[1] "2025-04-29 22:26:52 MDT" [1] "1410" "141114" "d318" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141114a.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 22:26:56 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.851, ave o2scale2 = 0.767" [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 > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.851, ave o2scale2 = 0.767" [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 > 200 )" [1] "2025-04-29 22:26:56 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:26:56 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:27:17 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:27:19 MDT" [1] "reading in recalculated plot titles" [1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1434 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:27:25 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.63 O2 = -477.3" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.4" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.946 co2off = 401.21 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: 9.03 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 2 176 185 0.1241517 0.1304148 0.1279794 3 -26.069156 527.6605 3 4 186 195 0.1311102 0.1373730 0.1349386 3 3.169297 379.6648 4 3 196 205 0.1380684 0.1443313 0.1432882 3 -6.636711 460.8126 6 4 476 485 0.3329420 0.3392124 0.3367739 2 3.193414 377.8706 7 2 486 495 0.3399079 0.3461713 0.3437356 2 -26.033906 526.6012 9 2 776 785 0.5417321 0.5479931 0.5455588 3 -26.064344 528.3980 10 4 786 795 0.5486885 0.5549520 0.5525178 3 3.171406 381.5331 11 5 796 805 0.5556473 0.5619104 0.5608673 NA -7.838812 442.2700 12 3 806 815 0.5626058 0.5688690 0.5678258 3 -6.613641 461.7752 14 4 1076 1085 0.7504777 0.7567373 0.7543032 2 3.208922 385.1125 15 2 1086 1095 0.7574329 0.7636960 0.7612619 2 -26.020867 526.6678 17 2 1376 1385 0.9592222 0.9654850 0.9630495 3 -26.036406 527.3748 18 4 1386 1395 0.9661806 0.9724433 0.9700088 3 3.188437 382.4508 19 3 1396 1405 0.9731389 0.9794034 0.9783589 3 -6.618531 461.1094 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.173742 1.302263 2.383729e-04 -0.008944337 0.004394472 0.7860265 3 1.173777 1.302294 2.923971e-04 0.696195172 0.005202994 3.0002177 4 1.173791 1.302328 -2.653875e-04 1.893300170 0.005992922 2.7690822 6 1.174497 1.303087 -8.350672e-04 0.571132273 0.004539501 1.7676891 7 1.174498 1.303092 -2.589294e-03 1.229981998 0.007567774 3.7158266 9 1.175628 1.304395 5.617307e-04 -0.747687171 0.003075864 1.9882722 10 1.175521 1.304278 1.986512e-03 -0.536732861 0.006014399 2.5257286 11 1.175469 1.304208 -5.617744e-03 -0.454895459 0.003977476 1.0253726 12 1.175478 1.304199 -1.312064e-03 2.307606775 0.004681335 3.0145232 14 1.176461 1.305340 9.227007e-05 -0.103693338 0.002267233 2.0463944 15 1.176522 1.305417 -3.457012e-03 -1.519786589 0.010152159 5.7383374 17 1.176548 1.305529 -5.682677e-04 1.385477749 0.003285690 4.2206675 18 1.176486 1.305458 1.242935e-03 0.510104150 0.005464782 1.7534335 19 1.176544 1.305510 -1.237455e-03 0.284556308 0.003370533 0.4865822 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 401.228 co2l1 = 0.945 co2l0 = 0" [1] "co2l0 = -197 co2l1 = 0.218" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "46 out of 117 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "71 out of 1252 1-min values rejected as stack air" [1] "71 out of 1252 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"