[1] "2025-04-29 20:42:57 MDT" [1] "1402" "140301" "d060" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140301a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 84141 63 [1] 84141 [1] 84141 [1] "testing skipping spike filter" [1] 84141 [1] 84141 [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 20:43:01 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.819, ave o2scale2 = 0.746" [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 = 0.819, ave o2scale2 = 0.746" [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] "5 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:43:02 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:43:02 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:43:16 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:43:18 MDT" [1] "reading in recalculated plot titles" [1] "Removed 5 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1 row(s) with low FLWTA" [1] "TEMP: 1394 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:43:22 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 = -475.9" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -633.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 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 = 0.441 co2off = 373.7 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: 3 minutes" [1] "Longest Cal: 9.02 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,] 13 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 185 194 0.1290359 0.1352958 0.1328615 3 -4.442633 302.0540 1.221251 3 4 195 204 0.1359912 0.1422546 0.1398193 3 58.214438 159.8005 1.221092 4 5 205 214 0.1429501 0.1492095 0.1481662 NA 32.846156 224.4539 1.220981 5 3 215 224 0.1499051 0.1561648 0.1551214 3 36.760578 238.2062 1.220793 7 4 485 494 0.3377292 0.3439888 0.3415544 2 58.222797 158.2800 1.219350 8 2 495 504 0.3446844 0.3509433 0.3485094 2 -4.272672 306.9893 1.219366 12 2 775 784 0.5661575 0.5724168 0.5699828 3 -4.264148 308.8269 1.219751 13 4 785 794 0.5731123 0.5793715 0.5769375 3 58.091680 160.1634 1.219745 14 3 795 804 0.5800671 0.5863264 0.5852834 3 36.620039 255.6863 1.220038 16 4 1075 1084 0.7748363 0.7810960 0.7786618 2 58.257297 154.6135 1.224724 17 2 1085 1094 0.7817914 0.7880511 0.7856171 2 -4.623133 305.7109 1.224869 18 5 1095 1104 0.7887467 0.7950065 0.7939634 NA 32.509375 226.4504 1.224823 20 2 1372 1380 0.9835116 0.9897713 0.9873870 2 -5.153493 305.2983 1.227047 21 4 1381 1390 0.9904709 0.9967298 0.9942957 2 58.252836 163.4937 1.227126 jfcv2 co2slp o2slp co2sd o2sd 2 1.340934 -0.008864468 1.02911298 0.022140920 5.6005710 3 1.340747 0.009334245 1.31923498 0.028485722 4.3196134 4 1.340613 -0.035253744 2.86048752 0.024969708 3.8712635 5 1.340398 0.002917881 3.34796210 0.007628347 4.6130783 7 1.338794 0.004881101 0.88703382 0.012846699 5.7534140 8 1.338829 -0.001731234 0.82514591 0.006763276 5.0931642 12 1.339310 -0.003804601 1.43463748 0.013140422 16.6448016 13 1.339329 0.008142654 1.66954039 0.023544184 4.9365430 14 1.339564 -0.006082503 2.43399684 0.017283674 4.3662877 16 1.344702 -0.004269376 0.01068626 0.013224907 5.1178783 17 1.344871 -0.001843015 0.86496186 0.006645474 2.8267590 18 1.344825 -0.057680303 -0.10124548 0.040835417 0.4432239 20 1.346981 0.009669787 1.38642016 0.025563664 15.7413227 21 1.347134 -0.001757112 0.16619595 0.012773391 4.2181808 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.641 co2l1 = 0.44 co2l0 = 0.012" [1] "co2l0 = -148.3 co2l1 = 0.217" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "86 out of 185 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "99 out of 1200 1-min values rejected as stack air" [1] "75 out of 1082 Line 1 1-min values rejected as stack air" [1] "24 out of 118 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"