[1] "2025-04-29 22:11:00 MDT" [1] "1409" "141011" "d284" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141011a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86160 63 [1] 86160 [1] 86160 [1] "testing skipping spike filter" [1] 86160 [1] 86160 [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 22:11:05 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.842, ave o2scale2 = 0.757" [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] "7 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.842, ave o2scale2 = 0.757" [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] "8 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:11:05 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:11:05 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:11:24 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:11:25 MDT" [1] "reading in recalculated plot titles" [1] "Removed 8 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1426 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:11:30 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 = -477.1" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.4" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.48 co2off = 392.71 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: 9.06 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 4 [2,] 5 6 [3,] 7 9 [4,] 10 11 [5,] 13 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 43 52 0.03099931 0.03729398 0.03485638 3 -33.450703 279.8764 3 4 53 62 0.03798947 0.04427049 0.04182531 3 24.118125 139.2631 4 5 63 72 0.04496759 0.05122688 0.05018350 NA 2.776563 201.5906 5 3 73 82 0.05192245 0.05818171 0.05713840 3 4.658516 212.8161 7 4 343 352 0.23973709 0.24599653 0.24356210 2 24.167742 138.2527 8 2 353 362 0.24669213 0.25295501 0.25051929 2 -33.391234 281.3992 10 2 643 652 0.44845590 0.45471490 0.45228075 3 -33.296102 282.6541 11 4 653 662 0.45541030 0.46167410 0.45923611 3 24.245234 138.1530 12 3 663 672 0.46237095 0.46863027 0.46758694 3 4.743883 211.9618 14 4 942 951 0.65729742 0.66355677 0.66112258 2 24.273352 148.4126 15 2 952 961 0.66425229 0.67051157 0.66807747 2 -33.300320 285.2677 16 5 962 971 0.67120718 0.67746644 0.67642317 NA 2.844687 196.3834 18 2 1242 1251 0.86598264 0.87224216 0.86980797 3 -33.536109 286.7243 19 4 1252 1261 0.87293767 0.87919867 0.87676338 3 24.024367 142.8019 20 3 1262 1271 0.87989468 0.88615396 0.88511057 3 4.534234 211.3453 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.187198 1.319165 0.0028604108 -1.81790579 0.008027558 5.0553038 3 1.187352 1.319378 0.0040179506 -0.87186573 0.013765819 3.9393559 4 1.187497 1.319545 -0.0038683915 0.26121946 0.002740039 0.8189870 5 1.187664 1.319744 -0.0049331184 1.26098110 0.012539881 1.7705697 7 1.188835 1.321009 0.0004910760 1.47200475 0.003720335 4.5430168 8 1.188932 1.321182 0.0013796290 1.39753976 0.010220927 6.0649539 10 1.190103 1.322335 -0.0064257238 0.00960068 0.016246460 2.3371437 11 1.190043 1.322285 0.0034723391 0.50863471 0.017460598 4.1727488 12 1.190138 1.322385 0.0009383668 0.45226610 0.006620655 0.5874551 14 1.190489 1.322713 0.0040589647 3.34679610 0.010323935 13.5774277 15 1.190372 1.322616 -0.0083358293 -0.33893339 0.022769601 3.4921628 16 1.190205 1.322368 -0.0076123128 5.24087966 0.005391689 7.0721819 18 1.185913 1.317526 -0.0001040668 -0.15257547 0.002701221 2.7118871 19 1.185440 1.317005 0.0071070910 -0.40056890 0.019128251 7.6423547 20 1.184921 1.316561 -0.0002453336 1.26132660 0.006921091 4.0225236 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 392.663 co2l1 = 0.48 co2l0 = 0.079" [1] "co2l0 = -145.19 co2l1 = 0.225" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "47 out of 104 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "57 out of 1219 1-min values rejected as stack air" [1] "57 out of 1219 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] "making html"