[1] "2025-04-29 20:55:33 MDT" [1] "1403" "140326" "d085" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140326a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86100 63 [1] 86100 [1] 86100 [1] "testing skipping spike filter" [1] 86100 [1] 86100 [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 20:55:37 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.83, ave o2scale2 = 0.755" [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] "2 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.83, ave o2scale2 = 0.755" [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] "2 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:55:38 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:55:38 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:55:56 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:55:57 MDT" [1] "reading in recalculated plot titles" [1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1432 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:56:00 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] "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 = 0.429 co2off = 369.09 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,] 3 5 [3,] 6 7 [4,] 9 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 3 4 216 225 0.1501026 0.1563654 0.1539312 2 82.58202 130.3816 1.202165 4 2 226 235 0.1570607 0.1633201 0.1608859 2 18.21093 271.7480 1.202288 6 2 511 520 0.3585448 0.3648040 0.3623698 3 17.95309 274.9650 1.203197 7 4 521 530 0.3654993 0.3717593 0.3693248 3 82.40609 130.2766 1.203205 8 3 531 540 0.3724549 0.3787141 0.3776707 3 60.30772 212.1738 1.203389 10 4 811 820 0.5672166 0.5734764 0.5710422 2 82.15569 128.8771 1.205271 11 2 821 830 0.5741718 0.5804345 0.5779992 2 17.72811 273.6575 1.205512 12 5 831 840 0.5811302 0.5873897 0.5863463 NA 56.02406 191.0362 1.205470 14 2 1111 1120 0.7759039 0.7821632 0.7797288 3 17.56898 271.9308 1.207926 15 4 1121 1130 0.7828586 0.7891215 0.7866865 3 82.02009 129.9776 1.207802 16 3 1131 1140 0.7898171 0.7960764 0.7950332 3 59.90392 211.3026 1.207863 20 4 1411 1420 0.9846019 0.9908612 0.9884272 2 81.91628 130.3533 1.210687 21 2 1421 1430 0.9915567 0.9978161 0.9953822 2 17.28917 272.4348 1.211098 jfcv2 co2slp o2slp co2sd o2sd 3 1.320806 0.0015750180 1.16331689 0.006227437 3.616328 4 1.320951 0.0049231908 1.44536572 0.012599578 4.578631 6 1.321979 -0.0055212117 0.05858755 0.015685704 2.825353 7 1.321975 0.0029922350 0.82727989 0.013292931 5.304620 8 1.322176 -0.0007876199 1.39068451 0.005496245 1.847549 10 1.324223 0.0066251995 0.94534047 0.021790526 2.660426 11 1.324504 -0.0073917781 0.28975095 0.018295160 3.626559 12 1.324477 -0.0532640333 -1.25102680 0.037741824 1.629105 14 1.327154 -0.0089180428 0.18233314 0.022439023 3.988175 15 1.327033 0.0096510478 1.33144453 0.026826221 4.160945 16 1.327092 -0.0007426544 0.88950977 0.007885817 1.248289 20 1.330237 -0.0044323504 0.97582845 0.013949486 4.051099 21 1.330705 -0.0051826804 0.78775888 0.013798605 3.515788 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 369.035 co2l1 = 0.428 co2l0 = -0.393" [1] "co2l0 = -142.65 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "55 out of 265 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "210 out of 1247 1-min values rejected as stack air" [1] "160 out of 1097 Line 1 1-min values rejected as stack air" [1] "50 out of 150 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"