[1] "2025-04-29 21:03:33 MDT" [1] "1404" "140413" "d103" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140413a.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 21:03:37 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.822, ave o2scale2 = 0.748" [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] "6 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.822, ave o2scale2 = 0.748" [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] "6 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 21:03:38 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:03:38 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:03:51 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:03:52 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 21:03:56 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 = -476.1" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -541.9" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -634.1" [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 = 0.408 co2off = 372.77 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 3 [2,] 4 5 [3,] 6 9 [4,] 10 11 [5,] 12 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 85 94 0.05932749 0.06559028 0.06315273 3 9.713937 274.5605 3 4 95 104 0.06628591 0.07254537 0.07011101 3 77.434438 133.2915 4 3 105 114 0.07324094 0.07950006 0.07845686 3 54.195828 213.4357 7 4 384 393 0.26804424 0.27430767 0.27187008 2 77.408070 131.9089 8 2 394 403 0.27500307 0.28126603 0.27882945 2 9.883195 271.5421 10 2 683 692 0.47672786 0.48298715 0.48055293 3 9.448281 272.7639 11 4 693 702 0.48368252 0.48994210 0.48750775 3 77.442570 132.0375 12 5 703 712 0.49063759 0.49689699 0.49585385 NA 50.281969 197.1704 13 3 713 722 0.49759259 0.50385530 0.50281197 3 54.155570 206.9002 15 4 980 989 0.68541921 0.69167888 0.68924475 2 77.494828 131.5386 16 2 990 999 0.69237422 0.69863709 0.69620255 2 9.363281 274.6594 18 2 1279 1288 0.89409606 0.90035535 0.89792128 3 9.745242 276.0459 19 4 1289 1298 0.90105116 0.90731053 0.90487650 3 77.057273 129.9128 20 3 1299 1308 0.90800587 0.91426563 0.91322259 3 53.966742 210.1544 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.218696 1.338836 0.007562878 0.24972109 0.020635766 3.421576 3 1.218331 1.338440 -0.001270716 0.58167731 0.018021998 3.280636 4 1.217911 1.337971 -0.006944024 0.72321069 0.018065720 1.138718 7 1.214308 1.334061 -0.004659560 1.00129306 0.012526999 5.720174 8 1.214709 1.334471 0.002575311 0.53104745 0.008028857 2.883595 10 1.217228 1.337211 0.003771304 -0.09062481 0.011342772 3.047291 11 1.217307 1.337276 -0.001520355 0.59028821 0.013107490 4.491393 12 1.217497 1.337502 -0.021652315 1.81908957 0.015335378 3.790005 13 1.217612 1.337636 -0.004626774 -1.54054426 0.013920711 2.010235 15 1.217989 1.337951 0.008099052 0.11336205 0.024026161 2.870815 16 1.218076 1.338052 -0.002333056 0.52431734 0.012910578 3.584350 18 1.215395 1.335178 -0.007888371 1.89780113 0.022404944 5.261484 19 1.215065 1.334831 0.009718787 0.52273767 0.027490115 3.523650 20 1.214961 1.334719 0.001006667 2.12557239 0.004387538 2.828878 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 372.72 co2l1 = 0.408 co2l0 = -0.206" [1] "co2l0 = -143.18 co2l1 = 0.224" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "31 out of 90 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "59 out of 1246 1-min values rejected as stack air" [1] "44 out of 1008 Line 1 1-min values rejected as stack air" [1] "15 out of 238 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"