[1] "2025-04-29 20:20:45 MDT" [1] "1401" "140123" "d023" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140123a.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 20:20:49 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.807, ave o2scale2 = 0.734" [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] "15 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.807, ave o2scale2 = 0.734" [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 1 RC FC 2 jog(s) with SP SD > 1000" [1] "17 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:20:50 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:20:50 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:21:07 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:21:08 MDT" [1] "reading in recalculated plot titles" [1] "Removed 17 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1419 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:21:18 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 = 0.455 co2off = 384.46 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.88 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 4 [2,] 5 6 [3,] 7 9 [4,] 10 11 [5,] 13 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 8 17 0.007377199 0.01364074 0.01120389 3 -6.108398 304.8744 3 4 18 27 0.014336169 0.02059586 0.01816152 3 54.791305 166.1957 4 5 28 37 0.021291262 0.02755072 0.02650747 NA 29.502688 226.7135 5 3 38 47 0.028246152 0.03450579 0.03346246 3 34.000492 242.5958 7 4 308 317 0.216059375 0.22231936 0.21988481 2 54.716766 163.6642 8 2 318 327 0.223014757 0.22927523 0.22683986 2 -5.819117 302.5720 10 2 608 617 0.424761806 0.43102124 0.42858719 3 -6.069500 303.8162 11 4 618 627 0.431717419 0.43797674 0.43554243 3 54.769625 156.9710 12 3 628 637 0.438672135 0.44493174 0.44388854 3 34.016094 242.5273 14 4 902 911 0.633445891 0.63970663 0.63727262 2 54.777781 167.5171 15 2 912 921 0.640401939 0.64666198 0.64422764 2 -6.181031 295.0867 16 5 922 931 0.647357031 0.65361629 0.65257324 NA 29.410438 238.8033 18 2 1201 1210 0.842130787 0.84839005 0.84595577 3 -6.026078 295.3499 19 4 1211 1218 0.849085648 0.85395370 0.85221505 3 54.667854 154.4730 20 3 1219 1228 0.856040191 0.86229957 0.86125632 3 33.879805 242.5567 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.240991 1.364632 0.005027406 2.87412835 0.013456400 7.280417 3 1.240960 1.364603 0.004862034 0.77802496 0.018140832 6.676148 4 1.240865 1.364504 -0.028336038 -2.17675250 0.020064155 3.055903 5 1.240958 1.364609 -0.001168717 0.02093115 0.011629101 1.842240 7 1.240148 1.363687 0.003580358 0.83082634 0.010750091 4.577355 8 1.240221 1.363780 -0.007434556 2.46218478 0.019054036 7.817388 10 1.239933 1.363439 -0.001267524 1.12934573 0.004466018 5.071111 11 1.239918 1.363395 0.007311946 0.38134150 0.018482859 5.905634 12 1.240001 1.363514 0.004278162 2.23837603 0.012751007 3.530910 14 1.238400 1.361614 -0.004012192 5.14975348 0.013227027 15.311894 15 1.238340 1.361539 -0.006411421 1.31415763 0.017181833 8.575243 16 1.238281 1.361313 -0.030334554 -9.93992077 0.021478368 15.084164 18 1.235925 1.358903 -0.007095731 2.90516155 0.020523064 11.295341 19 1.235838 1.358805 0.013323867 2.80339166 0.029676555 7.414918 20 1.235898 1.358746 -0.003517571 0.44780229 0.009660038 2.093856 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.386 co2l1 = 0.454 co2l0 = 0.031" [1] "co2l0 = -150.98 co2l1 = 0.23" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "63 out of 145 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "82 out of 1214 1-min values rejected as stack air" [1] "82 out of 1214 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"