[1] "2025-04-29 21:46:49 MDT" [1] "1406" "140808" "d220" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140808a.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 21:46:53 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.84, ave o2scale2 = 0.755" [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] "12 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.84, ave o2scale2 = 0.755" [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] "12 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:46:53 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:46:53 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:47:13 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:47:14 MDT" [1] "reading in recalculated plot titles" [1] "Removed 12 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1424 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:47:18 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 = -476.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.6" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.5" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.474 co2off = 392.06 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.51 minutes" [1] "Shortest Cal: 2 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 1 [2,] 2 5 [3,] 6 7 [4,] 8 10 [5,] 11 12 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 4 13 0.003571209 0.009830353 0.007396246 1 -20.30147 281.3574 4 2 294 303 0.205312124 0.211571586 0.209137218 3 -20.30351 280.9129 5 4 304 313 0.212266927 0.218526013 0.216091898 3 38.14720 138.3594 6 5 314 323 0.219221383 0.225484664 0.224441450 NA 15.85372 192.8868 7 3 324 333 0.226179977 0.232439815 0.231396434 3 18.33723 214.4454 9 4 594 603 0.413993056 0.420252546 0.417818428 2 38.03263 131.9843 10 2 604 613 0.420947917 0.427207176 0.424773119 2 -20.43379 279.7204 12 2 892 901 0.622708333 0.628967679 0.626533406 3 -20.65727 273.2962 13 4 902 911 0.629663050 0.635922743 0.633488122 3 37.76079 134.7513 14 3 912 921 0.636621528 0.642880758 0.641837399 3 17.95692 218.3280 16 4 1188 1197 0.831412124 0.837676939 0.835239945 2 37.62451 138.1915 17 2 1198 1205 0.838373032 0.844632523 0.842893779 2 -20.75696 273.7062 18 5 1206 1215 0.845328414 0.851591435 0.850545435 NA 15.33106 189.4653 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.201809 1.338211 -0.0044354389 -0.1013912 0.015515042 2.768210 4 1.202061 1.338497 0.0026781206 0.4028229 0.007823987 3.714012 5 1.201908 1.338325 0.0008714149 1.8003267 0.007682049 6.177717 6 1.201851 1.338251 -0.0091745028 2.4166233 0.006496544 3.504066 7 1.201769 1.338173 -0.0030240644 0.5811160 0.008495793 1.427265 9 1.198869 1.334898 -0.0029964254 0.2628664 0.010223039 1.719601 10 1.198426 1.334474 -0.0080029953 0.8613664 0.022068100 4.566080 12 1.186716 1.321522 -0.0026717392 -4.7815396 0.008502609 17.451999 13 1.186083 1.320851 0.0053855089 0.3573565 0.014732660 1.097138 14 1.185689 1.320381 -0.0051886142 7.3225395 0.013852731 10.246121 16 1.174822 1.308629 -0.0028678287 1.6258719 0.007612214 5.532965 17 1.175949 1.309862 -0.0042901526 2.5888428 0.008235752 5.940112 18 1.175556 1.309434 -0.0050910596 -4.4528657 0.003623922 5.781826 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.318 co2l1 = 0.473 co2l0 = 0.083" [1] "co2l0 = -144.47 co2l1 = 0.225" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "53 out of 803 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "750 out of 1243 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "750 out of 1243 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"