[1] "2025-04-29 20:14:45 MDT" [1] "1401" "140113" "d013" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140113a.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 20:14:49 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.82, ave o2scale2 = 0.745" [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] "106 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.82, ave o2scale2 = 0.745" [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] "105 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:14:50 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:14:50 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:15:07 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:15:08 MDT" [1] "reading in recalculated plot titles" [1] "Removed 106 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1330 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:15:17 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 = 0.457 co2off = 390.26 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.61 minutes" [1] "Shortest Cal: 7.01 minutes" [1] "Longest Cal: 9.03 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 4 [2,] 5 6 [3,] 7 9 [4,] 10 11 [5,] 12 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 83 92 0.05873843 0.06499769 0.06256338 3 -5.068109 298.4062 3 4 93 102 0.06569329 0.07195616 0.06951876 3 55.463219 159.5293 4 5 103 112 0.07265174 0.07891091 0.07786769 NA 29.829437 224.7256 5 3 113 122 0.07960648 0.08586638 0.08482331 3 34.782594 241.9363 7 4 383 392 0.26745885 0.27371875 0.27128432 2 55.454555 161.4403 8 2 393 402 0.27441435 0.28067373 0.27823942 2 -5.237180 302.5755 10 2 675 684 0.47615197 0.48241936 0.47997990 3 -5.205734 305.7665 11 4 685 694 0.48311386 0.48937350 0.48693908 3 55.344273 159.3035 12 3 695 704 0.49006895 0.49632813 0.49528499 3 34.656742 247.0724 15 4 974 981 0.68483678 0.68970495 0.68796633 2 55.273469 151.0186 16 2 982 991 0.69179164 0.69805093 0.69561655 2 -5.015141 306.2229 20 2 1239 1248 0.89352891 0.89979167 0.89735459 3 -4.714586 301.4522 21 4 1249 1255 0.90048727 0.90535773 0.90382692 3 55.131289 159.5052 22 3 1256 1265 0.90744444 0.91370718 0.91266390 3 34.634383 244.2545 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.220254 1.343090 2.837488e-04 2.137007 0.004023889 8.347339 3 1.220013 1.342822 4.340685e-03 2.807458 0.014311233 9.191279 4 1.219882 1.342666 -3.407247e-02 1.043078 0.024130019 2.184044 5 1.220039 1.342833 -3.971402e-03 1.040699 0.011913612 1.682745 7 1.221333 1.344290 1.219174e-03 1.890708 0.009590525 5.226197 8 1.221460 1.344458 1.699026e-03 2.682935 0.010890457 6.844691 10 1.222877 1.345830 9.495730e-06 3.666379 0.003641090 12.016619 11 1.222753 1.345691 7.196311e-03 2.515443 0.018392543 9.403307 12 1.222781 1.345736 -3.314126e-03 -1.300622 0.008594890 1.891728 15 1.221146 1.343925 6.716722e-03 -3.743648 0.012887721 9.230005 16 1.220744 1.343505 -1.401821e-02 1.025691 0.036462091 8.417676 20 1.214983 1.337298 -7.799820e-03 3.409011 0.020737570 9.503516 21 1.214889 1.337142 1.995515e-03 2.177620 0.009194095 5.120054 22 1.214723 1.337030 -2.359943e-03 -5.637448 0.006553901 7.302775 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.952 co2l1 = 0.457 co2l0 = 0.02" [1] "co2l0 = -148.63 co2l1 = 0.22" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "25 out of 105 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "80 out of 1129 1-min values rejected as stack air" [1] "60 out of 773 Line 1 1-min values rejected as stack air" [1] "20 out of 356 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"