[1] "2025-04-30 01:34:21 MDT" [1] "1605" "160616" "d168" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/160616a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 77384 63 [1] 77384 [1] 77384 [1] "testing skipping spike filter" [1] 77384 [1] 77384 [1] "recalculating jog averages" [1] "recalculating jog sds" [1] "recalculating jog slopes" [1] "Parsing MR flags" [1] "Calculating derived concentration values" [1] "2025-04-30 01:34:25 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.95, ave o2scale2 = 0.801" [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 = 0.95, ave o2scale2 = 0.801" [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] "6 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 01:34:26 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 01:34:26 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 01:34:37 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 01:34:38 MDT" [1] "reading in recalculated plot titles" [1] "Removed 6 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 2 row(s) with LiCO2A spikes in them" [1] "TEMP: 1279 0 TRUE" [1] "Removed 151 row(s) with -999.99 for a Licor jog SD" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 01:34:40 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 384.67 O2 = -522.7" [1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1" [1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.2" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.12 O2 = -572.1" [1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.947 co2off = 402.24 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.01 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.01 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 5 [3,] 6 7 [4,] 8 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 120 129 0.08626004 0.09251916 0.09008502 2 4.100922 90.30152 3 2 130 139 0.09321461 0.09947454 0.09704001 2 -18.633766 211.19986 5 2 420 429 0.29493519 0.30119465 0.29876038 3 -18.567703 209.45222 6 4 430 439 0.30189010 0.30815017 0.30571549 3 4.154695 88.81222 7 3 440 449 0.30884557 0.31510469 0.31406160 3 -9.406094 197.00777 9 4 720 729 0.50361921 0.50987850 0.50744427 2 4.232078 85.08731 10 2 730 739 0.51057407 0.51683333 0.51439907 2 -18.503359 210.38789 12 2 1020 1029 0.71229861 0.71855796 0.71612361 3 -18.444688 210.59547 13 4 1030 1039 0.71925347 0.72551308 0.72307862 3 4.266391 94.19826 14 3 1040 1049 0.72620836 0.73246768 0.73142439 3 -9.296508 194.06158 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.044263 1.239057 0.0004858451 0.20848904 0.004019033 2.3533576 3 1.044594 1.239429 -0.0011350944 0.34702177 0.005906522 4.0910586 5 1.050680 1.246438 -0.0010312063 -0.09639902 0.003297515 0.8625208 6 1.050685 1.246468 -0.0006634950 0.32718423 0.004876767 3.3714577 7 1.050828 1.246657 -0.0006568372 0.65840519 0.004584645 0.8975220 9 1.054589 1.251176 0.0008380170 0.88584773 0.003473874 2.4743491 10 1.054595 1.251199 -0.0006283422 -0.53678348 0.006897184 2.0899542 12 1.057763 1.255168 -0.0007606100 0.23604089 0.003235200 2.8680291 13 1.057810 1.255206 0.0003505904 -0.20093814 0.002566906 2.7422648 14 1.057835 1.255238 -0.0006264423 -0.37618581 0.004509593 1.9179300 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 402.209 co2l1 = 0.946 co2l0 = -0.012" [1] "co2l0 = -135.17 co2l1 = 0.211" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "166 out of 489 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "323 out of 994 1-min values rejected as stack air" [1] "12 out of 46 Line 1 1-min values rejected as stack air" [1] "311 out of 948 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"