[1] "2025-04-29 21:04:00 MDT" [1] "1404" "140414" "d104" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140414a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85387 63 [1] 85387 [1] 85387 [1] "testing skipping spike filter" [1] 85387 [1] 85387 [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 21:04:05 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.814, ave o2scale2 = 0.741" [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] "26 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.814, ave o2scale2 = 0.741" [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] "26 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 21:04:05 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:04:05 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:04:18 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:04:19 MDT" [1] "reading in recalculated plot titles" [1] "Removed 26 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1395 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:04:22 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" [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 = 0.404 co2off = 377.72 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.73 minutes" [1] "Shortest Cal: 7.01 minutes" [1] "Longest Cal: 9.02 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,] 4 6 [3,] 7 8 [4,] 9 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 146 155 0.1028108 0.1090705 0.1066362 2 77.089266 129.6640 1.216150 3 2 156 165 0.1097658 0.1160288 0.1135941 2 9.699547 270.0387 1.216353 4 5 166 175 0.1167241 0.1229871 0.1219436 NA 50.145031 194.9660 1.216494 6 2 445 454 0.3115243 0.3177844 0.3153500 3 9.543164 275.9717 1.222992 7 4 455 464 0.3184798 0.3247396 0.3223051 3 77.261687 137.0566 1.223361 8 3 465 474 0.3254352 0.3316979 0.3306546 3 53.987805 214.3759 1.223808 10 4 743 752 0.5202072 0.5264701 0.5240336 2 77.507023 130.5711 1.230891 11 2 753 762 0.5271655 0.5334249 0.5309907 2 9.024844 271.4676 1.230974 13 2 1023 1032 0.7286332 0.7348929 0.7324586 3 8.957172 274.9911 1.236596 14 4 1033 1041 0.7355882 0.7411525 0.7390659 3 77.518786 128.0424 1.236659 16 3 1050 1058 0.7501937 0.7557572 0.7550619 3 54.000402 215.6149 1.236608 18 4 1307 1315 0.9373030 0.9435625 0.9413764 2 77.662700 126.9766 1.237958 19 2 1316 1325 0.9442579 0.9505210 0.9480846 2 8.791047 276.4636 1.238128 jfcv2 co2slp o2slp co2sd o2sd 2 1.336023 -0.0059701426 1.66057306 0.016641196 4.9396605 3 1.336255 -0.0078837509 0.77296021 0.021345132 2.2100092 4 1.336432 -0.0322654462 0.58277527 0.022848388 2.1777505 6 1.343494 0.0088508749 0.37708736 0.021918246 3.5982268 7 1.343916 0.0008467661 0.01591005 0.013073880 6.9072369 8 1.344438 -0.0060673708 3.23700140 0.015069165 4.3099497 10 1.352322 0.0042787635 0.14309858 0.011569517 1.9041020 11 1.352414 -0.0011500321 -0.34400505 0.014370457 2.3939388 13 1.360776 0.0005942588 0.14129597 0.005154613 1.9407026 14 1.360920 0.0076463237 -1.32743469 0.019385980 7.5596874 16 1.360751 -0.0037668966 0.14515009 0.009146867 0.2764682 18 1.362375 -0.0034658489 1.13709975 0.014117011 5.2573989 19 1.362506 0.0032026134 3.08500151 0.010543900 9.2239593 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 372.913 co2l1 = 0.405 co2l0 = -0.21" [1] "co2l0 = -142.74 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "37 out of 150 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "113 out of 1208 1-min values rejected as stack air" [1] "113 out of 1208 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"