[1] "2025-04-29 21:10:03 MDT"
[1] "1404"   "140430" "d120"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140430a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 19833    63
[1] 19833
[1] 19833
[1] "testing skipping spike filter"
[1] 19833
[1] 19833
[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 21:10:04 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.824, ave o2scale2 = 0.749"
[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] "6 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.824, ave o2scale2 = 0.749"
[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] "6 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 21:10:04 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 21:10:04 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 21:10:07 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 21:10:08 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 7 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 323 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 21:10:09 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CC339495 description: HS CO2 = 376.62 O2 = -476.2"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -541.8"
[1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -634.1"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2"
[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 = 0.423  co2off = 361.12 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 8.01 minutes"
[1] "Average Cal: 8.01 minutes"
[1] "Shortest Cal: 7.01 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      2
[1] "calperiods"
  type posi pose      timei      timee      timea grp    co2sig    o2sig
2    4   49   58 0.03451968 0.04077894 0.03834465   2 74.705992 125.2662
3    2   59   67 0.04147454 0.04703825 0.04495174   2  9.322777 271.2179
     jfcv1    jfcv2       co2slp     o2slp      co2sd     o2sd
2 1.213570 1.333490 -0.003090074 1.5551103 0.01165719 4.241629
3 1.213685 1.333574 -0.007038637 0.1416961 0.01740046 3.332133
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 372.684  co2l1 = 0.422 co2l0 = 0"
[1] "co2l0 = -140.95  co2l1 = 0.219"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "32 out of 197 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "165 out of 272 1-min values rejected as stack air"
[1] "126 out of 233 Line 1 1-min values rejected as stack air"
[1] "39 out of 39 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"