[1] "2025-04-29 16:32:54 MDT" [1] "1206" "120610" "d162" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120610y.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 88617 63 [1] 88617 [1] 88617 [1] "testing skipping spike filter" [1] 88617 [1] 88617 [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 16:32:59 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.792, ave o2scale2 = 0.799" [1] "Removing 19 MR FC 1 jog(s) with WT SD > 1000" [1] "Removing 14 MR FC 2 jog(s) with WT SD > 1000" [1] "Removing 16 MR FC 1 jog(s) with SP SD > 1000" [1] "Removing 19 MR FC 2 jog(s) with SP SD > 1000" [1] "573 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.792, ave o2scale2 = 0.799" [1] "Removing 20 RC FC 1 jog(s) with WT SD > 1000" [1] "Removing 14 RC FC 2 jog(s) with WT SD > 1000" [1] "Removing 16 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 19 RC FC 2 jog(s) with SP SD > 1000" [1] "572 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 16:32:59 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 16:32:59 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 16:33:06 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 16:33:07 MDT" [1] "reading in recalculated plot titles" [1] "Removed 572 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 16 row(s) with high PFRIDGE" [1] "TEMP: 886 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 16:33:11 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 374.31 O2 = -450.5" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.95 O2 = -543.5" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.9" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2" [1] "position 5 cylinder CC339495 description: WT1 CO2 = 394.28 O2 = -550.6" [1] "position 6 cylinder CC339490 description: WT2 CO2 = 396.41 O2 = -582.4" [1] "Nominal linear calibrations:" [1] "co2scl = 0.989 co2off = 397.21 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 7.01 minutes" [1] "Average Cal: 5.98 minutes" [1] "Shortest Cal: 1 minutes" [1] "Longest Cal: 9.03 minutes" [1] "Removed 6 calibration row(s) with high SD" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 1 [2,] 2 3 [3,] 4 4 [4,] 5 7 [5,] 8 9 [6,] 10 11 [7,] 12 13 [8,] 14 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 19 26 0.08814109 0.0931557 0.09136489 1 18.472052 -58.77458 5 2 133 140 0.21451076 0.2193788 0.21764037 2 -13.006792 77.16474 7 3 146 153 0.22911574 0.2339838 0.23363601 2 7.819906 -70.33238 10 2 248 252 0.34595405 0.3508228 0.35012729 1 -12.986734 84.87940 13 2 351 357 0.46420946 0.4683820 0.46699098 3 -12.882200 87.89001 14 4 358 365 0.47185995 0.4767605 0.47501072 3 18.591365 -70.59538 15 3 366 369 0.48232755 0.4844138 0.48545686 3 8.010000 11.34975 17 4 478 483 0.59224216 0.5957198 0.59467650 2 18.644203 -61.88170 18 2 484 490 0.59641551 0.6026744 0.60086626 2 -12.790695 84.17026 20 2 598 603 0.71392653 0.7174095 0.71636441 2 -12.736125 87.85121 21 4 604 609 0.72089259 0.7250724 0.72367867 2 18.691431 -80.00514 24 4 718 725 0.83930645 0.8441813 0.84244035 2 18.731427 -68.36038 25 2 726 734 0.84696826 0.8525403 0.85045107 2 -12.647777 85.35471 27 2 849 857 0.96537847 0.9709522 0.96886183 2 -12.658536 86.02538 28 4 858 863 0.97443533 0.9779174 0.97687292 2 18.746812 -66.53916 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.269683 1.259117 -0.0039245093 -3.4847477 0.0079754914 14.516889 5 1.269427 1.258979 -0.0025963294 1.2276408 0.0049580532 10.729447 7 1.269094 1.258595 0.0102077039 -1.6806248 0.0202784041 1.190312 10 1.268829 1.258154 -0.0039871701 -2.7666104 0.0045237728 2.771048 13 1.271362 1.260765 -0.0011297215 0.1852327 0.0027801613 3.035509 14 1.271422 1.260808 -0.0014770204 -2.6303934 0.0036188346 9.295381 15 1.271712 1.261081 0.0072400449 13.7382488 0.0051265242 18.119625 17 1.273335 1.262934 -0.0043867584 6.1753600 0.0059597991 8.084279 18 1.273772 1.263349 -0.0026109119 2.0421903 0.0072827376 9.623248 20 1.274355 1.264052 -0.0002616232 -1.3717920 0.0005519851 2.658749 21 1.274431 1.264075 0.0013951950 3.9107034 0.0030264768 10.206495 24 1.275258 1.264970 -0.0013978759 0.3105825 0.0027486976 1.137674 25 1.275310 1.265026 -0.0035185400 1.3464296 0.0083860978 3.101517 27 1.275585 1.265566 0.0017418895 -0.4572132 0.0040866043 5.388381 28 1.275273 1.265179 0.0004861681 1.4303716 0.0019331268 2.509436 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.977 co2l1 = 0.988 co2l0 = 0.053" [1] "co2l0 = -93.82 co2l1 = 0.199" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "14 out of 25 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "11 out of 668 1-min values rejected as stack air" [1] "11 out of 668 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"