[1] "2025-04-29 16:33:16 MDT" [1] "1206" "120611" "d163" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120611b.hr" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120611c.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85769 63 [1] 85769 [1] 85769 [1] "testing skipping spike filter" [1] 85769 [1] 85769 [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 16:33:20 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.786, ave o2scale2 = 0.793" [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] "485 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.786, ave o2scale2 = 0.793" [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] "484 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 16:33:21 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 16:33:21 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 16:33:42 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 16:33:44 MDT" [1] "reading in recalculated plot titles" [1] "Removed 484 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 943 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 16:33:55 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -450.5" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.95 O2 = -543.5" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2" [1] "position 5 cylinder CC339495 description: WT1 CO2 = 394.28 O2 = -550.6" [1] "position 6 cylinder CC339490 description: WT2 CO2 = 396.41 O2 = -582.4" [1] "Nominal linear calibrations:" [1] "co2scl = 0.99 co2off = 377.54 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 6.12 minutes" [1] "Average Cal: 6.34 minutes" [1] "Shortest Cal: 2 minutes" [1] "Longest Cal: 10.35 minutes" [1] "Removed 5 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 5 5 [3,] 6 7 [4,] 8 10 [5,] 11 12 [6,] 13 14 [7,] 15 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 3 129 138 0.1214991 0.1280139 0.1269359 3 8.230297 -13.15474 3 2 139 146 0.1287323 0.1359184 0.1337627 3 -12.602625 95.89302 4 4 147 153 0.1366370 0.1409490 0.1395117 3 18.777500 -65.43194 5 5 154 163 0.1445092 0.1515080 0.1504520 NA 5.514375 -10.97996 10 4 337 341 0.3820867 0.3848722 0.3841758 1 18.779937 -62.96090 13 4 432 436 0.4968573 0.4996711 0.4989707 2 18.837437 -60.47286 14 2 437 440 0.5024600 0.5045519 0.5042034 2 -12.503437 76.58721 17 2 540 548 0.6216071 0.6278818 0.6255918 3 -12.495250 89.29609 18 4 549 555 0.6285804 0.6348505 0.6334571 3 18.859782 -70.63266 19 3 556 564 0.6355478 0.6411252 0.6404274 3 8.261482 -16.60294 21 4 673 680 0.7462911 0.7513084 0.7495167 2 18.887563 -69.03104 22 2 681 686 0.7534589 0.7570423 0.7559672 2 -12.480953 88.91701 24 2 807 816 0.8715994 0.8778734 0.8754337 2 -12.433867 87.67732 25 4 817 821 0.8813586 0.8841456 0.8834486 2 18.911917 -63.05163 28 4 940 943 0.9971235 0.9992166 0.9988679 1 18.968875 -72.16893 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.273541 1.263435 0.0102943890 -3.1618176 0.0273959629 5.667591 3 1.273345 1.263267 -0.0032854183 0.5536542 0.0096516069 4.599598 4 1.273167 1.263052 0.0046020374 -0.2909259 0.0079672180 1.038501 5 1.272768 1.262583 -0.1166880457 -2.6300299 0.0830850468 5.075389 10 1.271012 1.260851 0.0014645109 1.7120342 0.0015168326 2.312978 13 1.271875 1.261611 -0.0015471532 10.1704440 0.0015774287 10.289650 14 1.272250 1.261982 -0.0063522378 6.6134957 0.0045078057 4.693205 17 1.268980 1.258472 -0.0010375015 -0.2228304 0.0030069391 3.229141 18 1.268797 1.258366 0.0032820280 -5.3690361 0.0056522694 9.215705 19 1.268746 1.258291 0.0163261731 5.5188391 0.0355755269 6.069863 21 1.269709 1.259420 -0.0013635488 0.8079450 0.0037328776 4.765823 22 1.269599 1.259297 -0.0047418085 4.7818151 0.0063462126 7.006383 24 1.271625 1.261387 -0.0008278835 -0.4498174 0.0033473466 2.718890 25 1.271500 1.261293 0.0005604588 -2.0966233 0.0005636562 2.207394 28 1.274157 1.264186 0.0019912055 -3.4212087 0.0014142136 2.429844 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.676 co2l1 = 0.989 co2l0 = 0.077" [1] "co2l0 = -96.84 co2l1 = 0.234" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "28 out of 223 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "195 out of 718 1-min values rejected as stack air" [1] "195 out of 718 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"