[1] "2025-04-29 22:13:42 MDT" [1] "1409" "141016" "d289" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141016a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86220 63 [1] 86220 [1] 86220 [1] "testing skipping spike filter" [1] 86220 [1] 86220 [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 22:13:46 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.834, ave o2scale2 = 0.751" [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] "1 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.834, ave o2scale2 = 0.751" [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] "1 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:13:46 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:13:46 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:14:06 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:14:07 MDT" [1] "reading in recalculated plot titles" [1] "Removed 1 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1435 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:14:16 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.63 O2 = -477.1" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.4" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.48 co2off = 381.55 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.86 minutes" [1] "Shortest Cal: 7.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 4 6 [3,] 7 8 [4,] 9 12 [5,] 13 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 229 238 0.1595827 0.1658426 0.1634080 2 23.912781 136.6724 3 2 239 248 0.1665382 0.1727977 0.1703631 2 -33.671820 283.0791 4 5 249 258 0.1734931 0.1797561 0.1787113 NA 2.385000 201.1596 8 2 529 538 0.3682719 0.3745313 0.3720969 3 -33.635078 277.0558 9 4 539 548 0.3752269 0.3814862 0.3790521 3 23.956695 142.4552 10 3 549 558 0.3821817 0.3884444 0.3873984 3 4.411867 220.1805 12 4 828 837 0.5769398 0.5831990 0.5807648 2 23.959203 142.8748 13 2 838 847 0.5838946 0.5901539 0.5877198 2 -33.620672 279.1971 15 2 1128 1137 0.7856375 0.7918963 0.7894623 3 -33.661797 283.6856 16 4 1138 1147 0.7925922 0.7988515 0.7964173 3 23.927062 142.8351 17 5 1148 1157 0.7995470 0.8058066 0.8047633 NA 2.445750 206.9107 18 3 1158 1167 0.8065019 0.8127645 0.8117215 3 4.414773 216.7527 20 4 1428 1435 0.9943392 0.9992079 0.9974692 1 23.871937 138.3573 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.198397 1.329203 -0.0011900076 0.4168920 0.0035600712 3.595667 3 1.198562 1.329382 -0.0028236625 1.3622998 0.0106129363 3.658862 4 1.198605 1.329391 0.0002496567 -3.0489588 0.0001767767 4.075021 8 1.200146 1.331114 -0.0029922314 5.3868236 0.0077012979 14.767547 9 1.200032 1.330979 0.0011405146 0.7536730 0.0052400456 5.074580 10 1.200028 1.331062 -0.0059731318 5.3774549 0.0154526725 8.336608 12 1.200320 1.331460 0.0056436685 -1.6780899 0.0139766526 7.492721 13 1.200433 1.331578 -0.0065236652 -1.1804526 0.0199965050 3.153955 15 1.201144 1.332467 -0.0037919697 0.4801680 0.0095223978 3.747329 16 1.201158 1.332469 0.0040443173 -0.1128803 0.0122358245 2.893604 17 1.201214 1.332516 -0.0034947579 -1.8322061 0.0024748737 2.411361 18 1.201086 1.332438 0.0003619290 5.9154973 0.0045634096 9.580886 20 1.200916 1.332159 -0.0039794745 4.5298507 0.0082430842 8.673306 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 392.777 co2l1 = 0.48 co2l0 = 0.09" [1] "co2l0 = -145.94 co2l1 = 0.228" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "200 out of 345 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "145 out of 1256 1-min values rejected as stack air" [1] "145 out of 1138 Line 1 1-min values rejected as stack air" [1] "0 out of 118 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"