[1] "2025-04-29 22:50:35 MDT" [1] "1501" "150109" "d009" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/150109a.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 22:50:39 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.839, ave o2scale2 = 0.756" [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] "6 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.839, ave o2scale2 = 0.756" [1] "Removing 0 RC FC 1 jog(s) with WT SD > 1000" [1] "Removing 1 RC FC 2 jog(s) with WT SD > 1000" [1] "Removing 1 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000" [1] "8 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:50:40 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:50:40 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:50:54 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:50:55 MDT" [1] "reading in recalculated plot titles" [1] "Removed 8 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 249 row(s) with high TFRIDGE" [1] "TEMP: 1179 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:51:01 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 = -477.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.2" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.24 O2 = -635.1" [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 = 0.936 co2off = 390.45 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 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 2 [2,] 4 5 [3,] 6 9 [4,] 10 11 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 24 33 0.01834144 0.02460422 0.02216823 2 14.751023 130.9492 3 2 34 43 0.02529977 0.03155909 0.02912494 2 -14.760008 277.2035 4 5 44 53 0.03225469 0.03851389 0.03747077 NA 3.551375 197.6378 6 4 371 380 0.43595191 0.44221108 0.43977711 2 14.594008 135.7254 7 2 381 390 0.44290874 0.44916942 0.44673541 2 -14.912727 275.2225 9 2 671 680 0.64462416 0.65089164 0.64845556 3 -14.996141 275.8786 10 4 681 690 0.65158701 0.65784991 0.65541572 3 14.518398 132.1288 11 5 691 700 0.65854902 0.66480851 0.66376544 NA 3.337344 192.1373 12 3 701 710 0.66550394 0.67176354 0.67072038 3 4.633609 213.4207 14 4 969 978 0.85336808 0.85962792 0.85719370 2 14.426023 133.0075 15 2 979 988 0.86032355 0.86658727 0.86415009 2 -15.078312 277.5614 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.196482 1.327568 0.0017198935 0.09364770 0.004420798 2.139949 3 1.196502 1.327593 -0.0033546164 0.94674457 0.009868128 5.168195 4 1.196397 1.327490 -0.0024962556 2.14218056 0.001767767 3.017239 6 1.193003 1.323730 0.0003974839 0.09070382 0.001456757 2.490580 7 1.192919 1.323632 -0.0018803779 -0.45858997 0.005435184 5.426253 9 1.190358 1.320727 0.0001766624 -0.34567118 0.003228941 1.743174 10 1.190270 1.320621 -0.0003374826 -0.83377300 0.005125538 2.284523 11 1.190137 1.320482 -0.0044321445 -2.71888544 0.003137786 3.679102 12 1.190098 1.320443 -0.0005007231 3.84644262 0.002247705 5.289822 14 1.187830 1.317941 0.0024537314 0.43305160 0.006677516 5.126391 15 1.187823 1.317937 -0.0014124795 0.30743542 0.004708821 1.804973 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 390.604 co2l1 = 0.936 co2l0 = 0.001" [1] "co2l0 = -143.28 co2l1 = 0.222" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "53 out of 90 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "37 out of 1027 1-min values rejected as stack air" [1] "37 out of 1027 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"