[1] "2025-04-29 20:10:33 MDT" [1] "1401" "140105" "d005" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140105a.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 20:10:37 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.809, ave o2scale2 = 0.737" [1] "Removing 0 MR FC 1 jog(s) with WT SD > 1000" [1] "Removing 1 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] "26 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.809, ave o2scale2 = 0.737" [1] "Removing 1 RC FC 1 jog(s) with WT SD > 1000" [1] "Removing 1 RC FC 2 jog(s) with WT SD > 1000" [1] "Removing 1 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 1 RC FC 2 jog(s) with SP SD > 1000" [1] "28 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:10:37 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:10:37 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:10:52 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:10:54 MDT" [1] "reading in recalculated plot titles" [1] "Removed 28 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1408 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:10:58 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 = -475.6" [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 = 0.444 co2off = 372.66 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.35 minutes" [1] "Shortest Cal: 5.01 minutes" [1] "Longest Cal: 9.02 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 8 [4,] 9 10 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 5 2 241 247 0.1696632 0.1738402 0.1724468 3 -2.111363 299.7331 1.231405 6 4 248 257 0.1766216 0.1828850 0.1804503 3 60.069125 155.3912 1.231201 8 3 264 272 0.1905394 0.1961068 0.1954101 3 38.745857 237.6550 1.231192 10 4 529 538 0.3783681 0.3846279 0.3821938 2 59.956500 155.2420 1.232785 11 2 539 548 0.3853255 0.3915866 0.3891523 2 -2.358344 297.9470 1.232998 13 2 822 831 0.5870558 0.5933157 0.5908810 3 -2.478898 303.1026 1.236958 14 4 832 841 0.5940111 0.6002699 0.5978360 3 59.776187 159.7231 1.236915 15 3 842 851 0.6009653 0.6072247 0.6061816 3 38.443562 247.9465 1.237336 17 4 1116 1125 0.7957373 0.8020000 0.7995657 2 59.587664 153.1124 1.239550 18 2 1126 1135 0.8026956 0.8089583 0.8065232 2 -2.277109 300.0795 1.239799 19 5 1136 1145 0.8096539 0.8159167 0.8148733 NA 33.228875 222.3125 1.239820 jfcv2 co2slp o2slp co2sd o2sd 5 1.351775 -0.0021798567 0.09173233 0.003899720 20.862836 6 1.351619 0.0032126960 4.13488089 0.015439289 10.780398 8 1.351690 -0.0050662202 -0.23760266 0.012749985 1.054406 10 1.353619 0.0030889514 1.71836102 0.009877825 5.703122 11 1.353906 0.0042733669 2.87905288 0.012061274 8.696679 13 1.360251 -0.0142096086 2.23667402 0.036977595 6.556174 14 1.360217 0.0134361943 1.55930391 0.036050715 5.652872 15 1.360767 -0.0004769342 -2.89674122 0.005164698 4.645474 17 1.363031 0.0022394980 1.04604583 0.009749596 4.927725 18 1.363367 0.0038600252 -0.14205340 0.014056596 8.265906 19 1.363249 -0.0476705491 -1.85268175 0.033764349 2.733492 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 377.666 co2l1 = 0.444 co2l0 = -0.015" [1] "co2l0 = -148.11 co2l1 = 0.221" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "139 out of 250 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "111 out of 1243 1-min values rejected as stack air" [1] "67 out of 1127 Line 1 1-min values rejected as stack air" [1] "44 out of 116 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"