[1] "2025-04-29 21:23:45 MDT" [1] "1406" "140628" "d179" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140628a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85710 63 [1] 85710 [1] 85710 [1] "testing skipping spike filter" [1] 85710 [1] 85710 [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 21:23:49 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.833, ave o2scale2 = 0.751" [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] "0 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.833, ave o2scale2 = 0.751" [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 1 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000" [1] "2 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:23:49 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:23:49 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:24:10 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:24:11 MDT" [1] "reading in recalculated plot titles" [1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1425 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:24:14 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 = -476.5" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.7" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 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 = 0.468 co2off = 381.24 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 9.02 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 3 [2,] 4 5 [3,] 7 9 [4,] 10 11 [5,] 12 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 99 108 0.07015162 0.07641435 0.07398040 3 -9.592922 281.0695 3 4 109 118 0.07710998 0.08337373 0.08093887 3 49.409094 133.0086 4 3 119 128 0.08406904 0.09033192 0.08928872 3 29.419781 213.0492 6 4 399 408 0.27892144 0.28518469 0.28274912 2 49.529484 120.4741 7 2 409 418 0.28588044 0.29214271 0.28970799 2 -9.541023 278.2051 8 5 419 428 0.29283808 0.29910127 0.29805674 NA 27.607594 188.8043 10 2 699 708 0.48767020 0.49393015 0.49149551 3 -9.422188 276.2724 11 4 709 718 0.49462549 0.50088432 0.49845046 3 49.611648 134.4851 12 3 719 728 0.50157989 0.50783958 0.50679659 3 29.609070 221.0364 14 4 989 998 0.69621453 0.70247454 0.70004012 2 49.676000 136.6833 15 2 999 1008 0.70317017 0.70943330 0.70699795 2 -9.384492 279.2512 17 2 1289 1298 0.90497104 0.91123388 0.90879795 3 -9.252844 284.1671 18 4 1299 1308 0.91192940 0.91818955 0.91575493 3 49.746023 133.3202 19 5 1309 1318 0.91888487 0.92514450 0.92410105 NA 27.812406 206.0756 20 3 1319 1328 0.92583984 0.93210301 0.93105848 3 29.786211 211.3273 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.210392 1.342835 -0.0039599192 -1.3780933 0.010119198 7.327721 3 1.209823 1.342041 0.0052231317 0.8599428 0.014610837 4.153203 4 1.208832 1.341152 -0.0001850607 -5.0772002 0.005628868 7.392507 6 1.197960 1.329792 -0.0022294884 -1.5509394 0.009240207 11.181205 7 1.197703 1.329416 -0.0047267194 2.2575135 0.017778333 7.783581 8 1.197050 1.328710 -0.0021848600 -6.8494243 0.001546796 10.662681 10 1.198343 1.329604 -0.0016416631 -2.0884890 0.005854733 7.697837 11 1.198403 1.329635 0.0068111101 1.7218431 0.017483409 6.814780 12 1.198510 1.329858 -0.0006412745 -5.2193677 0.007188116 7.269759 14 1.197508 1.328998 -0.0047716193 -0.7054054 0.019455421 14.626867 15 1.197569 1.329032 -0.0007609226 2.7757782 0.012505554 13.775250 17 1.200036 1.331642 -0.0029766025 0.6554176 0.008293715 12.641879 18 1.200223 1.331867 0.0011268703 0.6117085 0.004375885 2.378212 19 1.200583 1.332271 -0.0050519751 5.9903047 0.003579728 8.312504 20 1.200773 1.332434 0.0035577175 0.9226881 0.010901238 3.729877 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 381.052 co2l1 = 0.468 co2l0 = 0.039" [1] "co2l0 = -142.03 co2l1 = 0.215" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "76 out of 355 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "279 out of 1218 1-min values rejected as stack air" [1] "279 out of 1218 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"