[1] "2025-04-29 21:48:30 MDT" [1] "1406" "140811" "d223" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140811a.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 21:48:34 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.837, ave o2scale2 = 0.755" [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] "3 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.837, ave o2scale2 = 0.755" [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] "3 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:48:34 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:48:34 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:48:54 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:48:56 MDT" [1] "reading in recalculated plot titles" [1] "Removed 3 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1433 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:48:59 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 = -476.8" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.6" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.5" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.473 co2off = 386.41 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.02 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 7 9 [4,] 10 11 [5,] 12 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 182 191 0.1268557 0.1331153 0.1306812 3 -20.52228 281.6714 1.191784 3 4 192 201 0.1338107 0.1400735 0.1376394 3 37.87538 135.0476 1.191612 4 3 202 211 0.1407689 0.1470288 0.1459855 3 18.07331 217.2129 1.191636 6 4 482 491 0.3355575 0.3418170 0.3393825 2 37.92973 122.0576 1.193938 7 2 492 501 0.3425124 0.3487762 0.3463408 2 -20.46817 283.0911 1.194069 8 5 502 511 0.3494716 0.3557312 0.3546878 NA 15.71162 193.8823 1.194100 10 2 779 788 0.5442615 0.5505208 0.5480866 3 -20.47343 283.0426 1.195841 11 4 789 798 0.5512165 0.5574792 0.5550438 3 37.95136 134.2381 1.195785 12 3 799 808 0.5581748 0.5644340 0.5633908 3 18.16461 219.4873 1.195801 14 4 1079 1088 0.7529757 0.7592357 0.7568013 2 37.92685 141.0216 1.196237 15 2 1089 1098 0.7599311 0.7661907 0.7637563 2 -20.45448 278.8885 1.196502 17 2 1379 1388 0.9616540 0.9679146 0.9654794 3 -20.46227 280.2672 1.197602 18 4 1389 1398 0.9686128 0.9748755 0.9724391 3 37.94830 138.6978 1.197550 19 5 1399 1408 0.9755709 0.9818306 0.9807871 NA 15.71116 195.7304 1.197801 20 3 1409 1418 0.9825260 0.9887889 0.9877439 3 18.15886 215.8702 1.197792 jfcv2 co2slp o2slp co2sd o2sd 2 1.321885 0.0043743521 -0.05199421 0.011268041 1.0217978 3 1.321689 0.0012219894 -0.33084848 0.009347426 1.7099197 4 1.321703 0.0003386505 0.16594535 0.006117707 0.4238638 6 1.324132 0.0026491346 -3.24629238 0.007239814 20.2653151 7 1.324249 -0.0037704509 0.78296916 0.012032172 2.4539932 8 1.324275 -0.0114822981 1.71718815 0.008131728 2.3739473 10 1.326149 -0.0000185946 -0.22169965 0.002878576 1.7468743 11 1.326102 0.0030548302 0.57848150 0.011372240 1.9315196 12 1.326127 -0.0039388894 0.47374767 0.010377460 0.6633515 14 1.326557 -0.0024981753 0.25146400 0.007181709 2.9377767 15 1.326847 -0.0006277430 0.49515297 0.007031652 1.5027766 17 1.328035 0.0033372726 -0.52912214 0.011175035 2.3305738 18 1.327986 0.0084350746 1.32297923 0.021217826 3.3063571 19 1.328260 -0.0067980541 -0.93295786 0.004817165 1.2834889 20 1.328245 0.0005743558 0.84988366 0.003681631 1.7729373 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.321 co2l1 = 0.473 co2l0 = 0.083" [1] "co2l0 = -142.94 co2l1 = 0.217" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "173 out of 601 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "428 out of 1226 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "428 out of 1226 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"