[1] "2025-04-30 03:28:49 MDT" [1] "1707" "170901" "d244" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170901a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 84300 63 [1] 84300 [1] 84300 [1] "testing skipping spike filter" [1] 84300 [1] 84300 [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 03:28:53 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.86, ave o2scale2 = 1.095" [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] "26 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.86, ave o2scale2 = 1.095" [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] "28 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 03:28:53 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 03:28:53 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 03:29:14 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 03:29:16 MDT" [1] "reading in recalculated plot titles" [1] "Removed 28 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1272 row(s) with low FLSP" [1] "TEMP: 104 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 03:29:19 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 396.87 O2 = -495.4" [1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 409.04 O2 = -699.1" [1] "position 4 cylinder CB08905 description: LT CO2 = 404.34 O2 = -653.2" [1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10100 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 4.478 co2off = 412.62 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 7.18 minutes" [1] "Average Cal: 60.21 minutes" [1] "Shortest Cal: 6.15 minutes" [1] "Longest Cal: 298.36 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 7 [4,] 8 9 [5,] 10 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 1 2 1 8 0.1017932 0.1067871 0.1050089 3 -4.046698 319.8326 1.160856 2 4 9 17 0.1074983 0.1131969 0.1110559 3 -1.325393 168.2120 1.160943 3 3 18 25 0.1139087 0.1188860 0.1185305 3 -4.843958 310.4641 1.161289 4 4 26 33 0.3096757 0.3146644 0.3128828 2 -1.304438 173.7064 1.164822 5 2 34 49 0.3153758 0.5225623 0.4337149 2 -4.008888 316.2285 1.166009 6 4 50 58 0.5232739 0.5289644 0.5268302 2 -1.288080 172.3086 1.166736 7 3 59 66 0.5296758 0.5346628 0.5343073 2 -4.794979 304.1799 1.166851 8 4 67 74 0.7254529 0.7304320 0.7286535 2 -1.294656 164.4584 1.163138 9 2 75 89 0.7311434 0.9383372 0.8584856 2 -4.023539 330.5760 1.161739 10 4 90 97 0.9390484 0.9440359 0.9422533 1 -1.309448 170.7371 1.160732 jfcv2 co2slp o2slp co2sd o2sd 1 0.9186720 9.588539e-05 0.398059060 0.0005265107 5.566592 2 0.9186557 3.047777e-04 1.904126233 0.0009919692 11.017232 3 0.9188432 -2.232261e-04 -5.042619094 0.0006922187 3.651246 4 0.9184339 -1.193055e-03 1.855696524 0.0025372229 4.161805 5 0.9175136 6.319927e-05 0.002540418 0.0096317777 9.303939 6 0.9166201 -2.832131e-05 -1.335110864 0.0003548663 6.431753 7 0.9166624 -7.788009e-04 9.221284326 0.0019751055 6.676380 8 0.9105730 -1.563606e-03 -0.475723349 0.0030302511 4.243166 9 0.9075999 -6.737303e-05 -0.033627705 0.0101580385 6.946995 10 0.9055553 -3.669525e-04 -0.251678394 0.0008618808 2.653739 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 414.877 co2l1 = 4.477 co2l0 = 0.017" [1] "co2l0 = -165.14 co2l1 = 0.235" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"