[1] "2025-04-29 18:11:21 MDT" [1] "1302" "130302" "d061" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130302a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85936 63 [1] 85936 [1] 85936 [1] "testing skipping spike filter" [1] 85936 [1] 85936 [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 18:11:25 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.754, ave o2scale2 = 0.76" [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 = 0.754, ave o2scale2 = 0.76" [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] "91 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 18:11:26 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 18:11:26 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 18:11:39 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 18:11:40 MDT" [1] "reading in recalculated plot titles" [1] "Removed 92 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1217 row(s) with low FLSP" [1] "TEMP: 122 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 18:11:50 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 = -448.5" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.97 O2 = -542.8" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -625.5" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2" [1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.38 co2off = 364.13 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 8.52 minutes" [1] "Average Cal: 47.71 minutes" [1] "Shortest Cal: 8.01 minutes" [1] "Longest Cal: 299.63 minutes" [1] "Removed 2 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 4 [3,] 5 7 [4,] 8 9 [5,] 10 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 9 0.04791363 0.05348027 0.05139373 3 -13.77023 203.88508 2 4 10 19 0.05417561 0.06043869 0.05800381 3 67.80610 44.67076 3 3 20 28 0.06113426 0.06670139 0.06600583 3 39.70187 110.55427 4 4 29 37 0.25667263 0.26224031 0.26015093 1 67.81128 44.46374 6 4 55 64 0.47170480 0.47796739 0.47553274 2 67.82027 41.95721 7 5 65 74 0.47866279 0.48492827 0.48388521 NA 23.17238 98.13947 8 3 75 83 0.48562387 0.49119112 0.49049587 2 39.77134 112.95641 9 4 84 92 0.67420255 0.67976904 0.67768037 2 67.83717 43.42035 10 2 93 104 0.68046536 0.81151852 0.73469524 2 -13.89668 203.44159 11 4 105 113 0.81221412 0.81847691 0.81589382 1 67.81478 49.00171 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.328425 1.318553 0.001705007 -0.56321944 0.006438078 2.205608 2 1.328229 1.318395 0.004696804 -0.53481453 0.023348317 2.314706 3 1.328087 1.318307 -0.002451351 -3.33414872 0.013864036 3.339584 4 1.326641 1.316800 -0.004144590 0.50977318 0.012695751 3.296185 6 1.326235 1.316247 0.011256038 0.18654640 0.028550295 3.434047 7 1.326306 1.316309 0.161035286 0.01024000 0.114020968 0.791223 8 1.326084 1.316123 -0.003579138 -1.90723724 0.017812495 2.114721 9 1.326509 1.316590 0.007894671 0.05813257 0.019286347 2.076280 10 1.326150 1.316447 0.001034859 -0.02185755 0.101633701 7.394551 11 1.325435 1.315947 0.003065923 -0.06674591 0.013799388 2.567083 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.79 co2l1 = 0.377 co2l0 = 0.118" [1] "co2l0 = -122.08 co2l1 = 0.225" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"