[1] "2025-04-29 20:45:40 MDT" [1] "1402" "140306" "d065" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140306a.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 20:45:44 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.832, ave o2scale2 = 0.757" [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] "284 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.832, ave o2scale2 = 0.757" [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] "285 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:45:44 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:45:44 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:46:01 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:46:02 MDT" [1] "reading in recalculated plot titles" [1] "Removed 285 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1150 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:46:06 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.62 O2 = -475.9" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -633.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2" [1] "position 5 cylinder CB09982 description: WT1 CO2 = 479.38 O2 = -1131.8" [1] "position 6 cylinder CB10019 description: WT2 CO2 = 407.52 O2 = -753.5" [1] "Nominal linear calibrations:" [1] "co2scl = 0.449 co2off = 392.14 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.01 minutes" [1] "Shortest Cal: 5.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 7 [4,] 8 9 [5,] 10 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 224 233 0.1576992 0.1639595 0.1615250 3 -4.519281 302.6950 1.208163 3 4 234 243 0.1646549 0.1709144 0.1684800 3 57.589445 164.9948 1.207845 5 3 251 260 0.1785683 0.1848314 0.1837883 3 36.383805 241.8134 1.208045 9 4 512 521 0.3663802 0.3726400 0.3702057 2 57.406055 162.1969 1.199317 10 2 522 529 0.3740337 0.3795978 0.3773955 2 -4.024648 284.7075 1.199654 12 4 722 726 0.5820250 0.5855023 0.5848067 2 57.439585 156.2402 1.203637 13 3 727 734 0.5889799 0.5952391 0.5948914 2 36.312990 237.0782 1.203799 15 4 912 916 0.7837732 0.7900328 0.7881783 2 57.360684 158.7037 1.198267 16 2 917 922 0.7928183 0.7969909 0.7959478 2 -3.960658 306.5648 1.197952 18 2 1142 1150 0.9931468 0.9987147 0.9966254 1 -3.951009 300.7535 1.197074 jfcv2 co2slp o2slp co2sd o2sd 2 1.326829 -0.0034869131 0.7746337 0.009372559 2.9808041 3 1.326491 0.0095661606 -0.7738899 0.028987209 3.2416482 5 1.326734 -0.0020986535 0.6959740 0.005861824 1.1557917 9 1.317723 0.0010915001 2.9010754 0.007079384 8.4307239 10 1.318091 -0.0005476624 4.0555191 0.004349230 26.8187824 12 1.322511 0.0188103429 0.5566370 0.021251989 0.5575415 13 1.322611 -0.0017503785 -4.4669023 0.005977225 3.1634464 15 1.316440 0.0034249949 0.1957820 0.013132972 0.7488568 16 1.316366 0.0003885785 -1.5757532 0.001012030 2.0648749 18 1.315545 -0.0040840321 3.5548457 0.009613997 8.2499027 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.598 co2l1 = 0.446 co2l0 = 0.012" [1] "co2l0 = -149.79 co2l1 = 0.227" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "119 out of 390 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "271 out of 1026 1-min values rejected as stack air" [1] "238 out of 968 Line 1 1-min values rejected as stack air" [1] "33 out of 58 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"