[1] "2025-04-29 18:17:38 MDT"
[1] "1303"   "130320" "d079"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130320a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 21720    63
[1] 21720
[1] 21720
[1] "testing skipping spike filter"
[1] 21720
[1] 21720
[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 18:17:39 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.787, ave o2scale2 = 0.797"
[1] "Removing 0 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 1 MR FC 2 jog(s) with SP SD > 1000"
[1] "65 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.787, ave o2scale2 = 0.797"
[1] "Removing 0 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 1 RC FC 2 jog(s) with SP SD > 1000"
[1] "65 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 18:17:39 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 18:17:39 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 18:17:42 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 18:17:43 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 65 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 6 row(s) with variable TFCELL"
[1] "TEMP: 290 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 18:17:44 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -448.3"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.97 O2 = -542.8"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.33 O2 = -625.5"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.408  co2off = 382.34 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 8.02 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    jfcv1
3    4  243  251 0.9646670 0.9702337 0.9681450   2 70.310295  45.55221 1.273118
4    2  252  261 0.9709306 0.9771898 0.9747556   2 -5.894031 194.94491 1.273543
     jfcv2       co2slp      o2slp      co2sd     o2sd
3 1.258564 0.0068037260 -0.4834665 0.01585279  1.73453
4 1.259051 0.0002781006 -2.9777487 0.01367157 11.47413
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 376.712  co2l1 = 0.407 co2l0 = 0"
[1] "co2l0 = -123.27  co2l1 = 0.24"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "5 out of 5 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "0 out of 241 1-min values rejected as stack air"
[1] "0 out of 0 Line 1 1-min values rejected as stack air"
[1] "0 out of 241 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "making html"