[1] "2025-04-29 20:10:00 MDT" [1] "1401" "140104" "d004" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140104a.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 20:10:04 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.809, ave o2scale2 = 0.737" [1] "Removing 0 MR FC 1 jog(s) with WT SD > 1000" [1] "Removing 1 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] "14 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.809, ave o2scale2 = 0.737" [1] "Removing 0 RC FC 1 jog(s) with WT SD > 1000" [1] "Removing 1 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] "14 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:10:05 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:10:05 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:10:22 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:10:23 MDT" [1] "reading in recalculated plot titles" [1] "Removed 14 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1422 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:10:28 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 = -475.6" [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 = 0.442 co2off = 377.66 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.02 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.02 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 4 181 190 0.1261667 0.1324295 0.1299952 2 60.802063 156.8935 1.239357 3 2 191 200 0.1331250 0.1393846 0.1369504 2 -2.293781 297.1368 1.239419 5 2 481 490 0.3348843 0.3411474 0.3387115 3 -2.038680 297.7798 1.237435 6 4 491 500 0.3418428 0.3481021 0.3456680 3 60.566664 163.7534 1.237346 7 3 501 510 0.3487980 0.3550571 0.3540141 3 39.146977 245.0445 1.237345 9 4 780 789 0.5435822 0.5498435 0.5474076 2 60.433242 160.9066 1.234527 10 2 790 799 0.5505408 0.5568000 0.5543660 2 -1.843422 301.2792 1.234622 11 5 800 809 0.5574963 0.5637553 0.5627122 NA 33.496500 220.6599 1.234408 13 2 1074 1083 0.7522650 0.7585278 0.7560919 3 -2.072156 299.1330 1.232087 14 4 1084 1093 0.7592234 0.7654830 0.7630487 3 60.362055 161.6285 1.232079 15 3 1094 1103 0.7661783 0.7724410 0.7713979 3 39.046391 243.6285 1.232509 17 4 1367 1376 0.9609330 0.9671930 0.9647586 2 60.278055 152.9985 1.232742 18 2 1377 1386 0.9678880 0.9741478 0.9717134 2 -2.092320 296.2713 1.232788 jfcv2 co2slp o2slp co2sd o2sd 2 1.362112 2.517978e-03 0.6196817 0.012482711 7.586911 3 1.362155 4.650608e-03 3.0383497 0.015860018 11.152754 5 1.360552 8.565879e-03 3.4450179 0.021647450 8.948282 6 1.360486 6.030885e-03 2.2209105 0.020267352 6.360122 7 1.360502 -7.352759e-05 -3.9159157 0.002760519 5.711009 9 1.357322 6.286786e-03 0.1284292 0.020922514 4.495767 10 1.357486 6.705851e-03 1.4574239 0.018101856 5.203306 11 1.357194 -5.442517e-02 -1.0673504 0.038537320 2.551616 13 1.352784 9.804831e-03 3.5361347 0.024322310 9.143649 14 1.352785 5.638903e-03 5.3019751 0.020558861 13.593364 15 1.353224 -4.368922e-03 -4.0442292 0.011399393 5.738789 17 1.353315 -2.984182e-03 2.5950144 0.011612918 7.586067 18 1.353375 -1.317107e-03 2.2087410 0.012069573 7.210333 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 377.545 co2l1 = 0.441 co2l0 = -0.017" [1] "co2l0 = -150.19 co2l1 = 0.229" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "111 out of 280 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "169 out of 1240 1-min values rejected as stack air" [1] "169 out of 1240 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"