[1] "2025-04-29 18:39:09 MDT"
[1] "1304"   "130505" "d125"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130505a.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] "2025-04-29 18:39:14 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.767, ave o2scale2 = 0.769"
[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] "112 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.767, ave o2scale2 = 0.769"
[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] "112 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 18:39:14 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 18:39:14 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 18:39:31 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 18:39:33 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 112 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 1231 row(s) with low FLWTA"
[1] "TEMP: 93 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 18:39:43 MDT"
[1] "Reading in cylinder log"
Read 78 records
[1] "Finding cylinder IDs"
Read 536 records
[1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -448"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.97 O2 = -542.7"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.33 O2 = -625.2"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2"
[1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.347  co2off = 383.45 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.01 minutes"
[1] "Average Cal: 7.01 minutes"
[1] "Shortest Cal: 3 minutes"
[1] "Longest Cal: 9.01 minutes"
[1] "Removed 1 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      2
[1] "calperiods"
  type posi pose      timei      timee      timea grp    co2sig     o2sig
2    2   70   79 0.04850385 0.05476380 0.05232959   2 -14.29485  96.56312
3    4   80   89 0.05545920 0.06171875 0.05928425   2  75.19076 -61.88726
     jfcv1    jfcv2     co2slp      o2slp      co2sd     o2sd
2 1.316780 1.314308 0.01126111  0.7126785 0.02872973 2.550821
3 1.316699 1.314213 0.02097161 -0.7870532 0.05406789 2.313703
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 379.267  co2l1 = 0.347 co2l0 = 0"
[1] "co2l0 = -98.31  co2l1 = 0.226"
[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 67 1-min values rejected as stack air"
[1] "0 out of 0 Line 1 1-min values rejected as stack air"
[1] "0 out of 67 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"