[1] "2025-04-29 20:40:50 MDT" [1] "1402" "140225" "d056" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140225a.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 20:40:54 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.816, ave o2scale2 = 0.743" [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] "29 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.816, ave o2scale2 = 0.743" [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] "29 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:40:54 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:40:54 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:41:11 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:41:13 MDT" [1] "reading in recalculated plot titles" [1] "Removed 29 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1406 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:41:16 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 = -475.9" [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 = 0.435 co2off = 373.74 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 8.35 minutes" [1] "Shortest Cal: 1 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 2 [2,] 3 6 [3,] 7 8 [4,] 9 11 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 3 4 210 219 0.1638342 0.1700972 0.1676628 2 58.985992 162.1107 1.219941 4 2 220 229 0.1707938 0.1770556 0.1746215 2 -4.317742 302.8699 1.219991 7 2 510 519 0.3725532 0.3788160 0.3763818 3 -4.375477 303.4887 1.220639 8 4 520 529 0.3795116 0.3857755 0.3833407 3 58.933797 159.0891 1.220427 9 5 530 539 0.3864711 0.3927348 0.3916883 NA 32.971719 229.3794 1.220429 10 3 540 549 0.3934301 0.3996898 0.3986464 3 37.252008 241.6156 1.220435 12 4 808 817 0.5812517 0.5875116 0.5850772 2 58.993203 163.7027 1.225943 13 2 818 827 0.5882071 0.5944664 0.5920321 2 -4.648055 293.3497 1.226314 15 2 1105 1114 0.7899396 0.7962025 0.7937659 3 -5.142969 306.3176 1.232021 16 4 1115 1124 0.7968980 0.8031569 0.8007228 3 59.009016 161.9566 1.232107 17 3 1125 1134 0.8038523 0.8101117 0.8090687 3 37.030336 240.8712 1.232298 jfcv2 co2slp o2slp co2sd o2sd 3 1.339366 -0.0016616542 1.6350945 0.004579949 4.516452 4 1.339406 0.0011985160 1.3591591 0.007817351 4.534738 7 1.340167 0.0045924244 1.1259434 0.011704745 4.399634 8 1.339940 -0.0002182738 2.6575462 0.016675097 6.680729 9 1.339935 -0.0547608219 1.7645241 0.039023455 2.388104 10 1.339958 -0.0050951349 -0.2043662 0.014225678 1.074724 12 1.345959 0.0042438018 2.0034948 0.012840877 5.378906 13 1.346379 -0.0028963107 -1.5976858 0.011963740 11.818174 15 1.352484 0.0026760861 1.4636606 0.008597848 5.829935 16 1.352596 0.0072345140 4.2466492 0.020610215 12.246712 17 1.352779 0.0002800420 -7.9181865 0.005386609 10.794952 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.648 co2l1 = 0.434 co2l0 = 0.014" [1] "co2l0 = -150.63 co2l1 = 0.229" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "141 out of 405 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "264 out of 1258 1-min values rejected as stack air" [1] "240 out of 1165 Line 1 1-min values rejected as stack air" [1] "24 out of 93 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"