[1] "2025-04-29 16:40:16 MDT" [1] "1206" "120625" "d177" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120625b.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 50136 63 [1] 50136 [1] 50136 [1] "testing skipping spike filter" [1] 50136 [1] 50136 [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 16:40:19 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.781, ave o2scale2 = 0.79" [1] "Removing 17 MR FC 1 jog(s) with WT SD > 1000" [1] "Removing 15 MR FC 2 jog(s) with WT SD > 1000" [1] "Removing 15 MR FC 1 jog(s) with SP SD > 1000" [1] "Removing 17 MR FC 2 jog(s) with SP SD > 1000" [1] "269 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.781, ave o2scale2 = 0.79" [1] "Removing 17 RC FC 1 jog(s) with WT SD > 1000" [1] "Removing 15 RC FC 2 jog(s) with WT SD > 1000" [1] "Removing 15 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 17 RC FC 2 jog(s) with SP SD > 1000" [1] "267 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 16:40:19 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 16:40:19 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 16:40:34 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 16:40:35 MDT" [1] "reading in recalculated plot titles" [1] "Removed 268 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 566 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 16:40:39 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -450.4" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.95 O2 = -543.4" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2" [1] "position 5 cylinder CC339495 description: WT1 CO2 = 394.28 O2 = -550.7" [1] "position 6 cylinder CC339490 description: WT2 CO2 = 396.42 O2 = -582.4" [1] "Nominal linear calibrations:" [1] "co2scl = 0.965 co2off = 377.89 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 7.02 minutes" [1] "Average Cal: 7.26 minutes" [1] "Shortest Cal: 6.02 minutes" [1] "Longest Cal: 9.09 minutes" [1] "Removed 2 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 4 [3,] 5 7 [4,] 8 9 [5,] 10 11 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 16 22 0.01484777 0.01972451 0.01805192 2 -12.673713 91.47259 3 4 23 30 0.02042118 0.02529780 0.02355599 2 19.466094 -71.88753 7 4 106 111 0.14028420 0.14447196 0.14325022 2 19.474438 -70.46192 8 2 112 119 0.14726094 0.15214198 0.15039996 2 -12.678562 91.53778 11 2 240 243 0.26582332 0.27070391 0.27035544 3 -12.715812 85.31015 12 4 244 251 0.27139994 0.27627914 0.27453641 3 19.457542 -69.52219 13 3 252 256 0.28046204 0.28465072 0.28720910 3 8.695854 29.35785 15 4 322 331 0.39003741 0.39634670 0.39389319 2 19.470844 -68.86207 16 2 332 338 0.39845061 0.40265738 0.40125517 2 -12.672488 87.43295 18 2 473 482 0.51562329 0.52192746 0.51947670 2 -12.642586 90.41245 19 4 483 492 0.52262737 0.52893756 0.52648379 2 19.488602 -70.92566 20 5 493 502 0.52963961 0.53594696 0.53489648 NA 7.811656 -15.97746 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.283424 1.269968 -0.0020993051 -2.990036e-01 0.0045117793 5.286329 3 1.283442 1.270021 0.0034372209 -1.072557e+00 0.0069817564 2.873979 7 1.280336 1.266904 -0.0001347878 -6.220251e-01 0.0005297159 2.349048 8 1.280169 1.266691 -0.0035899292 4.593158e-01 0.0071458030 1.222479 11 1.277285 1.263681 -0.0008718758 1.688856e-14 0.0006187184 0.000000 12 1.277142 1.263536 0.0041278418 -4.364255e-04 0.0082729479 3.159017 13 1.276922 1.263299 0.0016175345 8.689513e+00 0.0016349853 28.534494 15 1.279120 1.265689 -0.0016058063 4.574476e-01 0.0063309931 4.704329 16 1.279432 1.266001 -0.0042513845 1.212226e-01 0.0068942061 1.777226 18 1.280408 1.267129 0.0005757937 1.153161e+00 0.0029438453 3.862152 19 1.280450 1.267166 0.0010218384 3.952732e-01 0.0054108994 1.254840 20 1.280258 1.266956 -0.0010534578 4.893536e+00 0.0007513010 6.459705 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.54 co2l1 = 0.965 co2l0 = 0.005" [1] "co2l0 = -97.26 co2l1 = 0.222" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "9 out of 65 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "56 out of 390 1-min values rejected as stack air" [1] "5 out of 339 Line 1 1-min values rejected as stack air" [1] "51 out of 51 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"