[1] "2025-04-29 18:34:04 MDT" [1] "1304" "130427" "d117" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130427a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 44548 63 [1] 44548 [1] 44548 [1] "testing skipping spike filter" [1] 44548 [1] 44548 [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 18:34:06 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.77, ave o2scale2 = 0.772" [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] "187 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.77, ave o2scale2 = 0.772" [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] "187 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 18:34:06 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 18:34:06 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 18:34:16 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 18:34:17 MDT" [1] "reading in recalculated plot titles" [1] "Removed 188 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 554 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 18:34:23 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 = -448" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.97 O2 = -542.7" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.33 O2 = -625.3" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2" [1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.36 co2off = 369.09 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.01 minutes" [1] "Shortest Cal: 4.01 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 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 17 25 0.01165509 0.01791435 0.01552983 3 -13.54177 95.523253 3 4 26 35 0.01860981 0.02487266 0.02243814 3 72.27698 -66.381911 5 3 44 53 0.03252645 0.03878935 0.03774595 3 42.71856 9.690825 7 4 253 260 0.22183796 0.22670703 0.22496777 2 72.42095 -62.333627 8 2 261 265 0.22740243 0.23018403 0.22948856 2 -13.84250 98.572351 10 2 451 460 0.42926267 0.43552199 0.43308755 3 -14.00917 98.981738 11 4 461 470 0.43621759 0.44247682 0.44004254 3 72.55640 -60.379664 12 3 471 479 0.44317228 0.44873958 0.44804407 3 42.76453 8.047721 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.296647 1.292142 -0.011521104 0.6033757 0.031791230 1.677421 3 1.296871 1.292374 0.010529658 -0.9133576 0.028911961 3.232368 5 1.296692 1.292188 0.005310389 4.6326218 0.014641284 6.113249 7 1.298405 1.294035 0.001556282 1.0295878 0.003597399 1.966762 8 1.298388 1.294052 -0.022935112 -2.8781200 0.024307840 3.097007 10 1.301688 1.297541 -0.012844865 0.2116314 0.032647549 1.658339 11 1.301757 1.297623 0.007355690 -0.4913493 0.021803709 4.377979 12 1.302029 1.297918 0.006798830 1.5258227 0.016242821 1.668745 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.331 co2l1 = 0.36 co2l0 = 0.109" [1] "co2l0 = -98.33 co2l1 = 0.223" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "21 out of 218 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "197 out of 448 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "197 out of 448 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"