[1] "2025-04-29 22:43:38 MDT"
[1] "1411"   "141220" "d354"  
Read 2 records
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141220a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 83385    63
[1] 83385
[1] 83385
[1] "testing skipping spike filter"
[1] 83385
[1] 83385
[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 22:43:42 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.833, ave o2scale2 = 0.753"
[1] "Removing 1 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 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "51 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.833, ave o2scale2 = 0.753"
[1] "Removing 1 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 3 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] "53 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 22:43:43 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 22:43:43 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 22:43:54 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 22:43:56 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 53 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 275 manually filtered row(s) from a screenall period"
[1] "Removed 951 row(s) with low FLWTA"
[1] "TEMP: 109 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 22:43:58 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CC339495 description: HS CO2 = 376.63 O2 = -477.5"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.3"
[1] "position 3 cylinder CC339490 description: LS CO2 = 404.24 O2 = -635.1"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.932  co2off = 383.49 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.01 minutes"
[1] "Average Cal: 9.01 minutes"
[1] "Shortest Cal: 9.01 minutes"
[1] "Longest Cal: 9.01 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    jfcv1
2    4   20   29 0.9305470 0.9368067 0.9343721   2  18.10772 150.0401 1.212613
3    2   30   39 0.9375023 0.9437616 0.9413270   2 -11.55116 284.9246 1.212683
     jfcv2       co2slp     o2slp       co2sd     o2sd
2 1.344353  0.000558611 -5.746096 0.001538567 16.48703
3 1.344581 -0.002377833  1.180570 0.009266391 11.15106
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 387.38  co2l1 = 0.931 co2l0 = 0"
[1] "co2l0 = -149.16  co2l1 = 0.236"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "10 out of 10 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "0 out of 82 1-min values rejected as stack air"
[1] "0 out of 82 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"