[1] "2025-04-29 21:28:29 MDT" [1] "1406" "140706" "d187" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140706a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85959 63 [1] 85959 [1] 85959 [1] "testing skipping spike filter" [1] 85959 [1] 85959 [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 21:28:33 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.837, ave o2scale2 = 0.754" [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] "13 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.837, ave o2scale2 = 0.754" [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] "13 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:28:33 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:28:33 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:28:54 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:28:55 MDT" [1] "reading in recalculated plot titles" [1] "Removed 14 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "Removed 1283 row(s) with low FLSP" [1] "TEMP: 134 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:28:58 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.62 O2 = -476.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.7" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.4" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2" [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 = 0.471 co2off = 378.22 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.02 minutes" [1] "Average Cal: 57.2 minutes" [1] "Shortest Cal: 8.02 minutes" [1] "Longest Cal: 299.61 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 8 [4,] 9 10 [5,] 11 12 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 9 0.006340307 0.01190804 0.009819354 3 -14.75590 283.1108 2 4 10 19 0.012603414 0.01887474 0.016436209 3 44.01837 137.5367 3 3 20 29 0.019570168 0.02584042 0.024796021 3 24.11893 211.3326 4 4 30 39 0.214443287 0.22070605 0.218271940 2 44.00888 132.3075 5 2 40 58 0.221401534 0.42946644 0.331881044 2 -14.82010 282.4684 6 4 59 68 0.430162037 0.43642731 0.433991236 2 43.85563 132.4443 7 5 69 78 0.437124045 0.44338310 0.442339952 NA 22.06087 197.5705 8 3 79 87 0.444078733 0.44964604 0.448950627 2 23.96973 218.0845 9 4 88 97 0.631993750 0.63825723 0.635821549 2 43.66891 131.4130 10 2 98 115 0.638952749 0.84697801 0.755923555 2 -15.22354 279.3284 11 4 116 125 0.847673611 0.85393681 0.851499787 2 43.43248 133.0505 12 3 126 134 0.854632031 0.86020009 0.859504572 2 23.52039 212.4837 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.191914 1.323160 -8.518502e-04 1.086621034 0.0060232684 4.348192 2 1.192112 1.323417 4.197689e-03 0.958161860 0.0116244450 4.251703 3 1.192374 1.323634 -2.193888e-05 1.615250734 0.0079507017 3.040044 4 1.198261 1.330333 -1.270419e-03 0.540217083 0.0073681869 4.454803 5 1.199271 1.331492 -3.713564e-04 0.009259036 0.0587208653 5.262005 6 1.199835 1.332214 3.389214e-03 0.007003662 0.0103578514 4.568775 7 1.199677 1.332097 2.496152e-04 -0.319744856 0.0001767767 3.261768 8 1.199518 1.331941 -4.301629e-03 1.036813195 0.0103744801 1.292954 9 1.195925 1.327926 -1.023256e-03 0.817472282 0.0063798126 7.171655 10 1.194209 1.326101 -9.317234e-04 -0.011172996 0.1413859209 6.356221 11 1.193088 1.324953 1.172173e-02 0.285187941 0.0323623275 1.984734 12 1.192798 1.324742 1.450184e-03 -4.400408819 0.0061018604 4.452171 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 383.763 co2l1 = 0.468 co2l0 = 0.061" [1] "co2l0 = -142 co2l1 = 0.213" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"