[1] "2025-04-30 00:31:24 MDT"
[1] "1509"   "151030" "d303"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/151030a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 54360    63
[1] 54360
[1] 54360
[1] "testing skipping spike filter"
[1] 54360
[1] 54360
[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 00:31:27 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.884, ave o2scale2 = 0.788"
[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 0 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "3 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.884, ave o2scale2 = 0.788"
[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 0 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "2 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 00:31:27 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 00:31:27 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 00:31:37 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 00:31:38 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "TEMP: 902 0 TRUE"
[1] "Removed 566 row(s) with -999.99 for a Licor jog SD"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 00:31:40 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 384.68 O2 = -522.3"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.5"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.11 O2 = -572.1"
[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 = 0.945  co2off = 396.66 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  230  239 0.1608523 0.1671115 0.1646776   2   8.327805 368.9574 1.132331
3    2  240  249 0.1678071 0.1740664 0.1716325   2 -14.468398 488.5801 1.132277
4    5  250  259 0.1747618 0.1810210 0.1799780  NA  -4.552844 437.2378 1.132130
     jfcv2        co2slp      o2slp       co2sd     o2sd
2 1.270527  0.0018535877  0.1097316 0.005408372 1.026899
3 1.270478  0.0001315526  0.1466048 0.002255682 6.829346
4 1.270323 -0.0010612177 -1.3193686 0.000751301 2.965739
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 398.327  co2l1 = 0.944 co2l0 = 0"
[1] "co2l0 = -194.63  co2l1 = 0.212"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "22 out of 32 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "10 out of 282 1-min values rejected as stack air"
[1] "10 out of 46 Line 1 1-min values rejected as stack air"
[1] "0 out of 236 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "making html"