[1] "2025-04-29 20:12:39 MDT" [1] "1401" "140109" "d009" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140109a.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 20:12:43 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.798, ave o2scale2 = 0.727" [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] "4 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.798, ave o2scale2 = 0.727" [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] "6 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:12:44 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:12:44 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:13:02 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:13:04 MDT" [1] "reading in recalculated plot titles" [1] "Removed 6 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1430 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:13:13 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 = 0.44 co2off = 379.2 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.01 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 4 194 203 0.1368867 0.1431465 0.1407124 2 57.409836 153.1390 1.251408 3 2 204 213 0.1438419 0.1501019 0.1476673 2 -5.257641 294.4817 1.251403 5 2 492 501 0.3455913 0.3518507 0.3494163 3 -5.499836 298.2079 1.252717 6 4 502 511 0.3525463 0.3588061 0.3563714 3 57.366602 157.2662 1.252835 7 3 512 521 0.3595012 0.3657615 0.3647177 3 35.851742 242.8471 1.253028 9 4 792 801 0.5542881 0.5605475 0.5581132 2 57.148961 163.4960 1.253871 10 2 802 811 0.5612431 0.5675060 0.5650708 2 -5.430391 297.2534 1.253821 11 5 812 821 0.5682014 0.5744607 0.5734177 NA 30.533875 219.2487 1.253780 13 2 1092 1101 0.7629815 0.7692414 0.7668066 3 -5.802172 301.1797 1.254333 14 4 1102 1111 0.7699369 0.7761957 0.7737618 3 57.126445 158.8611 1.254249 15 3 1112 1121 0.7768913 0.7831505 0.7821073 3 35.617516 242.0008 1.254184 17 4 1390 1399 0.9716630 0.9779225 0.9754885 2 57.045695 153.9740 1.254376 18 2 1400 1409 0.9786181 0.9848773 0.9824430 2 -5.904820 297.7286 1.254510 jfcv2 co2slp o2slp co2sd o2sd 2 1.373602 0.002725733 3.2116173 0.008037505 8.315031 3 1.373612 -0.006970462 0.9692645 0.018450215 5.088544 5 1.375103 0.005870965 2.7068211 0.015970115 7.907598 6 1.375158 0.004504937 0.4413347 0.015528809 5.305875 7 1.375382 0.001073592 4.0300602 0.008377028 5.377283 9 1.376248 -0.004071657 2.8614435 0.013841656 8.433864 10 1.376167 -0.019288765 3.3172496 0.047514586 8.292462 11 1.376158 -0.046687750 0.6818324 0.033057242 2.675961 13 1.376846 0.004606113 1.2340557 0.011533083 5.466655 14 1.376698 0.007786023 1.9348193 0.022342515 8.271186 15 1.376683 -0.001019415 -0.5192053 0.005041873 7.025792 17 1.376900 0.003745490 0.8674649 0.010170831 2.586746 18 1.377072 -0.005254571 1.9380285 0.014424930 6.329989 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.087 co2l1 = 0.44 co2l0 = 0.025" [1] "co2l0 = -149.42 co2l1 = 0.227" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "41 out of 95 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "54 out of 1248 1-min values rejected as stack air" [1] "54 out of 1248 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"