[1] "2025-04-30 01:02:16 MDT"
[1] "1601"   "160106" "d006"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/160106a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 41820    63
[1] 23059
[1] 23059
[1] "testing skipping spike filter"
[1] 23059
[1] 23059
[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 01:02:18 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.88, ave o2scale2 = 0.782"
[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] "318 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.88, ave o2scale2 = 0.782"
[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] "317 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 01:02:18 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 01:02:18 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 01:02:26 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 01:02:27 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 317 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 378 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 01:02:28 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 = -522.4"
[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 = 394.12 O2 = -572.1"
[1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.949  co2off = 402.96 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.02 minutes"
[1] "Average Cal: 9.02 minutes"
[1] "Shortest Cal: 9.01 minutes"
[1] "Longest Cal: 9.02 minutes"
[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    jfcv1
2    2  254  263 0.1808589 0.1871179 0.1846837   3 -16.479414 492.6860 1.137530
3    4  264  273 0.1878133 0.1940761 0.1916418   3   6.213164 376.4900 1.137503
4    3  274  283 0.1947725 0.2010369 0.1999918   3  -7.354125 477.7107 1.137694
     jfcv2        co2slp     o2slp       co2sd     o2sd
2 1.280041  0.0015238214 1.3503488 0.003951144 3.524266
3 1.279982 -0.0007358928 1.1269467 0.005202585 4.383704
4 1.280194 -0.0010069418 0.8076773 0.002933413 2.328636
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 400.288  co2l1 = 0.948 co2l0 = -0.011"
[1] "co2l0 = -199.57  co2l1 = 0.221"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "0 out of 0 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "0 out of 336 1-min values rejected as stack air"
[1] "0 out of 336 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"