[1] "2025-04-29 22:38:24 MDT" [1] "1411" "141211" "d345" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141211a.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 22:38:28 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.853, ave o2scale2 = 0.77" [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] "46 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.853, ave o2scale2 = 0.77" [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] "46 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:38:28 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:38:28 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:38:50 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:38:51 MDT" [1] "reading in recalculated plot titles" [1] "Removed 46 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1390 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:38:56 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.63 O2 = -477.4" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.3" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.24 O2 = -635" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.945 co2off = 400.89 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.87 minutes" [1] "Shortest Cal: 7.01 minutes" [1] "Longest Cal: 9.1 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 5 [3,] 6 7 [4,] 8 10 [5,] 11 12 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 17 26 0.01184644 0.01816667 0.01570781 2 3.516703 383.3161 3 2 27 36 0.01886881 0.02518403 0.02272748 2 -25.749734 528.5146 6 2 302 311 0.22072659 0.22698579 0.22455156 3 -25.819242 529.5777 7 4 312 321 0.22768131 0.23394097 0.23150665 3 3.452914 384.6225 8 3 322 331 0.23463646 0.24089586 0.23985273 3 -6.347508 461.8311 10 4 586 595 0.42949306 0.43575619 0.43332071 2 3.410898 379.8811 11 2 596 605 0.43645159 0.44271493 0.44027984 2 -25.847570 531.1678 14 2 879 888 0.63823495 0.64449418 0.64205987 3 -25.972758 526.7443 15 4 889 898 0.64518981 0.65144881 0.64901463 3 3.304484 381.3492 16 3 899 906 0.65353484 0.65840373 0.65805602 3 -6.535750 461.1712 18 4 1173 1182 0.84696803 0.85322769 0.85079352 2 3.240875 383.4278 19 2 1183 1192 0.85392295 0.86018275 0.85774837 2 -26.040641 533.9951 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.182277 1.309973 0.0001791515 0.90231615 0.001664275 3.525550 3 1.182212 1.309880 -0.0030083918 0.00383228 0.007949250 1.370069 6 1.178207 1.305641 -0.0004613218 -1.03233781 0.002660357 3.752974 7 1.178303 1.305730 0.0028150206 -1.47556158 0.007731540 4.990618 8 1.178322 1.305770 -0.0009814832 0.84651611 0.003708316 1.551560 10 1.175020 1.302166 -0.0006928003 -2.01345030 0.002699607 6.386932 11 1.174935 1.302085 -0.0030812078 0.44261051 0.009536258 5.081479 14 1.168839 1.295174 -0.0003437032 -0.09237078 0.008001635 3.203793 15 1.168644 1.294957 0.0006432472 1.18953901 0.005622296 4.124339 16 1.168087 1.294365 -0.0024603566 -4.01172363 0.004634281 2.840736 18 1.164779 1.290483 0.0016343996 3.13596442 0.004918646 10.875942 19 1.164972 1.290679 -0.0007889870 -0.63037873 0.005204174 3.128088 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 401.046 co2l1 = 0.943 co2l0 = 0.001" [1] "co2l0 = -196.38 co2l1 = 0.216" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "24 out of 110 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "86 out of 1209 1-min values rejected as stack air" [1] "79 out of 1161 Line 1 1-min values rejected as stack air" [1] "7 out of 48 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"