[1] "2025-04-29 21:51:54 MDT" [1] "1406" "140817" "d229" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140817a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85665 63 [1] 85665 [1] 85665 [1] "testing skipping spike filter" [1] 85665 [1] 85665 [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 21:51:58 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.836, 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] "1 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.836, 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] "1 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:51:59 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:51:59 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:52:10 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:52:12 MDT" [1] "reading in recalculated plot titles" [1] "Removed 1 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "Removed 5 row(s) with variable TFCELL" [1] "Removed 1 row(s) with LiCO2A spikes in them" [1] "TEMP: 1418 21 TRUE" [1] "Removed 21 row(s) with -999.99 for a Licor jog SD" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:52:15 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 = -476.8" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.6" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.6" [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 = 386.28 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.03 minutes" [1] "Average Cal: 9.03 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.14 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,] 13 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 257 266 0.1785995 0.1848588 0.1824247 2 38.07412 137.3284 1.194076 3 2 267 276 0.1855544 0.1918137 0.1893796 2 -20.34347 284.3290 1.194101 5 2 557 566 0.3872905 0.3935532 0.3911191 3 -20.24837 280.7016 1.197306 6 4 567 576 0.3942489 0.4005080 0.3980736 3 38.15247 139.1496 1.197198 7 3 577 586 0.4012034 0.4074625 0.4064194 3 18.35081 213.8833 1.197308 10 4 855 864 0.5957026 0.6020486 0.5996042 2 38.21597 138.3816 1.199035 11 2 865 874 0.6027462 0.6090329 0.6065939 2 -20.22980 282.3067 1.199193 12 5 875 884 0.6097300 0.6159962 0.6149520 NA 15.96403 195.9562 1.199254 14 3 1049 1058 0.7566320 0.7629075 0.7618626 3 18.34610 216.1406 1.198077 15 2 1059 1068 0.7636044 0.7698777 0.7674387 3 -20.28829 280.2963 1.198005 16 4 1069 1078 0.7705752 0.7768429 0.7744054 3 38.14891 133.5719 1.198334 17 5 1079 1088 0.7775394 0.7838125 0.7827675 NA 15.04622 202.5891 1.199081 20 4 1349 1358 0.9656618 0.9719324 0.9694927 2 38.12311 139.2570 1.198504 21 2 1359 1368 0.9726296 0.9788986 0.9764611 2 -20.29514 281.0513 1.198740 jfcv2 co2slp o2slp co2sd o2sd 2 1.324137 0.0039878162 0.5968644 0.009892785 2.082034 3 1.324167 -0.0030908074 0.6236205 0.009721857 1.899087 5 1.327658 -0.0007199800 -0.1710154 0.004396432 1.043356 6 1.327535 -0.0017876162 0.7258802 0.009864314 2.742202 7 1.327666 0.0002526371 1.0262795 0.003155918 2.121504 10 1.329631 -0.0054973426 -0.4612398 0.015109644 2.318463 11 1.329758 -0.0036542191 -1.1998598 0.013905309 4.190726 12 1.329804 -0.0043031765 -3.2457150 0.003049398 4.387404 14 1.328762 -0.0006980890 -0.7131728 0.005259233 2.354982 15 1.328638 -0.0002807927 -2.6043981 0.011024169 8.222035 16 1.328945 0.0023607930 0.4282344 0.014076402 5.970897 17 1.329754 -0.0246054817 1.6034551 0.017456699 2.186031 20 1.329039 -0.0026632207 -0.5515954 0.009457715 3.241847 21 1.329293 -0.0031236411 1.3160250 0.009395380 3.567988 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.22 co2l1 = 0.473 co2l0 = 0.085" [1] "co2l0 = -144.07 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "106 out of 370 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "264 out of 1191 1-min values rejected as stack air" [1] "160 out of 356 Line 1 1-min values rejected as stack air" [1] "104 out of 835 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"