[1] "2025-04-30 03:10:41 MDT" [1] "1706" "170728" "d209" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/170728a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 84300 63 [1] 84300 [1] 84300 [1] "testing skipping spike filter" [1] 84300 [1] 84300 [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 03:10:45 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.871, ave o2scale2 = 0.946" [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 1 MR FC 2 jog(s) with SP SD > 1000" [1] "7 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.871, ave o2scale2 = 0.946" [1] "Removing 0 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] "9 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 03:10:45 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 03:10:45 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 03:11:06 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 03:11:08 MDT" [1] "reading in recalculated plot titles" [1] "Removed 9 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1395 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 03:11:10 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 CB10100 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10100 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 4.53 co2off = 423.38 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 8.2 minutes" [1] "Average Cal: 8.01 minutes" [1] "Shortest Cal: 6.14 minutes" [1] "Longest Cal: 8.21 minutes" [1] "Removed 2 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 9 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 251 259 0.1808578 0.1865526 0.1844183 3 -5.494616 347.8094 1.139566 3 4 260 268 0.1872639 0.1929648 0.1908245 3 -2.744580 180.1049 1.139708 4 3 269 277 0.1936762 0.1993657 0.1986545 3 -6.300259 314.8204 1.140013 6 4 543 551 0.3887485 0.3944486 0.3923123 2 -2.667116 177.8937 1.146548 7 2 552 560 0.3951599 0.4008488 0.3987155 2 -5.413848 344.1578 1.146767 9 2 834 842 0.5966680 0.6023657 0.6002265 3 -5.337518 335.2257 1.153143 10 4 843 849 0.6044994 0.6087668 0.6073443 3 -2.606713 168.5582 1.153259 12 3 859 867 0.6158904 0.6215796 0.6208686 3 -6.132937 311.2416 1.153718 15 2 1133 1141 0.8109430 0.8166432 0.8145092 1 -5.293018 338.6512 1.157673 jfcv2 co2slp o2slp co2sd o2sd 2 1.049609 8.520671e-04 1.74907939 0.002487319 7.930029 3 1.049596 8.706571e-04 -0.39470238 0.002142609 5.579075 4 1.049907 -4.357243e-05 -1.92534162 0.001469051 2.413053 6 1.055589 -9.335566e-04 3.92641284 0.003452511 9.713131 7 1.055707 -6.081835e-04 0.01803405 0.001440150 7.233237 9 1.061290 5.452956e-04 -1.95348791 0.001724031 16.227810 10 1.061290 -1.842963e-03 2.58365621 0.003401976 7.631683 12 1.061580 -7.956767e-04 -5.34985544 0.001955561 5.611829 15 1.065064 -1.137671e-03 1.20359611 0.002774914 3.871539 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 420.786 co2l1 = 4.442 co2l0 = 0.086" [1] "co2l0 = -163.68 co2l1 = 0.22" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "44 out of 135 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "91 out of 1266 1-min values rejected as stack air" [1] "91 out of 1266 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] "making html"