[1] "2025-04-29 20:22:40 MDT" [1] "1401" "140126" "d026" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140126a.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 20:22:45 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.814, 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] "74 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.814, ave o2scale2 = 0.74" [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] "74 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:22:45 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:22:45 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:23:03 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:23:04 MDT" [1] "reading in recalculated plot titles" [1] "Removed 74 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1362 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:23:16 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 = -475.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.08 O2 = -572.2" [1] "position 5 cylinder CB09982 description: WT1 CO2 = 479.38 O2 = -1131.8" [1] "position 6 cylinder CB10019 description: WT2 CO2 = 407.52 O2 = -753.5" [1] "Nominal linear calibrations:" [1] "co2scl = 0.462 co2off = 384.13 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.8 minutes" [1] "Shortest Cal: 7.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 4 6 [3,] 7 8 [4,] 9 12 [5,] 13 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 194 203 0.1378534 0.1441168 0.1416796 2 54.796023 162.0642 1.229765 3 2 204 213 0.1448123 0.1510713 0.1486372 2 -5.014695 302.2539 1.229964 4 5 214 223 0.1517674 0.1580301 0.1569845 NA 30.001719 223.4354 1.229964 6 2 493 502 0.3465628 0.3528219 0.3503880 3 -5.040820 302.3541 1.229903 7 4 503 512 0.3535174 0.3597771 0.3573430 3 54.810367 165.0422 1.229828 8 3 513 522 0.3604724 0.3667321 0.3656887 3 34.431898 246.1779 1.229941 10 4 784 793 0.5552824 0.5615420 0.5591080 2 54.838414 155.0513 1.229463 11 2 794 802 0.5622376 0.5678055 0.5657187 2 -4.941179 309.4110 1.229789 13 2 1070 1079 0.7639700 0.7702295 0.7677952 3 -4.980422 309.4139 1.229404 14 4 1080 1089 0.7709251 0.7771886 0.7747512 3 54.829805 157.4864 1.229226 15 5 1090 1099 0.7778840 0.7841470 0.7831036 NA 30.126000 220.8469 1.229059 16 3 1100 1109 0.7848425 0.7911053 0.7900619 3 34.451359 239.2708 1.229039 18 4 1337 1340 0.9740451 0.9789135 0.9785656 2 54.873875 162.9328 1.226815 19 2 1341 1347 0.9796093 0.9858681 0.9836427 2 -5.147379 303.2421 1.227048 jfcv2 co2slp o2slp co2sd o2sd 2 1.352002 0.0034795989 1.609527e+00 0.012667844 4.768011 3 1.352200 -0.0015711628 2.119173e+00 0.013222235 5.922758 4 1.352133 -0.0562033195 -3.448418e-01 0.039907339 5.659101 6 1.352165 -0.0046514862 2.150130e+00 0.013481032 5.970848 7 1.352080 0.0086428043 2.363394e+00 0.027322978 6.495612 8 1.352276 0.0034122532 1.082212e+00 0.009534649 1.685068 10 1.351594 -0.0015410078 3.548321e+00 0.012132267 16.343893 11 1.351988 0.0001646978 6.703293e+00 0.002383053 16.182857 13 1.351659 -0.0017205222 3.185438e+00 0.012849478 8.014320 14 1.351488 0.0072982161 1.985445e-02 0.022376507 2.193508 15 1.351312 -0.0324459235 2.196810e+00 0.022980970 3.131686 16 1.351308 -0.0012315252 -1.898543e+00 0.007779018 3.326624 18 1.348916 0.0054901635 1.584147e-14 0.003889087 0.000000 19 1.349236 0.0020994641 3.224761e+00 0.009415534 10.086362 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.949 co2l1 = 0.461 co2l0 = 0.017" [1] "co2l0 = -149.08 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "122 out of 215 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "93 out of 1180 1-min values rejected as stack air" [1] "93 out of 1180 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"