[1] "2025-04-29 17:38:21 MDT" [1] "1301" "130107" "d007" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130107a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 78410 63 [1] 78410 [1] 78410 [1] "testing skipping spike filter" [1] 78410 [1] 78410 [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 17:38:25 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.785, ave o2scale2 = 0.793" [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 1 MR FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000" [1] "317 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.785, ave o2scale2 = 0.793" [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 1 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000" [1] "317 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 17:38:25 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 17:38:25 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 17:38:32 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 17:38:33 MDT" [1] "reading in recalculated plot titles" [1] "Removed 317 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 916 row(s) with high PFRIDGE" [1] "Removed 4 row(s) with variable TFCELL" [1] "TEMP: 68 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 17:38:36 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 = 391.87 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 49.08 minutes" [1] "Shortest Cal: 5.01 minutes" [1] "Longest Cal: 298.48 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 7 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 1 2 1 10 0.1615406 0.1678003 0.1653660 3 -9.329461 206.06924 1.283342 2 4 11 19 0.1691911 0.1747550 0.1726687 3 65.476732 41.07922 1.282498 3 3 20 25 0.1754543 0.1789317 0.3984722 3 39.653672 93.18863 1.276051 4 4 26 35 0.6180127 0.6242720 0.6218377 2 65.740898 44.13648 1.269654 5 2 36 53 0.6256630 0.8329375 0.7545576 2 -9.145202 202.54633 1.267143 6 4 54 59 0.8364149 0.8398924 0.8388491 2 65.696141 41.50165 1.264618 7 3 60 68 0.8405880 0.8468507 0.8461552 2 39.936988 115.23094 1.264881 jfcv2 co2slp o2slp co2sd o2sd 1 1.267811 -0.034822124 0.14519378 0.08575972 2.732491 2 1.267083 0.010589276 2.51377963 0.02396582 6.451979 3 1.262715 0.017316692 -0.06010646 0.02262105 26.872823 4 1.258367 0.013263758 -0.76273039 0.03447712 3.005036 5 1.255321 0.002162075 -0.02316701 0.70745730 6.458577 6 1.252415 0.009454390 -2.47224701 0.01228899 3.690350 7 1.252729 0.008612651 -1.92439906 0.02372652 1.927700 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.423 co2l1 = 0.411 co2l0 = 0.084" [1] "co2l0 = -120.89 co2l1 = 0.217" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"