[1] "2025-04-29 20:18:59 MDT" [1] "1401" "140120" "d020" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140120a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86280 63 [1] 86280 [1] 86280 [1] "testing skipping spike filter" [1] 86280 [1] 86280 [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 20:19:03 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.812, ave o2scale2 = 0.738" [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] "5 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.812, ave o2scale2 = 0.738" [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] "5 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:19:04 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:19:04 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:19:21 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:19:22 MDT" [1] "reading in recalculated plot titles" [1] "Removed 5 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1431 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:19:33 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 = -475.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.7" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.08 O2 = -572.2" [1] "position 5 cylinder CB09982 description: WT1 CO2 = 479.38 O2 = -1131.8" [1] "position 6 cylinder CB10019 description: WT2 CO2 = 407.52 O2 = -753.5" [1] "Nominal linear calibrations:" [1] "co2scl = 0.456 co2off = 387.77 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.71 minutes" [1] "Shortest Cal: 5.06 minutes" [1] "Longest Cal: 9.03 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 9 [4,] 10 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 221 230 0.1543905 0.1606578 0.1582181 3 -6.127680 305.1542 1.234604 3 4 231 240 0.1613532 0.1676134 0.1651789 3 54.706367 155.5474 1.234478 4 3 241 250 0.1683088 0.1745680 0.1735248 3 33.922477 244.2295 1.234587 6 4 521 530 0.3631170 0.3693762 0.3669421 2 54.640281 160.1362 1.232831 7 2 531 540 0.3700718 0.3763314 0.3738970 2 -5.884422 302.8173 1.232855 9 2 816 825 0.5718071 0.5780704 0.5756337 3 -5.928102 306.3590 1.231420 10 4 826 835 0.5787657 0.5850245 0.5825906 3 54.644836 159.9777 1.231319 11 5 836 845 0.5857201 0.5919794 0.5909363 NA 29.555125 225.2952 1.231283 12 3 846 855 0.5926772 0.5989410 0.5978984 3 33.930687 240.0672 1.231128 14 4 1116 1125 0.7804966 0.7867566 0.7843222 2 54.623242 161.3386 1.230374 15 2 1126 1135 0.7874519 0.7937118 0.7912772 2 -5.882000 301.7493 1.230442 17 2 1416 1425 0.9891852 0.9954572 0.9930172 2 -5.929258 305.4225 1.229892 18 4 1426 1431 0.9961659 0.9996775 0.9986343 2 54.574125 155.7146 1.229770 jfcv2 co2slp o2slp co2sd o2sd 2 1.358010 -2.829055e-03 0.4157239 0.009178259 4.019386 3 1.357883 7.418848e-03 0.6897496 0.021924674 3.936165 4 1.358039 6.278359e-03 5.0888854 0.016383379 6.661069 6 1.356061 -7.415302e-04 1.5182854 0.008357391 4.131451 7 1.356091 -4.339558e-03 1.9308577 0.012876289 7.419533 9 1.354526 -5.030535e-05 2.6634919 0.005188408 6.974809 10 1.354398 9.207647e-03 0.6480763 0.024820155 3.576104 11 1.354441 -3.694919e-02 -3.4410719 0.026162951 4.958469 12 1.354245 -6.083645e-03 -0.6020242 0.016301943 2.172827 14 1.353465 5.414677e-03 1.5724838 0.013646667 4.944985 15 1.353555 -1.158781e-02 1.3414133 0.029832120 5.837539 17 1.352853 8.924744e-04 0.9411668 0.005381167 5.015301 18 1.352787 1.301826e-02 -1.2129793 0.019289664 4.460584 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.345 co2l1 = 0.456 co2l0 = 0.031" [1] "co2l0 = -148.35 co2l1 = 0.219" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "84 out of 198 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "114 out of 1273 1-min values rejected as stack air" [1] "114 out of 1273 Line 1 1-min values rejected as stack air" [1] "0 out of 0 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"