[1] "2025-04-29 21:33:07 MDT" [1] "1406" "140714" "d195" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140714a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85920 63 [1] 85920 [1] 85920 [1] "testing skipping spike filter" [1] 85920 [1] 85920 [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 21:33:11 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.828, ave o2scale2 = 0.745" [1] "Removing 1 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 1 MR FC 2 jog(s) with SP SD > 1000" [1] "10 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.828, ave o2scale2 = 0.745" [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] "10 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:33:11 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:33:11 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:33:30 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:33:32 MDT" [1] "reading in recalculated plot titles" [1] "Removed 10 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "Removed 1 row(s) with LiCO2A spikes in them" [1] "TEMP: 1420 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:33:36 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 = -476.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.7" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.4" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2" [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 = 0.472 co2off = 385.71 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 9.03 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.08 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 5 [3,] 6 7 [4,] 9 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 209 218 0.1457906 0.1520533 0.1496190 2 39.30666 136.3660 1.204038 3 2 219 228 0.1527488 0.1590120 0.1565767 2 -19.17794 282.9298 1.203692 5 2 508 517 0.3547269 0.3609899 0.3585530 3 -19.02102 282.9284 1.211964 6 4 518 527 0.3616856 0.3679605 0.3655185 3 39.49277 129.4579 1.212140 7 3 528 537 0.3686558 0.3749183 0.3738753 3 19.66022 221.5301 1.212448 9 4 808 817 0.5635116 0.5697743 0.5673390 2 39.45662 133.1228 1.214961 10 2 818 827 0.5704698 0.5767326 0.5742980 2 -19.02153 283.0818 1.214644 11 5 828 837 0.5774279 0.5836908 0.5826475 NA 17.17234 201.5418 1.214625 13 2 1105 1114 0.7725313 0.7787913 0.7763568 3 -19.15874 277.9755 1.208163 14 4 1115 1124 0.7794869 0.7857500 0.7833130 3 39.30810 138.8916 1.207829 15 3 1125 1134 0.7864455 0.7927083 0.7916623 3 19.47163 218.2533 1.207798 17 4 1394 1403 0.9812148 0.9875174 0.9850672 2 39.10506 138.2080 1.201027 18 2 1404 1413 0.9882176 0.9945185 0.9920680 2 -19.36591 278.2825 1.200959 jfcv2 co2slp o2slp co2sd o2sd 2 1.337856 -0.0025106078 0.6462052 0.007075407 3.775909 3 1.337498 -0.0067573847 -0.4235749 0.019828675 2.649108 5 1.346749 0.0012013940 1.5355753 0.005129435 4.508400 6 1.346931 0.0037365664 -1.3849934 0.011343842 7.059077 7 1.347328 0.0011281885 5.5943096 0.006194666 7.773229 9 1.349765 -0.0026164463 -0.7728467 0.007271520 4.330172 10 1.349428 -0.0006773779 0.9916800 0.007805819 2.842799 11 1.349378 -0.0301447949 -2.3863882 0.021345786 3.142360 13 1.342021 -0.0039124670 1.1703212 0.011593103 5.114876 14 1.341631 0.0037314866 2.4449779 0.013942481 6.411764 15 1.341611 -0.0058810884 -3.6021410 0.015472954 4.814562 17 1.334286 0.0005301839 1.2932837 0.003628846 5.006693 18 1.334210 0.0000997928 0.6097100 0.004506188 3.398560 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 385.674 co2l1 = 0.472 co2l0 = 0.084" [1] "co2l0 = -143.35 co2l1 = 0.219" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "154 out of 413 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "259 out of 1238 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "259 out of 1238 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"