[1] "2025-04-29 20:20:05 MDT" [1] "1401" "140122" "d022" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140122a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86280 63 [1] 86280 [1] 86280 [1] "testing skipping spike filter" [1] 86280 [1] 86280 [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 20:20:09 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.806, ave o2scale2 = 0.733" [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] "10 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.806, ave o2scale2 = 0.733" [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] "10 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:20:09 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:20:09 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:20:27 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:20:28 MDT" [1] "reading in recalculated plot titles" [1] "Removed 10 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1426 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:20:41 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 = -475.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.8" [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 = 0.453 co2off = 379.59 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: 9.03 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 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 246 255 0.1724986 0.1787576 0.1763235 3 -6.382547 301.6108 1.241804 3 4 256 265 0.1794529 0.1857127 0.1832784 3 54.729164 159.0937 1.241609 4 3 266 275 0.1864080 0.1926672 0.1916242 3 33.839891 250.4728 1.241469 6 4 544 553 0.3812244 0.3874954 0.3850583 2 54.763305 160.4708 1.241053 7 2 554 563 0.3881910 0.3944504 0.3920161 2 -6.202688 296.0187 1.241211 8 5 564 573 0.3951458 0.4014087 0.4003657 NA 29.494906 227.8143 1.241182 10 2 842 851 0.5899560 0.5962189 0.5937850 3 -5.578883 303.6693 1.240825 11 4 852 861 0.5969144 0.6031759 0.6007419 3 54.760156 160.6575 1.240793 12 3 862 871 0.6038716 0.6101308 0.6090875 3 34.139055 247.9335 1.241028 14 4 1138 1147 0.7986392 0.8048986 0.8024644 2 54.858453 162.8666 1.240695 15 2 1148 1157 0.8055938 0.8118531 0.8094191 2 -6.242234 298.2439 1.240736 jfcv2 co2slp o2slp co2sd o2sd 2 1.365744 0.0048259564 3.569086688 0.012435133 9.085476 3 1.365529 0.0059169656 2.894479055 0.015080104 7.856196 4 1.365360 -0.0038379726 1.565674267 0.010919692 2.261847 6 1.364943 0.0056248430 1.257889566 0.015093438 4.048557 7 1.365042 0.0146144343 -0.852733772 0.037022782 9.947121 8 1.365068 -0.0200357856 -0.753654065 0.014186330 2.609940 10 1.364562 -0.0048148917 1.658039093 0.014247315 6.879323 11 1.364488 0.0084630156 1.730631479 0.026468753 5.424530 12 1.364779 0.0001214158 -0.431255465 0.008826669 4.276018 14 1.364326 0.0058026376 3.713398757 0.015877522 9.244323 15 1.364340 0.0010625408 0.009591308 0.008611775 4.359378 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.406 co2l1 = 0.454 co2l0 = 0.03" [1] "co2l0 = -150.53 co2l1 = 0.228" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "14 out of 120 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "106 out of 1269 1-min values rejected as stack air" [1] "106 out of 1269 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"