[1] "2025-04-30 01:14:57 MDT"
[1] "1601"   "160209" "d040"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/160209a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 52415    63
[1] 52415
[1] 52415
[1] "testing skipping spike filter"
[1] 52415
[1] 52415
[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 01:14:59 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.902, ave o2scale2 = 0.793"
[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 1 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "130 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.902, ave o2scale2 = 0.793"
[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 1 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "130 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 01:14:59 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 01:14:59 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 01:15:04 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 01:15:06 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 130 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 5 row(s) with low FLSP"
[1] "Removed 21 row(s) with high TFRIDGE"
[1] "Removed 2 row(s) with variable TFCELL"
[1] "TEMP: 713 0 TRUE"
[1] "Removed 426 row(s) with -999.99 for a Licor jog SD"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 01:15:07 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 384.67 O2 = -522.5"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.3"
[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 = 0.943  co2off = 398.85 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: 9.02 minutes"
[1] "Longest Cal: 9.02 minutes"
[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  236  245 0.9634624 0.9697254 0.9672898   2   4.403344 -272.1855
3    2  246  255 0.9704207 0.9766837 0.9742491   2 -18.390523 -159.2952
     jfcv1    jfcv2       co2slp      o2slp       co2sd     o2sd
2 1.092007 1.240883 -0.001567677 -0.8983120 0.004232633 3.346948
3 1.092208 1.241080 -0.001608726  0.9079155 0.007362348 2.611775
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 402.027  co2l1 = 0.944 co2l0 = 0"
[1] "co2l0 = -55.22  co2l1 = 0.224"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "46 out of 85 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "39 out of 260 1-min values rejected as stack air"
[1] "39 out of 260 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"