[1] "2025-04-29 16:37:18 MDT" [1] "1206" "120618" "d170" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120618b.hr" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120618c.hr" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120618d.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 78708 63 [1] 78708 [1] 78708 [1] "testing skipping spike filter" [1] 78708 [1] 78708 [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 16:37:22 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.781, ave o2scale2 = 0.787" [1] "Removing 0 MR FC 1 jog(s) with WT SD > 1000" [1] "Removing 1 MR FC 2 jog(s) with WT SD > 1000" [1] "Removing 1 MR FC 1 jog(s) with SP SD > 1000" [1] "Removing 1 MR FC 2 jog(s) with SP SD > 1000" [1] "471 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.781, ave o2scale2 = 0.787" [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 1 RC FC 2 jog(s) with SP SD > 1000" [1] "469 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 16:37:22 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 16:37:22 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 16:37:30 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 16:37:32 MDT" [1] "reading in recalculated plot titles" [1] "Removed 470 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1 row(s) with variable TFCELL" [1] "TEMP: 838 0 TRUE" [1] "Removed 60 row(s) with -999.99 for a Licor jog SD" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 16:37:38 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -450.4" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.95 O2 = -543.4" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2" [1] "position 5 cylinder CC339495 description: WT1 CO2 = 394.28 O2 = -550.7" [1] "position 6 cylinder CC339490 description: WT2 CO2 = 396.42 O2 = -582.4" [1] "Nominal linear calibrations:" [1] "co2scl = 0.972 co2off = 392.93 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 4.02 minutes" [1] "Average Cal: 5.24 minutes" [1] "Shortest Cal: 1 minutes" [1] "Longest Cal: 9.12 minutes" [1] "Removed 6 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 5 [3,] 6 7 [4,] 8 9 [5,] 10 11 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 4 4 126 132 0.2667582 0.2709568 0.2695487 2 18.468963 -69.718381 5 2 133 137 0.2732966 0.2760869 0.2753908 2 -13.456979 84.093161 7 2 239 245 0.3942483 0.3984294 0.3970355 3 -13.424813 85.070579 8 4 246 250 0.3991261 0.4019138 0.4012164 3 18.507938 -75.868136 9 3 251 260 0.4060955 0.4123644 0.4113194 3 7.824375 -2.755474 11 4 378 384 0.5175676 0.5238397 0.5211911 2 18.588258 -72.300407 12 2 385 394 0.5245366 0.5308726 0.5283867 2 -13.342078 96.777064 19 4 631 636 0.7733350 0.7768206 0.7757756 2 18.730125 -66.283485 20 2 637 640 0.7817018 0.7837922 0.7834439 2 -13.120156 94.376415 22 2 729 733 0.8991174 0.9019043 0.9012073 2 -12.986979 96.275478 23 4 734 738 0.9046926 0.9074800 0.9067832 2 18.824250 -67.416931 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 4 1.277744 1.266561 -0.0011873561 0.2832556 0.002063731 2.315482 5 1.277970 1.266798 -0.0057050871 6.6413766 0.006430619 6.876459 7 1.279811 1.268383 -0.0019867116 -0.2246520 0.003446012 9.218370 8 1.279732 1.268331 0.0081531706 3.5114473 0.008808066 3.530989 9 1.280018 1.268483 0.0043970596 4.4789126 0.010836034 6.522493 11 1.281354 1.270060 0.0012623836 2.1983997 0.004458507 8.085059 12 1.281513 1.270333 -0.0005224098 1.8561102 0.007610990 5.002579 19 1.284635 1.273732 0.0027402562 -3.1425319 0.003573266 4.366099 20 1.284841 1.274132 0.0040501807 -20.4629238 0.002872621 14.513484 22 1.286855 1.276136 -0.0039854225 -11.7409157 0.004134616 11.836898 23 1.286743 1.276108 0.0033945895 -5.8214525 0.003478169 8.367634 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 387.212 co2l1 = 0.972 co2l0 = 0.008" [1] "co2l0 = -97.05 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "18 out of 160 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "142 out of 590 1-min values rejected as stack air" [1] "142 out of 590 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"