[1] "2025-04-30 01:21:08 MDT"
[1] "1602"   "160223" "d054"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/160223a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 86220    63
[1] 86220
[1] 86220
[1] "testing skipping spike filter"
[1] 86220
[1] 86220
[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 01:21:12 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.899, ave o2scale2 = 0.793"
[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 0 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000"
[1] "96 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.899, ave o2scale2 = 0.793"
[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 1 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "99 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 01:21:12 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 01:21:12 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 01:21:30 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 01:21:32 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 99 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 1070 row(s) with low FLWTA"
[1] "TEMP: 267 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 01:21:37 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 384.67 O2 = -522.5"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.3"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.12 O2 = -572.1"
[1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.947  co2off = 403.82 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 8.51 minutes"
[1] "Average Cal: 8.51 minutes"
[1] "Shortest Cal: 8.02 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
2    4  244  250 0.9786191 0.9841864 0.9822391   2   6.497762 -266.3724
3    2  251  258 0.9855774 0.9918363 0.9891704   2 -16.266177 -148.6960
     jfcv1    jfcv2       co2slp      o2slp       co2sd     o2sd
2 1.111742 1.260345  0.000497933 -3.3835864 0.001914378 9.026752
3 1.111591 1.260218 -0.001014287  0.4084447 0.004381320 5.088234
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 400.042  co2l1 = 0.945 co2l0 = 0"
[1] "co2l0 = -58.97  co2l1 = 0.215"
[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 245 1-min values rejected as stack air"
[1] "0 out of 245 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] "making html"