[1] "2025-04-29 20:39:09 MDT" [1] "1402" "140222" "d053" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140222a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85918 63 [1] 85918 [1] 85918 [1] "testing skipping spike filter" [1] 85918 [1] 85918 [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 20:39:13 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.811, ave o2scale2 = 0.739" [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] "5 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.811, ave o2scale2 = 0.739" [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] "7 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:39:13 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:39:13 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:39:31 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:39:32 MDT" [1] "reading in recalculated plot titles" [1] "Removed 7 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1 row(s) with low FLWTA" [1] "TEMP: 1421 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:39:37 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 = 0.429 co2off = 378.69 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: 9.02 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 7 9 [4,] 10 11 [5,] 12 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 45 54 0.03303359 0.03929685 0.03686088 3 -3.818867 301.3029 3 4 55 64 0.03999213 0.04625532 0.04382019 3 60.337727 161.0361 4 3 65 74 0.04695061 0.05321354 0.05217048 3 38.292000 242.6691 6 4 345 354 0.24177315 0.24803296 0.24559831 2 60.261352 159.7281 7 2 355 364 0.24872827 0.25498785 0.25255362 2 -4.092461 299.9684 8 5 365 374 0.25568356 0.26194656 0.26090107 NA 33.878500 222.3642 10 2 645 654 0.45050958 0.45677286 0.45433865 3 -4.318453 304.6465 11 4 655 664 0.45746832 0.46372798 0.46129351 3 60.189516 158.2417 12 3 665 674 0.46442344 0.47068255 0.46963937 3 38.045688 241.0746 14 4 937 946 0.65915637 0.66541557 0.66298163 2 60.141758 155.1630 15 2 947 956 0.66611111 0.67237083 0.66993673 2 -4.406289 300.5729 17 2 1237 1246 0.86787509 0.87413782 0.87170347 3 -4.723562 306.3555 18 4 1247 1256 0.87483880 0.88110185 0.87866416 3 60.034625 158.3961 19 5 1257 1266 0.88179745 0.88805634 0.88701321 NA 33.479906 228.0492 20 3 1267 1276 0.88875185 0.89501068 0.89396764 3 37.836969 241.4945 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.228272 1.348505 4.301691e-04 2.4034470 0.014827559 6.051593 3 1.228269 1.348513 6.434625e-03 2.0939273 0.020704229 5.837741 4 1.228399 1.348668 2.555075e-03 -3.1651756 0.007542883 4.189177 6 1.230091 1.350424 -1.033201e-04 -0.4081864 0.002498200 3.781060 7 1.230235 1.350596 -1.086359e-02 1.4410394 0.027511198 4.799521 8 1.230241 1.350592 -5.428062e-02 1.0305603 0.038537320 2.122854 10 1.232848 1.353326 5.337191e-03 0.5833855 0.014850285 3.499048 11 1.232807 1.353295 -3.725585e-05 0.9345487 0.008863974 5.971961 12 1.232837 1.353301 5.246782e-04 -3.2116915 0.007576323 4.354097 14 1.234433 1.355163 1.213256e-03 2.3629584 0.007416683 6.352795 15 1.234551 1.355267 -4.543007e-03 1.0046731 0.013184471 4.477700 17 1.237353 1.358241 4.307956e-03 1.4738627 0.014676040 4.079120 18 1.237160 1.358088 2.521377e-03 1.1275626 0.016165785 3.180479 19 1.237118 1.358058 -4.725343e-02 -2.8973952 0.033454990 4.881678 20 1.237162 1.358053 -2.952699e-03 1.0670069 0.011036516 2.489071 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.479 co2l1 = 0.429 co2l0 = 0.009" [1] "co2l0 = -148.8 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "52 out of 140 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "88 out of 1214 1-min values rejected as stack air" [1] "88 out of 1214 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"