[1] "2025-04-29 22:52:04 MDT" [1] "1501" "150112" "d012" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/150112a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86020 63 [1] 86020 [1] 86020 [1] "testing skipping spike filter" [1] 86020 [1] 86020 [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 22:52:08 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.842, ave o2scale2 = 0.759" [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] "33 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.842, ave o2scale2 = 0.759" [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] "33 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:52:08 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:52:08 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:52:19 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:52:20 MDT" [1] "reading in recalculated plot titles" [1] "Removed 33 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1234 row(s) with low FLSP" [1] "Removed 9 row(s) with high TFRIDGE" [1] "TEMP: 156 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:52:24 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 = -477.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.2" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.24 O2 = -635.1" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.937 co2off = 399.5 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 53.32 minutes" [1] "Shortest Cal: 8.01 minutes" [1] "Longest Cal: 299.49 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 7 [4,] 8 9 [5,] 10 12 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 18 0.02646733 0.2344462 0.1434137 3 -15.607645 276.2305 2 4 19 28 0.23514161 0.2414119 0.2389714 3 13.850539 131.1608 3 3 29 37 0.24210723 0.2476711 0.2469756 3 3.964366 208.4315 4 4 38 46 0.43765535 0.4432210 0.4411341 2 13.848607 130.6986 5 2 47 64 0.44391652 0.6518926 0.5608606 2 -15.655816 274.6655 6 4 65 74 0.65258796 0.6588484 0.6564140 2 13.838023 131.9807 7 3 75 83 0.65954387 0.6651076 0.6644121 2 3.960312 210.6931 8 4 84 92 0.85502266 0.8605867 0.8585001 2 13.826973 130.2849 9 2 93 101 0.86128241 0.8668466 0.8647602 2 -15.667179 272.3022 11 3 105 114 0.96343255 0.9696921 0.9686488 3 3.927367 210.6994 12 2 115 124 0.97038767 0.9766505 0.9742165 3 -15.661289 280.8201 13 4 125 134 0.97734954 0.9836130 0.9811755 3 13.821570 133.7125 14 5 135 144 0.98430830 0.9905789 0.9895296 NA 2.818312 200.6650 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.186170 1.316595 -2.138053e-04 -0.01021963 0.033180266 5.078955 2 1.186257 1.316690 1.143925e-03 1.02144944 0.005252438 3.265557 3 1.186332 1.316668 8.268394e-04 1.77872586 0.002628824 1.795688 4 1.187663 1.318226 4.297060e-04 -1.23265566 0.004318491 3.727273 5 1.188504 1.319131 -7.588304e-05 -0.00836283 0.012155363 2.474811 6 1.189001 1.319671 1.492634e-03 1.16327434 0.007337141 3.133048 7 1.189158 1.319756 -1.274865e-03 -1.30198397 0.002837160 1.420698 8 1.190242 1.321105 1.334884e-03 -0.78161259 0.004209497 3.181044 9 1.190434 1.321264 -3.895967e-03 -3.60547512 0.009630506 9.581283 11 1.190906 1.322044 3.023668e-04 6.21410202 0.004921758 12.426075 12 1.190969 1.322066 7.125378e-04 1.89696064 0.002729415 9.025368 13 1.190803 1.321942 2.124290e-03 -1.58577848 0.007148336 4.959924 14 1.190972 1.322068 -2.593126e-03 9.13791163 0.001856155 13.469265 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 391.286 co2l1 = 0.936 co2l0 = 0.017" [1] "co2l0 = -142.72 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"