[1] "2025-04-29 21:24:19 MDT" [1] "1406" "140629" "d180" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140629a.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 21:24:23 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.824, ave o2scale2 = 0.742" [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 1 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 = 0.824, ave o2scale2 = 0.742" [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 2 RC FC 2 jog(s) with SP SD > 1000" [1] "3 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:24:24 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:24:24 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:24:44 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:24:45 MDT" [1] "reading in recalculated plot titles" [1] "Removed 3 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1433 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:24:49 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 = -476.5" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.7" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -634.4" [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 = 0.468 co2off = 380.85 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: 9.02 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,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 161 170 0.1137350 0.1199942 0.1175602 2 49.931367 134.8727 1.207844 3 2 171 180 0.1206935 0.1269526 0.1245186 2 -9.147672 279.1982 1.208349 5 2 461 470 0.3224734 0.3287328 0.3262984 3 -9.057914 281.6561 1.212782 6 4 471 480 0.3294282 0.3356881 0.3332535 3 49.983297 125.7977 1.212591 7 3 481 490 0.3363833 0.3426463 0.3416007 3 29.958437 213.2877 1.212908 9 4 760 769 0.5311968 0.5374595 0.5350246 2 50.046195 136.0600 1.215983 10 2 770 779 0.5381550 0.5444178 0.5419837 2 -9.035914 273.2629 1.215910 11 5 780 789 0.5451134 0.5513727 0.5503298 NA 28.117000 206.1590 1.216286 13 2 1060 1069 0.7399710 0.7462303 0.7437959 3 -9.057500 283.8575 1.217070 14 4 1070 1079 0.7469258 0.7531884 0.7507542 3 50.022859 132.0791 1.217611 15 3 1080 1089 0.7538839 0.7601468 0.7591036 3 30.026227 214.5276 1.217977 17 4 1360 1369 0.9487413 0.9550045 0.9525694 2 50.021406 139.8606 1.218389 18 2 1370 1379 0.9556998 0.9619630 0.9595272 2 -9.021445 283.1422 1.218697 jfcv2 co2slp o2slp co2sd o2sd 2 1.340124 -5.531605e-03 1.2112028 0.016005630 5.754428 3 1.340671 -5.747942e-03 -0.3077588 0.015775410 7.588804 5 1.345333 -7.497991e-03 -2.2408462 0.020082140 6.497840 6 1.345019 3.152896e-03 -0.6870010 0.009771311 4.422848 7 1.345438 -1.318950e-03 -0.7431132 0.004863999 1.720747 9 1.349236 -5.412148e-03 2.1624450 0.013492079 7.535322 10 1.349192 -6.206291e-03 -0.8624974 0.019674129 4.901516 11 1.349369 7.740969e-03 2.3264267 0.005480078 3.068271 13 1.350990 -3.808296e-03 3.8833105 0.010171849 24.572653 14 1.351242 6.283631e-03 0.8055560 0.016111454 12.277175 15 1.351355 -6.012236e-05 0.1834219 0.004445721 2.416209 17 1.352027 6.868982e-04 4.2550547 0.005470293 12.745571 18 1.352210 -2.572433e-03 -0.8289922 0.008993763 8.750421 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 380.869 co2l1 = 0.467 co2l0 = 0.038" [1] "co2l0 = -142.84 co2l1 = 0.218" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "69 out of 210 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "141 out of 1251 1-min values rejected as stack air" [1] "141 out of 1251 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"