[1] "2025-04-30 00:01:13 MDT"
[1] "1505"   "150520" "d140"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/150520a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 47160    63
[1] 47160
[1] 47160
[1] "testing skipping spike filter"
[1] 47160
[1] 47160
[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 00:01:16 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.842, ave o2scale2 = 0.756"
[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 2 MR FC 2 jog(s) with SP SD > 1000"
[1] "25 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.842, ave o2scale2 = 0.756"
[1] "Removing 2 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 2 RC FC 2 jog(s) with SP SD > 1000"
[1] "23 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 00:01:16 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 00:01:16 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 00:01:19 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 00:01:20 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 23 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 761 0 TRUE"
[1] "Removed 648 row(s) with -999.99 for a Licor jog SD"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 00:01:22 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 = -522.1"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 406.19 O2 = -648.6"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.11 O2 = -572.2"
[1] "position 5 cylinder CB09982 description: WT1 CO2 = 479.38 O2 = -1131.8"
[1] "position 6 cylinder CB10019 description: WT2 CO2 = 407.52 O2 = -753.5"
[1] "Nominal linear calibrations:"
[1] "co2scl = 1  co2off = 461.99 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 10.14 minutes"
[1] "Average Cal: 10.14 minutes"
[1] "Shortest Cal: 7.32 minutes"
[1] "Longest Cal: 12.96 minutes"
[1] "Removed 1 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      1
[1] "calperiods"
  type posi pose     timei     timee     timea grp  co2sig    o2sig   jfcv1
2    4  102  107 0.1027131 0.1077942 0.1064236   1 -66.551 378.5401 1.18554
     jfcv2      co2slp    o2slp       co2sd     o2sd
2 1.322464 0.001735713 5.594258 0.003075864 15.75144
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 406.189  co2l1 = 0 co2l0 = 0"
[1] "co2l0 = 0  co2l1 = 0"
[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 99 1-min values rejected as stack air"
[1] "0 out of 99 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"