[1] "2025-04-29 19:49:02 MDT" [1] "1311" "131113" "d317" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/131113a.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 19:49:06 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.811, ave o2scale2 = 0.737" [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] "44 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.811, ave o2scale2 = 0.737" [1] "Removing 1 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 1 RC FC 2 jog(s) with SP SD > 1000" [1] "44 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 19:49:07 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 19:49:07 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 19:49:28 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 19:49:29 MDT" [1] "reading in recalculated plot titles" [1] "Removed 44 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1392 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 19:49:39 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 = -446.5" [1] "position 2 cylinder CB08911 description: MS CO2 = 405.33 O2 = -624.3" [1] "position 3 cylinder CB08905 description: LS CO2 = 394.98 O2 = -542.2" [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 = 0.436 co2off = 377.94 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.73 minutes" [1] "Shortest Cal: 7.02 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 2 [2,] 3 4 [3,] 5 8 [4,] 9 10 [5,] 11 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 156 165 0.1100837 0.1163433 0.1139091 2 -15.80055 297.7632 1.228413 3 4 166 175 0.1170387 0.1232983 0.1208639 2 31.40227 211.2539 1.228418 6 4 455 464 0.3187882 0.3250473 0.3226130 2 31.42604 207.9091 1.229275 7 2 465 474 0.3257431 0.3320022 0.3295679 2 -15.82645 304.1342 1.229458 9 2 750 759 0.5276436 0.5339032 0.5314691 3 -16.22627 298.6486 1.233502 10 4 760 769 0.5345985 0.5408584 0.5384239 3 31.25797 210.3103 1.233285 11 5 770 779 0.5415538 0.5478130 0.5467699 NA 23.13028 186.1013 1.233707 12 3 780 789 0.5485092 0.5547685 0.5537251 3 56.18295 128.7006 1.234004 14 4 1041 1049 0.7370486 0.7426168 0.7405286 2 31.21860 207.1905 1.238637 15 2 1050 1059 0.7433122 0.7495718 0.7471374 2 -16.51501 303.3017 1.238828 17 2 1325 1331 0.9450811 0.9513405 0.9486978 3 -16.68188 295.6029 1.241638 18 4 1332 1340 0.9520359 0.9582990 0.9557154 3 31.21821 214.7959 1.240879 19 3 1341 1348 0.9589944 0.9638668 0.9635191 3 56.17360 135.6351 1.240473 jfcv2 co2slp o2slp co2sd o2sd 2 1.350603 -0.0043494243 0.32237398 0.016410180 3.3324248 3 1.350583 0.0040657327 1.94939117 0.010419705 5.9995014 6 1.351549 -0.0030467228 -1.97616613 0.010934461 7.9776010 7 1.351796 -0.0017314950 -2.01029984 0.014421139 8.8801457 9 1.356032 -0.0053359210 -4.91287553 0.016435064 15.6837275 10 1.355792 -0.0006001193 -2.96437024 0.008241676 8.6304471 11 1.356304 -0.0894246370 -0.65525665 0.063330251 1.2821228 12 1.356598 0.0027674463 -8.06314544 0.007383805 11.4078083 14 1.361562 -0.0014461013 -2.55874849 0.006649410 8.0933597 15 1.361704 -0.0052584873 1.64902388 0.014226619 6.9329908 17 1.364631 0.0088590166 0.46772331 0.028437364 1.5131536 18 1.363889 0.0066336417 0.07436775 0.020772911 9.4243168 19 1.363465 -0.0077342190 0.30839378 0.014704255 0.2184126 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 381.354 co2l1 = 0.433 co2l0 = 0.156" [1] "co2l0 = -141.75 co2l1 = 0.218" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "10 out of 10 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "0 out of 1218 1-min values rejected as stack air" [1] "0 out of 1218 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"