[1] "2025-04-30 02:48:02 MDT"
[1] "1704"   "170427" "d117"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170427a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 84300    63
[1] 84300
[1] 84300
[1] "testing skipping spike filter"
[1] 84300
[1] 84300
[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 02:48:06 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 1.142, ave o2scale2 = 0.882"
[1] "Removing 3 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 8 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "287 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 1.142, ave o2scale2 = 0.882"
[1] "Removing 3 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 1 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 9 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "288 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 02:48:07 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 02:48:07 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 02:48:27 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 02:48:29 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 288 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 1116 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 02:48:32 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CC339495 description: HS CO2 = 396.87 O2 = -495.4"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CC339490 description: LS CO2 = 409.04 O2 = -699.1"
[1] "position 4 cylinder CB08905 description: LT CO2 = 404.34 O2 = -653.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CB10100 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 4.492  co2off = 378.12 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 7.19 minutes"
[1] "Average Cal: 6.96 minutes"
[1] "Shortest Cal: 2.05 minutes"
[1] "Longest Cal: 8.22 minutes"
[1] "Removed 11 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      1
[2,]        2      2
[3,]        3      3
[1] "calperiods"
   type posi pose     timei     timee     timea grp   co2sig    o2sig     jfcv1
3     2  158  164 0.1395670 0.1438337 0.1424113   1 5.007625 352.7063 0.8958205
6     2  384  391 0.3403138 0.3453023 0.3435158   1 5.029771 341.6249 0.8891694
11    2  617  625 0.5539444 0.5596427 0.5575092   1 5.047964 376.0223 0.8761594
      jfcv2        co2slp     o2slp        co2sd     o2sd
3  1.134311 -0.0009765108 -1.660599 0.0016729699 17.87521
6  1.134914 -0.0002294339  6.869072 0.0005764475 24.76490
11 1.134487  0.0012882293  8.075855 0.0029261432 26.21512
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 396.866  co2l1 = 0 co2l0 = 0"
[1] "co2l0 = -89.05  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 964 1-min values rejected as stack air"
[1] "0 out of 964 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"