[1] "2025-04-29 17:38:40 MDT" [1] "1301" "130108" "d008" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130108a.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 17:38:44 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.787, ave o2scale2 = 0.795" [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 0 MR FC 2 jog(s) with SP SD > 1000" [1] "91 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.787, ave o2scale2 = 0.795" [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] "88 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 17:38:44 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 17:38:44 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 17:38:59 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 17:39:01 MDT" [1] "reading in recalculated plot titles" [1] "Removed 88 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1235 row(s) with high PFRIDGE" [1] "TEMP: 111 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 17:39:10 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 = -448.9" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.96 O2 = -543" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -625.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2" [1] "position 5 cylinder CB09982 description: WT1 CO2 = 479.38 O2 = -1131.8" [1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.414 co2off = 378.06 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 66.32 minutes" [1] "Shortest Cal: 6.01 minutes" [1] "Longest Cal: 299.54 minutes" [1] "Removed 1 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 3 [3,] 4 5 [4,] 6 7 [5,] 8 9 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 4 1 7 0.03707176 0.04193984 0.04040994 2 65.704059 46.34042 2 2 8 24 0.04472188 0.25064931 0.18084810 2 -8.848983 202.76015 3 4 25 34 0.25134491 0.25760463 0.25517022 1 65.894242 44.67087 5 4 42 51 0.45339933 0.45965865 0.45722444 2 65.746727 46.88093 6 2 52 71 0.46035425 0.66836808 0.57587866 2 -8.685771 201.02492 7 4 72 81 0.66906343 0.67532295 0.67288854 2 66.071008 36.54853 8 3 82 91 0.68297277 0.68923235 0.68818914 2 40.190609 112.95830 9 4 92 101 0.87077546 0.87703822 0.87460435 2 66.102281 42.89401 10 2 102 111 0.87773380 0.88399306 0.88155910 2 -9.202016 205.31075 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.268012 1.255544 -0.0096545925 0.6356678168 0.01916983 2.954733 2 1.267914 1.255334 -0.0006117014 0.0099159729 0.62117531 5.217593 3 1.268093 1.255429 0.0021030094 0.5852456654 0.01076465 2.490371 5 1.269692 1.256893 -0.0065570902 0.4542452713 0.02033944 2.886910 6 1.271478 1.258731 -0.0018639566 0.0004482788 0.63928342 5.906983 7 1.272756 1.260025 0.0013423256 -0.4327384052 0.01064837 8.155407 8 1.272922 1.260218 0.0083326979 -2.4652508929 0.02366677 3.377339 9 1.276664 1.264164 -0.0084671113 0.2817351774 0.02106461 3.120619 10 1.276570 1.264074 -0.0221217038 1.8663532835 0.05449498 5.500564 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.166 co2l1 = 0.412 co2l0 = 0" [1] "co2l0 = -121.98 co2l1 = 0.222" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"