[1] "2025-04-29 16:36:15 MDT" [1] "1206" "120616" "d168" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120616g.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 79599 63 [1] 79599 [1] 79599 [1] "testing skipping spike filter" [1] 79599 [1] 79599 [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 16:36:19 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.777, ave o2scale2 = 0.782" [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] "100 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.777, ave o2scale2 = 0.782" [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] "100 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 16:36:19 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 16:36:19 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 16:36:40 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 16:36:42 MDT" [1] "reading in recalculated plot titles" [1] "Removed 101 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1225 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 16:36:52 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 = -450.4" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.95 O2 = -543.4" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.8" [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 = 396.42 O2 = -582.4" [1] "Nominal linear calibrations:" [1] "co2scl = 0.995 co2off = 391.68 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.03 minutes" [1] "Average Cal: 8.77 minutes" [1] "Shortest Cal: 2.01 minutes" [1] "Longest Cal: 10.03 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 4 [3,] 5 6 [4,] 8 9 [5,] 10 12 [6,] 13 14 [7,] 16 18 [8,] 19 20 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 4 13 0.003078819 0.009392101 0.006916529 3 -11.621375 91.412065 3 4 14 23 0.010108391 0.016553443 0.014046976 3 19.608180 -64.863580 4 3 24 33 0.017269531 0.023715654 0.022641356 3 9.141156 -2.867111 7 2 160 170 0.136667795 0.143635098 0.140848315 1 -11.611160 88.046894 9 2 275 283 0.254426071 0.260697569 0.258407817 2 -11.608997 93.366856 10 4 284 293 0.261394676 0.267664931 0.265226421 2 19.607922 -73.692774 11 5 294 303 0.268361892 0.274632176 0.273586690 NA 6.569219 -12.197527 13 4 450 459 0.379847367 0.386120631 0.383680877 2 19.607984 -60.318269 14 2 460 469 0.386816638 0.393088889 0.390649476 2 -11.614609 89.047755 16 2 624 633 0.505283189 0.511555093 0.509116468 3 -11.647977 90.734872 17 4 634 643 0.512251591 0.518523698 0.516084288 3 19.569383 -68.939817 18 3 644 653 0.519221412 0.525491696 0.524447338 3 9.111352 -2.837139 20 4 803 812 0.630722020 0.637001910 0.634559230 2 19.574891 -66.882505 21 2 813 822 0.637699074 0.643970718 0.641532100 2 -11.663320 89.637901 22 5 823 832 0.644667332 0.650935966 0.649891247 NA 6.562594 -17.608571 24 2 983 992 0.756174103 0.762446007 0.760007100 3 -11.651852 91.137419 25 4 993 1002 0.763142679 0.769416725 0.766976168 3 19.588820 -67.323687 26 3 1003 1012 0.770113947 0.776384635 0.775339388 3 9.118344 -1.489699 28 4 1163 1172 0.881627112 0.887899797 0.885460041 2 19.602656 -70.523543 29 2 1173 1182 0.888596730 0.894868576 0.892429243 2 -11.632156 88.698806 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.289243 1.281068 0.0012418716 1.27581531 0.003509871 4.220062 3 1.289029 1.280825 -0.0009747227 1.06124568 0.005593108 3.124783 4 1.289196 1.280964 0.0005338761 -0.25599743 0.003301278 1.322775 7 1.289028 1.280765 -0.0021566266 0.61416654 0.006608995 4.081565 9 1.290522 1.282320 -0.0022331317 1.72925048 0.006693799 5.004370 10 1.290470 1.282293 0.0020039905 1.57284062 0.007381410 6.527722 11 1.290724 1.282583 -0.0250965251 -0.69558149 0.017810252 1.302287 13 1.288670 1.280440 -0.0015106944 2.15280892 0.004083360 8.217786 14 1.288292 1.279996 -0.0006329038 -1.38936850 0.006383900 5.365784 16 1.285798 1.277392 0.0000169394 3.52940536 0.002500209 10.977742 17 1.285534 1.277056 0.0032389582 -0.05948352 0.009012605 3.578431 18 1.285469 1.277007 0.0043660315 -8.75752682 0.011260359 13.121078 20 1.285333 1.276986 -0.0007630917 -0.50131427 0.004170842 3.857384 21 1.285426 1.277091 -0.0037080049 1.60973753 0.009504313 6.146140 22 1.285307 1.276976 -0.0238619372 -1.71944805 0.016926369 2.355385 24 1.286128 1.277626 -0.0005167029 -0.36630463 0.003493287 2.805481 25 1.285970 1.277471 0.0023250189 1.67062338 0.006480864 6.084324 26 1.285844 1.277351 0.0020393705 -2.51864625 0.005872340 3.931093 28 1.281742 1.273077 -0.0021912414 3.15037570 0.007075328 9.132837 29 1.281625 1.272945 -0.0017481948 1.57245766 0.004573556 5.682196 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 385.865 co2l1 = 0.993 co2l0 = 0.018" [1] "co2l0 = -97.03 co2l1 = 0.225" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "26 out of 100 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "74 out of 935 1-min values rejected as stack air" [1] "74 out of 935 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"