[1] "2025-04-30 03:27:43 MDT" [1] "1707" "170830" "d242" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170830a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 84240 63 [1] 84240 [1] 84240 [1] "testing skipping spike filter" [1] 84240 [1] 84240 [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 03:27:47 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.86, ave o2scale2 = 1.056" [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] "32 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.86, ave o2scale2 = 1.056" [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] "32 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 03:27:47 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 03:27:47 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 03:28:07 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 03:28:09 MDT" [1] "reading in recalculated plot titles" [1] "Removed 32 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1266 row(s) with low FLSP" [1] "TEMP: 105 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 03:28:11 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 = 4.509 co2off = 412.57 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 7.18 minutes" [1] "Average Cal: 60.22 minutes" [1] "Shortest Cal: 6.15 minutes" [1] "Longest Cal: 298.41 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 6 [4,] 7 8 [5,] 9 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 8 0.02220755 0.02719213 0.02541168 3 -4.004635 312.8836 2 4 9 17 0.02790402 0.03361574 0.03146765 3 -1.291696 175.7932 3 3 18 25 0.03432717 0.03930457 0.03894913 3 -4.794375 294.2859 4 4 26 33 0.23010625 0.23510153 0.23331998 2 -1.256042 163.0533 5 2 34 49 0.23581322 0.44304288 0.35417469 2 -3.950786 325.3518 6 4 50 57 0.44375457 0.44873403 0.44695575 1 -1.229333 168.1282 8 4 65 72 0.64598235 0.65096337 0.64918417 2 -1.224938 169.8430 9 2 73 88 0.65167506 0.85890642 0.77004458 2 -3.972982 329.4661 10 4 89 97 0.85961791 0.86531840 0.86318080 2 -1.281268 164.5341 11 3 98 105 0.86603012 0.87100955 0.87065383 2 -4.799427 313.5603 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.167040 0.9585597 0.0016106380 -5.69862322 0.0031221028 14.975475 2 1.166962 0.9584569 0.0002678920 1.78654637 0.0009631414 15.945728 3 1.167020 0.9583319 0.0001813926 -26.37892461 0.0013169567 19.094164 4 1.166897 0.9549837 0.0013092794 1.94118351 0.0025716807 6.370600 5 1.166951 0.9526978 0.0000703978 -0.02730315 0.0108679441 15.735272 6 1.166840 0.9508856 0.0012621790 -1.23923444 0.0025674241 7.800219 8 1.165135 0.9465471 0.0003066830 -3.17862648 0.0008803408 14.044894 9 1.159934 0.9397691 -0.0002043512 -0.01505244 0.0309174462 12.686305 10 1.155621 0.9343525 0.0003738011 -3.26396311 0.0010236235 8.196693 11 1.155586 0.9342042 0.0001760870 11.12629542 0.0009956285 8.059904 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 414.673 co2l1 = 4.478 co2l0 = -0.031" [1] "co2l0 = -164.39 co2l1 = 0.233" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"