[1] "2025-04-29 20:58:19 MDT" [1] "1403" "140401" "d091" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140401a.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 20:58:24 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.808, ave o2scale2 = 0.735" [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] "160 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.808, ave o2scale2 = 0.735" [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] "160 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:58:24 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:58:24 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:58:47 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:58:49 MDT" [1] "reading in recalculated plot titles" [1] "Removed 160 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1276 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:58:56 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 = -476.1" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -541.9" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -634" [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 = 0.387 co2off = 384.26 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 8.01 minutes" [1] "Average Cal: 7.8 minutes" [1] "Shortest Cal: 5.01 minutes" [1] "Longest Cal: 9.01 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 5 [3,] 6 8 [4,] 9 10 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 179 187 0.1534167 0.1596759 0.1574903 3 11.169007 271.3585 1.223799 3 4 188 193 0.1617625 0.1652396 0.1641964 3 81.799141 129.6928 1.223859 5 3 201 208 0.1742808 0.1805404 0.1801927 3 57.493240 207.1887 1.225186 7 4 409 418 0.3620567 0.3683160 0.3658818 2 81.767570 137.8494 1.232696 8 2 419 426 0.3704026 0.3752708 0.3735319 2 10.796344 274.3844 1.233272 10 2 690 697 0.5706970 0.5755659 0.5738271 3 10.469344 274.9523 1.241403 11 4 698 705 0.5783474 0.5839114 0.5818250 3 81.868076 126.9735 1.241463 12 3 706 713 0.5853021 0.5908657 0.5905180 3 57.350164 216.0268 1.241948 14 4 965 974 0.7793377 0.7855971 0.7831627 2 81.928109 123.1294 1.248576 15 2 975 984 0.7862924 0.7925512 0.7901173 2 10.102555 269.7357 1.248764 16 5 985 992 0.7946386 0.7995093 0.7991614 NA 52.554438 191.1962 1.249205 18 2 1260 1269 0.9880001 0.9942593 0.9918253 2 9.996391 270.5018 1.250633 19 4 1270 1276 0.9949549 0.9991281 0.9977371 2 81.792750 126.7076 1.250651 jfcv2 co2slp o2slp co2sd o2sd 2 1.345497 0.002305808 3.956643e+00 0.005905806 9.987916 3 1.345675 -0.021564187 -4.741199e-01 0.028683908 3.321686 5 1.347054 -0.005268043 -4.785661e+00 0.012295732 3.389049 7 1.355102 0.004904240 2.158585e+00 0.015017120 7.793342 8 1.355726 -0.001841827 2.539080e-01 0.003669075 2.761352 10 1.364190 -0.006595777 4.986355e-01 0.016304656 5.477530 11 1.364275 0.005892863 3.976174e+00 0.014723533 9.847541 12 1.364823 -0.008665923 4.854828e-14 0.020482113 0.000000 14 1.371911 -0.005491081 1.961618e-01 0.020721682 3.582243 15 1.372156 -0.005428787 9.282856e-01 0.015884468 6.446153 16 1.372642 -0.287609699 4.945713e+00 0.203735141 3.503413 18 1.373911 -0.009816515 8.170578e-01 0.024315099 2.950161 19 1.373925 0.024673842 2.691908e+00 0.044017752 7.089829 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 372.572 co2l1 = 0.387 co2l0 = -0.234" [1] "co2l0 = -142.37 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "83 out of 115 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "32 out of 1112 1-min values rejected as stack air" [1] "32 out of 1112 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"