[1] "2025-04-29 22:08:05 MDT" [1] "1408" "140926" "d269" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140926a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 73955 63 [1] 73955 [1] 73955 [1] "testing skipping spike filter" [1] 73955 [1] 73955 [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 22:08:09 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.822, 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] "179 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.822, 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] "179 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:08:09 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:08:09 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:08:26 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:08:27 MDT" [1] "reading in recalculated plot titles" [1] "Removed 179 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1053 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:08:32 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 = -477" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.5" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.7" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.479 co2off = 378.44 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 7.93 minutes" [1] "Shortest Cal: 1 minutes" [1] "Longest Cal: 9.01 minutes" [1] "Removed 3 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 5 [3,] 6 7 [4,] 8 9 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 130 138 0.1272408 0.1335000 0.1314138 2 28.076728 136.8482 3 2 139 148 0.1341956 0.1404551 0.1380209 2 -29.723063 283.1197 6 2 396 403 0.3366142 0.3421781 0.3403234 3 -29.841102 287.9479 7 4 404 413 0.3428734 0.3491331 0.3466990 3 27.923141 142.6520 8 3 414 422 0.3498287 0.3560880 0.3553926 3 8.307519 220.3002 10 4 675 684 0.5446030 0.5508623 0.5484279 2 27.829539 136.7291 11 2 685 694 0.5515579 0.5578168 0.5553826 2 -29.968680 282.0826 14 4 950 958 0.7602343 0.7664936 0.7639105 2 27.767007 135.9941 16 3 966 975 0.7741444 0.7804039 0.7793606 2 8.233852 218.5517 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.215511 1.348952 -0.0020322566 -4.2827663 0.008927946 11.660703 3 1.215920 1.349422 -0.0043488441 -0.8609447 0.015351426 7.229474 6 1.216825 1.350603 0.0013183310 2.7252446 0.004064621 6.494582 7 1.217089 1.350802 0.0027727918 1.1329202 0.012104675 17.207980 8 1.216707 1.350410 -0.0036508794 7.5642163 0.009957876 7.626136 10 1.217159 1.350847 -0.0005890244 -0.3504085 0.003829796 3.979322 11 1.217247 1.350948 -0.0007268492 0.9121220 0.019304753 10.975673 14 1.216898 1.350555 0.0046145141 0.7212491 0.017403505 4.077803 16 1.217931 1.351768 -0.0024937425 -0.7606528 0.007844964 1.457192 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 390.946 co2l1 = 0.477 co2l0 = 0.105" [1] "co2l0 = -143.58 co2l1 = 0.217" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "193 out of 268 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "75 out of 903 1-min values rejected as stack air" [1] "75 out of 903 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"