[1] "2025-04-30 00:23:47 MDT"
[1] "1508"   "151012" "d285"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/151012a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 38724    63
[1] 38724
[1] 38724
[1] "testing skipping spike filter"
[1] 38724
[1] 38724
[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 00:23:49 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.866, ave o2scale2 = 0.77"
[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] "56 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.866, ave o2scale2 = 0.77"
[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] "56 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-30 00:23:49 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-30 00:23:49 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-30 00:23:55 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-30 00:23:56 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 57 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 551 row(s) with low FLSP"
[1] "TEMP: 37 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-30 00:23:58 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 = 406.19 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 = 0.938  co2off = 374.67 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 8.02 minutes"
[1] "Average Cal: 8.27 minutes"
[1] "Shortest Cal: 8.01 minutes"
[1] "Longest Cal: 9.03 minutes"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      1
[2,]        2      4
[1] "calperiods"
  type posi pose      timei      timee      timea grp     co2sig    o2sig
1    4    1    9 0.08603148 0.09159884 0.08951234   1 22.1598214 364.6917
2    2   10   18 0.29478356 0.30034795 0.29826152   3 -0.7291696 477.7845
3    4   19   28 0.30104554 0.30731296 0.30487607   3 22.3002266 368.6477
4    3   29   37 0.30800828 0.31357584 0.31287915   3  8.5765714 466.2023
     jfcv1    jfcv2      co2slp     o2slp       co2sd      o2sd
1 1.156712 1.298615 0.006681203  9.219194 0.015425072 21.307084
2 1.156769 1.298963 0.002382452  2.756664 0.005688955 10.093409
3 1.156777 1.298780 0.005148063  5.982367 0.013458556 15.099405
4 1.156868 1.298632 0.003021192 -9.092418 0.006927774  9.134153
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 385.406  co2l1 = 0.934 co2l0 = 0.017"
[1] "co2l0 = -202.48  co2l1 = 0.234"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "NO SAMPLE PERIODS"
[1] "JGOFS data found"
[1] "making html"