[1] "2025-04-29 23:10:45 MDT"
[1] "1502"   "150218" "d049"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/150218a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 85500    63
[1] 85500
[1] 85500
[1] "testing skipping spike filter"
[1] 85500
[1] 85500
[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 23:10:49 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.843, ave o2scale2 = 0.759"
[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] "24 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.843, ave o2scale2 = 0.759"
[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 0 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 1 RC FC 2 jog(s) with SP SD > 1000"
[1] "26 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 23:10:49 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 23:10:49 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 23:11:09 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 23:11:10 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 26 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 1310 row(s) with low FLSP"
[1] "TEMP: 88 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 23:11:15 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 = -477.8"
[1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1"
[1] "position 3 cylinder CC339490 description: LS CO2 = 404.24 O2 = -635.3"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CB10019 description: WT2 CO2 = 407.52 O2 = -753.5"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.936  co2off = 385.87 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 8.02 minutes"
[1] "Average Cal: 80.91 minutes"
[1] "Shortest Cal: 7.02 minutes"
[1] "Longest Cal: 300.6 minutes"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      2
[2,]        3      4
[3,]        5      6
[4,]        7      8
[1] "calperiods"
  type posi pose     timei     timee     timea grp     co2sig    o2sig    jfcv1
1    4    1    9 0.1695799 0.1751470 0.1730580   2  14.423205 135.3087 1.186919
2    2   10   27 0.1758426 0.3839051 0.2928340   2 -15.130691 280.1005 1.186420
3    4   28   37 0.3846007 0.3908634 0.3884287   2  14.335930 130.8836 1.185908
4    3   38   46 0.3915590 0.3971262 0.3964307   2   2.657866 227.4416 1.185923
5    4   47   54 0.5860835 0.5909560 0.5892151   2  14.284302 131.9584 1.187164
6    2   55   71 0.5916516 0.8004028 0.7164844   2 -15.210592 278.3676 1.187436
7    4   72   80 0.8010995 0.8066633 0.8045770   2  14.279045 135.0927 1.187496
8    3   81   88 0.8157084 0.8205810 0.8202312   2   2.598417 228.2448 1.187698
     jfcv2        co2slp        o2slp       co2sd     o2sd
1 1.319153  2.975162e-03 -0.297563237 0.006582975 1.757050
2 1.318502 -3.597096e-04 -0.002201944 0.055111627 3.603148
3 1.317840  2.386747e-03 -0.263072505 0.007257573 1.703572
4 1.317930  2.030734e-03 -1.146560379 0.005518250 1.213345
5 1.319154  3.267426e-03 -0.500895732 0.006304812 2.464238
6 1.319610 -2.277955e-05 -0.004203034 0.009313215 3.325736
7 1.319841  2.728390e-03  1.392137208 0.007016323 6.438475
8 1.319967  1.614501e-03 -7.923871374 0.003439128 5.644345
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 390.831  co2l1 = 0.936 co2l0 = 0"
[1] "co2l0 = -142.62  co2l1 = 0.217"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "NO SAMPLE PERIODS"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"