[1] "2025-04-30 02:20:09 MDT" [1] "1701" "170127" "d027" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170127a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 49815 63 [1] 49815 [1] 49815 [1] "testing skipping spike filter" [1] 49815 [1] 49815 [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 02:20:11 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 1.077, ave o2scale2 = 0.867" [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] "38 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 1.077, ave o2scale2 = 0.867" [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 2 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000" [1] "38 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 02:20:11 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 02:20:11 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 02:20:16 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 02:20:17 MDT" [1] "reading in recalculated plot titles" [1] "Removed 38 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 6 row(s) with variable TFCELL" [1] "TEMP: 784 676 TRUE" [1] "Removed 676 row(s) with -999.99 for a Licor jog SD" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 02:20:18 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 384.67 O2 = -523.1" [1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1" [1] "position 3 cylinder CB08911 description: LS CO2 = 406.17 O2 = -647.9" [1] "position 4 cylinder CB08905 description: LT CO2 = 404.34 O2 = -653.2" [1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = 398.16 O2 = -1524.9" [1] "Nominal linear calibrations:" [1] "co2scl = 0.985 co2off = 427.39 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.27 minutes" [1] "Average Cal: 9.34 minutes" [1] "Shortest Cal: 8.23 minutes" [1] "Longest Cal: 10.23 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 6 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 3 3 11 0.8371229 0.8434277 0.8426397 3 -32.01704 221.7905 3 2 12 21 0.8442159 0.8513172 0.8485527 3 -40.82563 222.4117 4 4 22 31 0.8521051 0.8591976 0.8564389 3 -18.33652 107.3204 7 3 50 58 0.9549141 0.9606283 0.9599188 3 -32.78723 194.4789 8 2 59 68 0.9613377 0.9677470 0.9652462 3 -41.62425 226.9314 9 4 69 78 0.9684566 0.9749276 0.9724107 3 -19.15672 115.4038 10 5 79 88 0.9756407 0.9821161 0.9810353 NA -20.99309 118.6850 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 0.9271623 1.152230 0.014287507 4.5821322 0.035139875 5.211646 3 0.9271230 1.151989 0.012968127 1.1401758 0.036228834 10.171320 4 0.9270790 1.151780 0.014199997 -2.5109021 0.039713201 15.174838 7 0.9265939 1.151143 0.016564391 -13.8406335 0.037061406 14.166276 8 0.9269031 1.151374 0.012146848 2.0813747 0.030805807 9.766250 9 0.9270984 1.151520 0.016142195 0.9905786 0.041336665 4.203360 10 0.9273154 1.151674 0.001386322 -4.4773199 0.001016466 6.495895 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 424.091 co2l1 = 0.954 co2l0 = -1.434" [1] "co2l0 = -140.72 co2l1 = 0.224" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"