[1] "2025-04-29 20:28:37 MDT" [1] "1401" "140204" "d035" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140204a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85739 63 [1] 85739 [1] 85739 [1] "testing skipping spike filter" [1] 85739 [1] 85739 [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 20:28:41 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.807, ave o2scale2 = 0.735" [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] "49 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.807, ave o2scale2 = 0.735" [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] "48 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:28:42 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:28:42 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:28:51 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:28:52 MDT" [1] "reading in recalculated plot titles" [1] "Removed 48 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 2 row(s) with variable TFCELL" [1] "TEMP: 1377 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:28:59 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 = -475.8" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -633.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 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 = 0.458 co2off = 367.68 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 8.42 minutes" [1] "Shortest Cal: 1 minutes" [1] "Longest Cal: 9.74 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 6 [3,] 7 8 [4,] 9 9 [5,] 11 12 [6,] 13 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 14 23 0.009741927 0.01600231 0.01356778 2 55.954641 157.8580 3 2 24 33 0.016697917 0.02295732 0.02052308 2 -4.258711 301.7205 5 2 314 323 0.218436169 0.22470012 0.22226289 3 -4.562383 306.9915 6 4 324 333 0.225395544 0.23165856 0.22922179 3 56.027742 156.5747 7 5 334 343 0.232354138 0.23861693 0.23757384 NA 31.107062 226.3727 8 3 344 353 0.239312558 0.24557280 0.24452941 3 35.366500 242.1073 10 4 614 623 0.427155093 0.43341814 0.43098166 2 56.051734 163.0792 11 2 624 633 0.434113571 0.44037277 0.43793877 2 -4.521617 301.5144 14 4 793 801 0.581724132 0.58798843 0.58580159 1 56.005943 166.2931 15 5 802 811 0.588683825 0.59516881 0.59411700 NA 30.242375 222.4875 17 4 1072 1081 0.776782610 0.78304410 0.78060931 2 55.948430 148.4398 18 2 1082 1091 0.783740567 0.78999939 0.78756535 2 -4.002961 305.4171 20 2 1360 1367 0.985576360 0.99044876 0.98870752 2 -4.190708 300.1885 21 4 1368 1377 0.992545312 0.99930906 0.99670074 2 56.116656 166.0305 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.242315 1.365320 0.001653533 0.42252866 0.004927799 4.629532 3 1.242425 1.365435 -0.001418262 1.81879339 0.009991287 9.997564 5 1.241485 1.364336 -0.009924739 -0.04839328 0.024674000 7.162791 6 1.241307 1.364145 0.011085375 0.90051863 0.028425546 6.446141 7 1.241234 1.364066 -0.024591187 -1.25669230 0.017412504 2.195776 8 1.241292 1.364191 -0.003168688 -1.64356662 0.009620535 3.526760 10 1.240144 1.363017 0.004492570 3.00632664 0.012483371 7.748858 11 1.240152 1.363072 -0.003327960 2.14815086 0.011417378 12.030376 14 1.237789 1.360979 0.003083477 0.77845172 0.008678466 7.097073 15 1.237987 1.361242 -0.032954687 2.98819562 0.023334524 7.008719 17 1.235799 1.358846 -0.005507386 4.36735086 0.015855213 12.607461 18 1.235702 1.358727 -0.015737846 0.75638857 0.039520281 3.867108 20 1.232527 1.355062 0.016681986 3.79894405 0.032277742 9.933650 21 1.232781 1.355367 0.007676897 0.70479277 0.025559040 10.761434 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.594 co2l1 = 0.458 co2l0 = 0.013" [1] "co2l0 = -148.57 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "70 out of 185 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "115 out of 1191 1-min values rejected as stack air" [1] "115 out of 1191 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"