[1] "2025-04-29 20:48:33 MDT" [1] "1402" "140312" "d071" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140312a.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 20:48:37 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.829, ave o2scale2 = 0.754" [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] "144 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.829, ave o2scale2 = 0.754" [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] "144 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:48:38 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:48:38 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:48:54 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:48:55 MDT" [1] "reading in recalculated plot titles" [1] "Removed 144 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1292 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:48:59 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 = -476" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -633.9" [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 = 0.451 co2off = 373.05 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.23 minutes" [1] "Shortest Cal: 4.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 7 [4,] 9 10 [5,] 11 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 3 12 0.002376157 0.008635446 0.006201121 3 -4.081055 302.9367 3 4 13 22 0.009331105 0.015590365 0.013156207 3 57.178953 160.9467 4 3 23 32 0.016285909 0.022545139 0.021501888 3 36.279555 246.0264 6 4 303 312 0.211101852 0.217364641 0.214929691 2 57.194172 159.3112 7 2 313 322 0.218060185 0.224319965 0.221885731 2 -3.603961 299.6464 9 2 595 601 0.421885822 0.426058970 0.424667841 2 -3.968638 306.4385 10 4 602 611 0.426754398 0.433013976 0.430579395 2 57.127828 162.6035 11 5 612 621 0.433709491 0.439972483 0.438927937 NA 31.975687 229.7936 15 4 835 844 0.628481481 0.634740770 0.632306720 2 57.239039 161.1937 16 2 845 851 0.636132031 0.641695862 0.639470492 2 -4.326175 307.5684 18 2 1088 1097 0.837184722 0.843449971 0.841013549 3 -4.580688 304.6376 19 4 1098 1106 0.844145544 0.850405353 0.848319238 3 57.286599 162.9562 20 3 1107 1114 0.852491898 0.857363773 0.857016102 3 36.039563 226.1088 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.205709 1.325322 0.0088432966 2.0865817 0.022125818 6.355506 3 1.205652 1.325263 0.0019452967 1.0077428 0.006468825 3.092775 4 1.205586 1.325200 -0.0004851695 -1.6567041 0.006825915 2.872553 6 1.206120 1.325764 0.0024124010 1.9001834 0.006477360 6.365089 7 1.206155 1.325787 0.0024745083 2.1081501 0.006913685 6.829919 9 1.205825 1.325405 0.0012230357 -0.1849598 0.007636953 4.806817 10 1.205241 1.324866 0.0050541693 1.3761398 0.017237015 4.811335 11 1.205263 1.324887 -0.0370925440 2.3361249 0.026251339 3.249690 15 1.206528 1.326244 0.0029533703 0.1446698 0.009796930 1.879174 16 1.206871 1.326543 -0.0020814522 1.8404842 0.005888847 4.867487 18 1.207897 1.327671 -0.0030631784 0.9570239 0.015204961 6.117904 19 1.207626 1.327339 0.0017558795 -1.1327959 0.012127234 3.624192 20 1.207808 1.327597 -0.0006810597 -9.6801977 0.004552472 6.853775 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.487 co2l1 = 0.45 co2l0 = 0.012" [1] "co2l0 = -149.41 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "77 out of 387 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "310 out of 1122 1-min values rejected as stack air" [1] "308 out of 849 Line 1 1-min values rejected as stack air" [1] "2 out of 273 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"