[1] "2025-04-29 20:18:24 MDT" [1] "1401" "140119" "d019" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140119a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85860 63 [1] 85860 [1] 85860 [1] "testing skipping spike filter" [1] 85860 [1] 85860 [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 20:18:28 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.808, ave o2scale2 = 0.734" [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] "22 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.808, ave o2scale2 = 0.734" [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] "22 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:18:28 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:18:28 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:18:45 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:18:47 MDT" [1] "reading in recalculated plot titles" [1] "Removed 22 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1408 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:18:55 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 = -475.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.7" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.08 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 = 0.454 co2off = 379.55 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.07 minutes" [1] "Average Cal: 9.05 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 6 [3,] 7 8 [4,] 9 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 160 169 0.1112650 0.1175278 0.1150938 2 54.806828 159.7632 1.239350 3 2 170 179 0.1182239 0.1244905 0.1220530 2 -6.063516 304.3598 1.239506 5 2 460 469 0.3200199 0.3262800 0.3238452 3 -6.039484 302.6844 1.239158 6 4 470 479 0.3269755 0.3332384 0.3308018 3 54.734289 155.7946 1.239157 7 5 480 489 0.3339339 0.3401968 0.3391536 NA 29.670437 223.2409 1.239296 8 3 490 499 0.3408924 0.3471522 0.3461090 3 34.005836 239.3487 1.239294 10 4 738 747 0.5284387 0.5347408 0.5322900 2 54.754836 158.5413 1.238046 11 2 748 757 0.5354413 0.5417442 0.5392921 2 -6.194266 302.2460 1.238096 13 2 1034 1043 0.7371643 0.7434653 0.7410146 3 -6.196008 304.1190 1.236808 14 4 1044 1053 0.7441655 0.7504677 0.7480168 3 54.713609 163.0899 1.236692 15 3 1054 1063 0.7511683 0.7574730 0.7564211 3 33.886430 244.8231 1.236795 17 4 1332 1341 0.9459105 0.9522130 0.9497618 2 54.742578 162.8062 1.235509 18 2 1342 1351 0.9529132 0.9592158 0.9567646 2 -6.248742 300.7936 1.235540 19 5 1352 1361 0.9599163 0.9662245 0.9651742 NA 29.253125 221.5323 1.235191 jfcv2 co2slp o2slp co2sd o2sd 2 1.363273 -0.0016183082 0.5024390 0.009894068 2.5028052 3 1.363464 -0.0044944981 2.8689113 0.011456232 7.4726083 5 1.362933 0.0006088920 4.5951974 0.005094394 11.7784917 6 1.362922 0.0011769694 -1.1225840 0.008737232 5.6862456 7 1.363067 -0.0370709382 2.1919943 0.026251339 4.2675304 8 1.363066 0.0008416857 -1.1066328 0.003848112 2.9367382 10 1.361841 0.0013806097 3.4331576 0.008142079 9.9327333 11 1.361883 -0.0033314315 2.3027384 0.010963248 5.8470134 13 1.360421 -0.0030072549 2.4880820 0.010502627 6.4768795 14 1.360272 0.0043442866 2.4695894 0.017151138 6.6046461 15 1.360395 -0.0021805003 -0.6258840 0.006140054 1.0498640 17 1.358872 0.0072010596 1.8033074 0.021587259 7.2418314 18 1.358966 0.0046608938 1.9150371 0.014655015 5.3547633 19 1.358576 -0.0250423571 0.2172515 0.017854446 0.5552054 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.421 co2l1 = 0.453 co2l0 = 0.031" [1] "co2l0 = -149.39 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "175 out of 515 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "340 out of 1216 1-min values rejected as stack air" [1] "340 out of 1216 Line 1 1-min values rejected as stack air" [1] "0 out of 0 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"