[1] "2025-04-29 21:42:41 MDT" [1] "1406" "140730" "d211" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140730a.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 21:42:45 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.822, ave o2scale2 = 0.74" [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] "0 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.822, ave o2scale2 = 0.74" [1] "Removing 1 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 1 RC FC 2 jog(s) with SP SD > 1000" [1] "2 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:42:45 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:42:45 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:43:05 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:43:07 MDT" [1] "reading in recalculated plot titles" [1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1434 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:43:13 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 = -476.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.6" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.5" [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 = 0.473 co2off = 386.23 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 9.02 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.04 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 6 [3,] 7 8 [4,] 9 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 18 27 0.01430321 0.02056600 0.01813117 2 38.33222 136.3196 3 2 28 37 0.02126157 0.02752474 0.02508932 2 -20.09441 281.9468 5 2 318 327 0.22307066 0.22933058 0.22689616 3 -20.05505 281.2616 6 4 328 337 0.23002587 0.23628579 0.23385103 3 38.37971 137.3875 7 5 338 347 0.23698116 0.24323999 0.24219699 NA 16.16528 195.6195 8 3 348 357 0.24393539 0.25019841 0.24915537 3 18.56105 221.4908 10 4 618 627 0.43183958 0.43811019 0.43567050 2 38.37957 134.9495 11 2 628 637 0.43880677 0.44506597 0.44263184 2 -20.06588 280.9490 13 2 918 927 0.64063947 0.64690284 0.64446842 3 -19.99462 282.9924 14 4 928 937 0.64759838 0.65386852 0.65142831 3 38.45431 135.8120 15 3 938 947 0.65456933 0.66084586 0.65980213 3 18.68523 212.6933 17 4 1218 1227 0.84942130 0.85568426 0.85325022 2 38.49573 140.6183 18 2 1228 1237 0.85638362 0.86264690 0.86020948 2 -19.94163 280.8908 19 5 1238 1247 0.86334230 0.86960535 0.86856142 NA 16.21291 199.9370 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.214909 1.349112 0.0011121098 0.714248500 0.004511147 2.4291968 3 1.214956 1.349168 -0.0008884301 0.584600828 0.013060041 3.9970125 5 1.215398 1.349614 -0.0056584111 0.088515796 0.014134259 1.5402540 6 1.215380 1.349606 0.0031373689 -0.009657843 0.014744587 1.0754570 7 1.215489 1.349722 -0.0093008739 0.973046921 0.006584932 1.6816957 8 1.215343 1.349560 -0.0006426400 0.381446150 0.002327398 1.1470424 10 1.215241 1.349458 -0.0014630753 -0.227397735 0.007559174 3.1061700 11 1.215132 1.349326 -0.0061803437 -0.123874115 0.017225882 0.9662091 13 1.217606 1.352020 0.0003930881 0.141115563 0.005274649 1.1238817 14 1.217355 1.351756 0.0025511026 0.363737463 0.012449586 1.8043900 15 1.217748 1.352201 0.0036959977 1.823381126 0.010811232 3.3286497 17 1.221273 1.356067 -0.0029221037 0.479268442 0.008830367 2.0338216 18 1.221656 1.356479 -0.0019069651 0.956825340 0.008990225 3.6100982 19 1.221357 1.356207 -0.0105475576 0.787802016 0.007468815 1.1596211 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.097 co2l1 = 0.473 co2l0 = 0.08" [1] "co2l0 = -143.87 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "159 out of 842 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "683 out of 1242 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "683 out of 1242 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"