[1] "2025-04-29 21:37:09 MDT" [1] "1406" "140721" "d202" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140721a.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 21:37:13 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.814, ave o2scale2 = 0.733" [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] "4 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.814, ave o2scale2 = 0.733" [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] "4 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:37:13 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:37:13 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:37:35 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:37:36 MDT" [1] "reading in recalculated plot titles" [1] "Removed 4 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1432 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:37:41 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 = -476.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.6" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.5" [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 = 0.472 co2off = 385.93 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: 9.03 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 9 [4,] 10 11 [5,] 12 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 55 64 0.03816056 0.04442361 0.04198775 3 -19.36966 279.8378 3 4 65 74 0.04511916 0.05138194 0.04894676 3 39.09009 136.8825 4 3 75 84 0.05207743 0.05834028 0.05729688 3 19.26850 223.7704 6 4 355 364 0.24692694 0.25319783 0.25075722 2 39.00629 135.5354 7 2 365 374 0.25389314 0.26015602 0.25771992 2 -19.45663 280.1143 9 2 655 664 0.45571137 0.46197454 0.45953868 3 -19.60668 280.3943 10 4 665 674 0.46266994 0.46893261 0.46649748 3 38.83552 138.9965 11 5 675 684 0.46962795 0.47589054 0.47484750 NA 16.58444 197.2326 12 3 685 694 0.47658857 0.48285223 0.48180655 3 19.02183 218.5619 14 4 955 964 0.66447225 0.67073600 0.66830112 2 38.82476 136.0738 15 2 965 974 0.67143142 0.67769447 0.67525887 2 -19.66365 280.9735 17 2 1251 1260 0.87320781 0.87947106 0.87703363 3 -19.61105 281.1766 18 4 1261 1270 0.88016664 0.88642593 0.88399154 3 38.84870 134.4586 19 3 1271 1280 0.88712153 0.89338464 0.89233874 3 19.02045 216.0405 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.236382 1.372323 -0.0007236920 0.56167360 0.005773529 2.1869498 3 1.236238 1.372178 0.0082519761 -0.99717236 0.022355836 5.1728280 4 1.236273 1.372245 -0.0026875306 4.16576976 0.007233201 5.5097716 6 1.232201 1.367769 0.0032830369 -0.23360051 0.009668093 3.4322750 7 1.232256 1.367855 -0.0058063067 -0.90710686 0.015896795 4.0545850 9 1.229193 1.364546 -0.0023350035 -0.05653922 0.007061863 1.1105388 10 1.229032 1.364378 0.0031605735 0.26535602 0.009741350 4.4032751 11 1.228749 1.364077 -0.0091128495 0.17063389 0.006452349 0.7659002 12 1.228737 1.364041 0.0006303506 0.65700852 0.004912260 0.8543920 14 1.225701 1.360752 -0.0021729133 1.68659180 0.006587701 5.3309383 15 1.225459 1.360492 -0.0090981874 0.65856835 0.024601125 7.8682621 17 1.224259 1.359245 -0.0043105141 -0.61591046 0.011071387 2.0495783 18 1.223806 1.358758 0.0013528976 0.08296992 0.009748422 1.5129227 19 1.224194 1.359190 -0.0054464185 1.43026808 0.016061073 3.5889467 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 385.87 co2l1 = 0.472 co2l0 = 0.084" [1] "co2l0 = -143.91 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "261 out of 700 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "439 out of 1250 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "439 out of 1250 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"