[1] "2025-04-30 00:11:27 MDT" [1] "1505" "150611" "d162" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/150611a.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] "2025-04-30 00:11:31 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.866, ave o2scale2 = 0.778" [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] "29 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.866, ave o2scale2 = 0.778" [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] "31 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 00:11:31 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 00:11:31 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 00:11:49 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 00:11:50 MDT" [1] "reading in recalculated plot titles" [1] "Removed 31 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1405 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 00:11:53 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 384.68 O2 = -522.1" [1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1" [1] "position 3 cylinder CB08911 description: LS CO2 = 406.19 O2 = -648.6" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.11 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 = 1.014 co2off = 474.15 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: 9.02 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 2 116 125 0.08711450 0.09337731 0.09094316 3 -88.21775 476.9465 3 4 126 135 0.09407292 0.10033565 0.09790077 3 -66.99127 365.3753 4 3 136 145 0.10103116 0.10729398 0.10625062 3 -79.66279 470.6039 6 4 405 414 0.29588006 0.30214416 0.29970943 2 -66.94588 367.0428 7 2 415 424 0.30284265 0.30910556 0.30666879 2 -88.16682 479.0128 9 2 697 706 0.50462193 0.51088183 0.50844728 3 -88.13057 482.2381 10 4 707 716 0.51157714 0.51784002 0.51540296 3 -66.90703 364.9522 11 5 717 726 0.51853533 0.52479517 0.52375142 NA -78.96172 439.3244 12 3 727 736 0.52549274 0.53175353 0.53071043 3 -79.58913 471.2465 14 4 997 1006 0.71339355 0.71965295 0.71721901 2 -66.86716 367.1436 15 2 1007 1016 0.72034838 0.72660856 0.72417401 2 -88.09863 477.4692 17 2 1294 1303 0.92213194 0.92839491 0.92595942 3 -88.08623 478.8079 18 4 1304 1313 0.92909031 0.93535399 0.93291816 3 -66.84906 362.4322 19 3 1314 1323 0.93604939 0.94231247 0.94126905 3 -79.52637 471.2900 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.148938 1.278146 0.0005482905 0.72538983 0.002935505 3.3347815 3 1.149196 1.278434 0.0039044424 0.76569843 0.010004896 4.0310753 4 1.149473 1.278744 -0.0004358231 -0.44252089 0.002331351 1.0197867 6 1.152880 1.283053 -0.0001464190 0.19425860 0.002490481 2.6690202 7 1.153049 1.283274 0.0005320926 0.05830595 0.006131050 4.2030690 9 1.155847 1.286884 0.0006410970 1.15567256 0.001803530 4.5480188 10 1.155852 1.286903 0.0007435243 0.60854341 0.003616986 3.0638668 11 1.155955 1.287031 0.0019325077 -0.94548090 0.001370019 1.2509512 12 1.156082 1.287197 0.0031361980 2.48489400 0.008279199 3.2692346 14 1.158062 1.289641 0.0009391530 1.01591047 0.002982464 5.4018483 15 1.158148 1.289765 -0.0016944213 0.95097238 0.005407237 5.0204374 17 1.161607 1.293933 -0.0001786824 1.79762255 0.003210950 5.8478989 18 1.161781 1.294138 0.0055205517 0.05881616 0.015394804 3.7272206 19 1.162148 1.294549 0.0008967091 -0.03694606 0.007830974 0.5360987 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 473.998 co2l1 = 1.014 co2l0 = 1.993" [1] "co2l0 = -197.78 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "42 out of 335 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "293 out of 1223 1-min values rejected as stack air" [1] "293 out of 1223 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"