd
2 1.298834 1.288112 -0.002035171 -0.5694198 0.01233995 2.368608
3 1.298709 1.288006  0.009891664  0.1458631 0.02400726 2.013352
5 1.298795 1.288013 -0.003788860 -2.0270824 0.01348019 2.037116
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 377.601  co2l1 = 0.397 co2l0 = 0.049"
[1] "co2l0 = -122.09  co2l1 = 0.22"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "5 out of 5 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "0 out of 264 1-min values rejected as stack air"
[1] "0 out of 0 Line 1 1-min values rejected as stack air"
[1] "0 out of 264 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "making html"