[1] "2025-04-29 20:24:28 MDT" [1] "1401" "140129" "d029" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140129a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86280 63 [1] 86280 [1] 86280 [1] "testing skipping spike filter" [1] 86280 [1] 86280 [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 20:24:32 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.811, ave o2scale2 = 0.738" [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] "2 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.811, ave o2scale2 = 0.738" [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] "2 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:24:32 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:24:32 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:24:50 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:24:51 MDT" [1] "reading in recalculated plot titles" [1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1434 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:25:08 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 = 0.459 co2off = 379.08 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.02 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.03 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 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 4 4 239 248 0.1669479 0.1732114 0.1707766 2 55.138516 161.9927 1.235038 5 2 249 258 0.1739067 0.1801767 0.1777382 2 -5.529102 305.7995 1.235126 7 2 539 548 0.3756563 0.3819156 0.3794816 3 -5.166797 304.0948 1.233637 8 4 549 558 0.3826111 0.3888709 0.3864368 3 55.154367 159.8437 1.233406 9 3 559 568 0.3895664 0.3958295 0.3947863 3 34.567906 234.0827 1.233469 11 4 839 848 0.5843455 0.5906049 0.5881705 2 55.151031 159.8827 1.232740 12 2 849 858 0.5913002 0.5975592 0.5951252 2 -4.976305 306.8286 1.232649 13 5 859 868 0.5982547 0.6045144 0.6034714 NA 30.188687 211.8836 1.232770 15 2 1139 1148 0.7930377 0.7992973 0.7968631 3 -4.832648 302.1608 1.231610 16 4 1149 1158 0.7999930 0.8062519 0.8038176 3 55.175547 155.2628 1.231681 17 3 1159 1168 0.8069475 0.8132063 0.8121633 3 34.678500 238.3292 1.231796 jfcv2 co2slp o2slp co2sd o2sd 4 1.357775 -0.0016817127 0.9995982 0.010947457 4.713582 5 1.357845 -0.0091471277 3.4027818 0.025441173 8.897938 7 1.356335 -0.0042598769 2.7989388 0.012333252 8.105420 8 1.356079 0.0051295787 0.3749665 0.014690499 2.800901 9 1.356134 0.0002328125 3.1764642 0.001862458 6.999526 11 1.355191 0.0043905350 1.6380195 0.011459556 4.821462 12 1.355109 -0.0040972793 2.8323881 0.013542198 8.848782 13 1.355262 -0.0290850081 2.7326316 0.020594485 4.005476 15 1.353774 -0.0030168051 1.4452959 0.010177276 5.275589 16 1.353971 0.0063472205 -2.8002472 0.017442852 10.401467 17 1.354108 0.0020773509 -6.9101627 0.007769345 9.125923 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.985 co2l1 = 0.458 co2l0 = 0.019" [1] "co2l0 = -148.45 co2l1 = 0.219" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "97 out of 250 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "153 out of 1273 1-min values rejected as stack air" [1] "144 out of 1215 Line 1 1-min values rejected as stack air" [1] "9 out of 58 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"