[1] "2025-04-30 00:35:39 MDT" [1] "1509" "151109" "d313" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/151109a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86280 63 [1] 86280 [1] 86280 [1] "testing skipping spike filter" [1] 86280 [1] 86280 [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 00:35:43 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.887, ave o2scale2 = 0.788" [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] "89 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.887, ave o2scale2 = 0.788" [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] "88 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 00:35:44 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 00:35:44 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 00:36:00 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 00:36:02 MDT" [1] "reading in recalculated plot titles" [1] "Removed 88 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1232 row(s) with low FLSP" [1] "TEMP: 116 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 00:36:05 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 384.68 O2 = -522.3" [1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1" [1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.4" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.11 O2 = -572.1" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.944 co2off = 395.47 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 8.02 minutes" [1] "Average Cal: 61.11 minutes" [1] "Shortest Cal: 7.01 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 3 [2,] 4 5 [3,] 6 6 [4,] 7 8 [5,] 9 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 9 0.1368505 0.1424144 0.1403277 3 -15.585839 486.8173 2 4 10 19 0.1431100 0.1493690 0.1469348 3 7.205211 370.3388 3 3 20 28 0.1500645 0.1556285 0.1549329 3 -6.418420 484.6654 4 4 29 37 0.3455534 0.3511175 0.3490310 2 7.180071 374.4347 5 2 38 55 0.3518135 0.5598249 0.4687761 2 -15.604438 490.7302 6 4 56 65 0.5605203 0.5667801 0.5643455 1 7.218766 371.2197 8 4 73 81 0.7629259 0.7684934 0.7664053 2 7.105527 372.8386 9 2 82 99 0.7691887 0.9771944 0.8861483 2 -15.725211 485.3131 10 4 100 108 0.9778898 0.9834572 0.9813675 2 7.062143 369.3890 11 3 109 116 0.9925069 0.9973751 0.9970273 2 -6.537885 477.1644 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.128969 1.270633 3.877746e-04 -0.189082255 0.0028371276 1.769529 2 1.128754 1.270325 5.920489e-04 0.946559658 0.0044888176 3.926014 3 1.128631 1.269996 1.622744e-03 1.429884642 0.0046426625 1.527035 4 1.129200 1.270693 9.360491e-05 0.197859267 0.0006696825 3.686112 5 1.131004 1.272764 1.075554e-04 0.015589601 0.0180642949 6.075033 6 1.132219 1.274222 3.066465e-03 0.100316774 0.0097264339 2.875273 8 1.125269 1.266266 -2.313158e-03 -0.417830990 0.0053231336 2.587312 9 1.125123 1.265589 -1.737053e-04 0.002602082 0.0263812776 4.276709 10 1.125095 1.265149 2.601100e-03 1.015729451 0.0063061761 4.519933 11 1.125653 1.265733 2.002455e-03 10.571237774 0.0048656026 7.487764 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 399.427 co2l1 = 0.944 co2l0 = -0.014" [1] "co2l0 = -196.77 co2l1 = 0.216" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"