[1] "2025-04-29 20:47:00 MDT" [1] "1402" "140309" "d068" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140309a.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 20:47:04 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.824, ave o2scale2 = 0.75" [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] "37 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.824, ave o2scale2 = 0.75" [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] "37 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:47:04 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:47:04 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:47:21 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:47:22 MDT" [1] "reading in recalculated plot titles" [1] "Removed 37 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1399 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:47:26 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 = -475.9" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -633.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 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 = 0.446 co2off = 373.74 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.95 minutes" [1] "Shortest Cal: 8.01 minutes" [1] "Longest Cal: 9.05 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 7 9 [4,] 10 11 [5,] 12 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 105 113 0.08052763 0.08609167 0.08400525 3 -4.182518 305.5846 3 4 114 123 0.08748264 0.09374728 0.09131159 3 57.384289 165.9447 4 3 124 132 0.09444271 0.10072436 0.09979698 3 36.250728 240.5432 6 4 378 387 0.28926927 0.29552894 0.29309439 2 57.562898 168.1758 7 2 388 397 0.29622451 0.30248727 0.30005153 2 -4.390539 304.8870 8 5 398 407 0.30318287 0.30944239 0.30839918 NA 32.340906 226.9899 12 2 678 687 0.49800718 0.50426684 0.50183266 3 -4.508758 302.5859 13 4 688 697 0.50496224 0.51123950 0.50880326 3 57.458328 162.8638 14 3 698 707 0.51193657 0.51819580 0.51715274 3 36.281070 239.6587 16 4 978 987 0.70670440 0.71296331 0.71052930 2 57.519047 160.9995 17 2 988 997 0.71365862 0.71991843 0.71748425 2 -4.940234 305.1718 19 2 1278 1287 0.91541444 0.92167419 0.91924009 3 -4.959617 307.8766 20 4 1288 1297 0.92236965 0.92862862 0.92619466 3 57.451039 163.2176 21 5 1298 1307 0.92932407 0.93558333 0.93454000 NA 32.302469 232.0717 22 3 1308 1317 0.93627894 0.94254164 0.94149837 3 36.058844 240.5648 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.208444 1.328006 -0.010170868 2.46941638 0.022381334 5.888318 3 1.208300 1.327806 0.005913617 0.06587486 0.016842162 4.647052 4 1.208276 1.327861 0.003165442 2.76651754 0.008565455 4.479322 6 1.212427 1.332215 -0.003365859 0.32369542 0.010315608 4.097934 7 1.213001 1.332867 0.010467750 -3.62826769 0.025959682 13.134562 8 1.212972 1.332845 -0.037016230 4.11518837 0.026207145 6.125598 12 1.213240 1.333095 0.007545534 1.53248175 0.019015367 5.515440 13 1.213364 1.333242 0.003438220 0.29402756 0.010819787 3.837306 14 1.213562 1.333468 -0.002238567 1.30911863 0.006126497 2.045373 16 1.215583 1.335620 0.004019491 4.42829224 0.011534679 11.349210 17 1.215803 1.335885 0.003051619 2.59107144 0.011640626 6.984612 19 1.216917 1.337042 -0.005801295 0.07886132 0.014932117 1.015155 20 1.216870 1.336986 0.004243349 1.33827189 0.015835508 4.624330 21 1.217085 1.337202 -0.035130413 -3.55536676 0.024881320 8.009161 22 1.217074 1.337232 -0.002906276 -0.38377614 0.008344160 1.707772 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.693 co2l1 = 0.445 co2l0 = 0.014" [1] "co2l0 = -150.75 co2l1 = 0.227" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "151 out of 350 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "199 out of 1190 1-min values rejected as stack air" [1] "143 out of 725 Line 1 1-min values rejected as stack air" [1] "56 out of 465 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "making html"