[1] "2025-04-29 22:09:25 MDT"
[1] "1409"   "141007" "d280"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141007a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 10080    63
[1] 10080
[1] 10080
[1] "testing skipping spike filter"
[1] 10080
[1] 10080
[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 22:09:25 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.823, ave o2scale2 = 0.742"
[1] "Removing 2 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 0 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 1 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 2 MR FC 2 jog(s) with SP SD > 1000"
[1] "24 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.823, ave o2scale2 = 0.742"
[1] "Removing 1 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 1 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 2 RC FC 2 jog(s) with SP SD > 1000"
[1] "22 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 22:09:25 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 22:09:25 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 22:09:28 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 22:09:28 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 22 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 128 row(s) with low FLSP"
[1] "TEMP: 16 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 22:09:29 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 = -477.1"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.5"
[1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.8"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2"
[1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.479  co2off = 401.9 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 7.01 minutes"
[1] "Average Cal: 7.01 minutes"
[1] "Shortest Cal: 6.01 minutes"
[1] "Longest Cal: 8.01 minutes"
[1] "Removed 1 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      1
[1] "calperiods"
  type posi pose     timei     timee     timea grp   co2sig    o2sig    jfcv1
1    4    1    7 0.9643507 0.9685234 0.9671325   1 25.15496 119.6889 1.216512
     jfcv2      co2slp    o2slp      co2sd     o2sd
1 1.349559 0.008862769 2.991129 0.01725366 7.989497
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 404.231  co2l1 = 0 co2l0 = 0"
[1] "co2l0 = 0  co2l1 = 0"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "NO SAMPLE PERIODS"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"