[1] "2025-04-29 22:23:59 MDT" [1] "1410" "141109" "d313" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141109a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85396 63 [1] 85396 [1] 85396 [1] "testing skipping spike filter" [1] 85396 [1] 85396 [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 22:24:03 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.837, ave o2scale2 = 0.754" [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 1 MR FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000" [1] "15 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.837, ave o2scale2 = 0.754" [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 1 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000" [1] "15 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:24:03 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:24:03 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:24:15 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:24:16 MDT" [1] "reading in recalculated plot titles" [1] "Removed 15 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 2 row(s) with variable TFCELL" [1] "TEMP: 1404 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:24:20 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.63 O2 = -477.2" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.4" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.946 co2off = 400.94 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 8.62 minutes" [1] "Shortest Cal: 3.01 minutes" [1] "Longest Cal: 9.03 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 6 [3,] 7 8 [4,] 10 11 [5,] 12 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 181 190 0.1264350 0.1326979 0.1302630 2 3.500680 385.5082 3 2 191 200 0.1333932 0.1396562 0.1372207 2 -25.725805 524.2990 6 2 481 490 0.3354345 0.3417051 0.3392702 3 -25.701891 530.5742 7 4 491 500 0.3424005 0.3486642 0.3462298 3 3.514422 382.5838 8 5 501 510 0.3493621 0.3556266 0.3545808 NA -7.524594 444.2524 9 3 511 520 0.3563221 0.3625856 0.3615414 3 -6.275492 464.7044 12 2 742 751 0.5387011 0.5449641 0.5425280 2 -25.669094 536.3308 13 4 752 761 0.5456597 0.5519226 0.5494876 2 3.543789 384.7319 14 5 762 771 0.5526181 0.5588810 0.5578380 NA -7.691969 431.1795 16 4 1032 1041 0.7404942 0.7467537 0.7443193 2 3.558602 379.0594 17 2 1042 1051 0.7474491 0.7537122 0.7512754 2 -25.655820 530.6962 19 2 1332 1341 0.9492206 0.9554838 0.9530480 3 -25.718680 529.6740 20 4 1342 1351 0.9561794 0.9624421 0.9600070 3 3.487086 380.8095 21 3 1352 1361 0.9631376 0.9694005 0.9683571 3 -6.300461 463.9411 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.190136 1.321721 1.920864e-05 0.469420948 0.003554178 6.440474 3 1.190213 1.321806 -1.445266e-03 0.466123339 0.006083720 2.595738 6 1.193548 1.325527 -1.856273e-04 0.538015235 0.001484199 2.579703 7 1.193557 1.325506 1.521306e-03 0.408562922 0.005497133 3.540851 8 1.193637 1.325594 -2.300900e-03 1.461147392 0.001635184 2.767704 9 1.193791 1.325771 1.491095e-03 0.492048823 0.004418968 1.248558 12 1.194920 1.328320 -2.220653e-03 -5.108926399 0.006173821 21.483657 13 1.195384 1.328742 2.456107e-04 -0.790342004 0.005431692 4.450399 14 1.195701 1.329052 -3.308227e-03 -6.805568420 0.002342291 9.021570 16 1.198214 1.331568 1.555757e-05 -1.114098744 0.002160403 3.357156 17 1.198280 1.331629 -1.104952e-03 0.623919836 0.006980317 2.100513 19 1.197260 1.330400 -9.804750e-04 2.142051879 0.003261388 6.097119 20 1.197038 1.330174 -1.204973e-03 -0.737547531 0.004560963 3.186549 21 1.196895 1.330023 -2.479039e-03 -0.004887382 0.006604748 1.853822 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 400.908 co2l1 = 0.945 co2l0 = 0.001" [1] "co2l0 = -196.28 co2l1 = 0.216" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "178 out of 480 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "302 out of 1206 1-min values rejected as stack air" [1] "268 out of 1172 Line 1 1-min values rejected as stack air" [1] "34 out of 34 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"