[1] "2025-04-29 20:16:29 MDT" [1] "1401" "140116" "d016" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140116a.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 20:16:33 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] "6 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] "6 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:16:33 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:16:33 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:16:50 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:16:51 MDT" [1] "reading in recalculated plot titles" [1] "Removed 6 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1430 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:17:03 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 = -633.7" [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 = 0.451 co2off = 379.6 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.01 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 2 [2,] 4 6 [3,] 7 8 [4,] 9 12 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 269 278 0.1893485 0.1956077 0.1931738 2 55.090328 162.4301 1.234624 3 2 279 288 0.1963034 0.2025629 0.2001288 2 -5.983039 301.9327 1.234790 4 5 289 298 0.2032583 0.2095178 0.2084747 NA 29.568750 222.6529 1.234776 6 2 568 577 0.3980706 0.4043301 0.4018961 3 -6.172078 307.8596 1.236113 7 4 578 587 0.4050255 0.4112857 0.4088513 3 55.049680 161.2720 1.236020 8 3 588 597 0.4119811 0.4182407 0.4171976 3 34.154328 248.1281 1.236203 10 4 867 876 0.6067466 0.6130058 0.6105717 2 55.098437 157.9679 1.237912 11 2 877 886 0.6137014 0.6199607 0.6175264 2 -6.276617 302.0246 1.238108 13 2 1166 1175 0.8154277 0.8216873 0.8192529 3 -6.641867 299.2931 1.240639 14 4 1176 1185 0.8223827 0.8286423 0.8262078 3 55.098062 158.1593 1.240608 15 5 1186 1195 0.8293377 0.8356007 0.8345574 NA 29.249937 224.1971 1.240764 16 3 1196 1205 0.8362963 0.8425556 0.8415123 3 33.999070 243.0970 1.241091 jfcv2 co2slp o2slp co2sd o2sd 2 1.358155 -1.326459e-05 3.1934072 0.006875548 9.185417 3 1.358341 9.678160e-04 3.6417352 0.010041873 9.327024 4 1.358382 -4.269308e-02 -0.9848267 0.030228815 3.758279 6 1.359720 6.963018e-05 3.1962647 0.007248749 24.876418 7 1.359683 8.020804e-03 1.4157502 0.020899751 5.743892 8 1.359856 1.309063e-04 0.8480546 0.003445324 1.516141 10 1.361730 2.380490e-03 1.8470352 0.009301138 5.679571 11 1.361929 2.186296e-03 1.7779916 0.007651990 7.767652 13 1.364636 1.746344e-04 2.2301699 0.011520045 6.740867 14 1.364630 3.087125e-03 0.1817728 0.016766050 7.466332 15 1.364755 -3.606489e-02 -2.2193905 0.025544232 4.390891 16 1.365096 -4.588939e-03 -2.1706754 0.011492255 2.862513 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.458 co2l1 = 0.45 co2l0 = 0.032" [1] "co2l0 = -149.4 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "87 out of 285 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "198 out of 1263 1-min values rejected as stack air" [1] "198 out of 1263 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"