[1] "2025-04-29 21:23:29 MDT"
[1] "1406"   "140627" "d178"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140627a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 53348    63
[1] 53348
[1] 53348
[1] "testing skipping spike filter"
[1] 53348
[1] 53348
[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 21:23:31 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.821, ave o2scale2 = 0.741"
[1] "Removing 1 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 2 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 2 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "8 MR delta diff NA values ( most likely because WTDIFF > 1000 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.821, ave o2scale2 = 0.741"
[1] "Removing 1 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 2 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 2 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "8 RC delta diff NA values ( most likely because WTDIFF > 1000 )"
[1] "2025-04-29 21:23:32 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 21:23:32 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 21:23:38 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 21:23:39 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 8 row(s) with NAs in them ( most likely because WTDIFF > 1000 )"
[1] "Removed 378 row(s) with low FLWTA"
[1] "Removed 31 row(s) with variable TFCELL"
[1] "TEMP: 471 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 21:23:40 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 = -476.5"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.7"
[1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -634.4"
[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 = 0.469  co2off = 367.87 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.02 minutes"
[1] "Average Cal: 7.26 minutes"
[1] "Shortest Cal: 2 minutes"
[1] "Longest Cal: 9.02 minutes"
[1] "Removed 1 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        2      3
[1] "calperiods"
  type posi pose     timei     timee     timea grp    co2sig    o2sig    jfcv1
2    5    4   13 0.6734832 0.6797457 0.6787010  NA 26.361094 198.3733 1.222405
4    4  274  283 0.8613963 0.8676557 0.8652216   2 49.076109 143.6189 1.222536
5    2  284  293 0.8683510 0.8746160 0.8721803   2 -9.902492 279.3105 1.222279
     jfcv2       co2slp     o2slp       co2sd      o2sd
2 1.357401  0.007802422 -9.754362 0.005524272 20.849839
4 1.354202 -0.004603011 -1.580895 0.011737158  8.520789
5 1.353963 -0.002813882 -1.376824 0.009786643 15.528498
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 381.256  co2l1 = 0.468 co2l0 = 0"
[1] "co2l0 = -147.37  co2l1 = 0.235"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "9 out of 73 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "64 out of 413 1-min values rejected as stack air"
[1] "64 out of 413 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"