[1] "2025-04-29 20:12:06 MDT" [1] "1401" "140108" "d008" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140108a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86220 63 [1] 86220 [1] 86220 [1] "testing skipping spike filter" [1] 86220 [1] 86220 [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 20:12:10 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.802, ave o2scale2 = 0.73" [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] "11 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.802, ave o2scale2 = 0.73" [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 0 RC FC 2 jog(s) with SP SD > 1000" [1] "13 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:12:10 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:12:10 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:12:27 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:12:28 MDT" [1] "reading in recalculated plot titles" [1] "Removed 13 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1423 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:12:34 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 = -475.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.7" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.08 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 = 383.35 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.02 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.07 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 2 125 134 0.09297917 0.09924274 0.09680633 3 -4.131586 291.8310 3 4 135 144 0.09993811 0.10620139 0.10376454 3 58.005945 154.2253 4 3 145 154 0.10689693 0.11315622 0.11211285 3 36.782773 235.4184 6 4 425 434 0.30170619 0.30796606 0.30553176 2 57.826375 155.3465 7 2 435 444 0.30866146 0.31492127 0.31248672 2 -3.604008 294.1169 8 5 445 454 0.31561675 0.32187972 0.32083406 NA 31.656156 221.4749 10 2 725 734 0.51042538 0.51672512 0.51427275 3 -4.253867 298.9771 11 4 735 742 0.51742703 0.52370139 0.52173003 3 57.753823 159.6115 12 3 743 752 0.52439699 0.53065651 0.52961356 3 36.490844 236.6011 14 4 1020 1029 0.71928545 0.72554815 0.72311318 2 57.627344 155.8791 15 2 1030 1039 0.72624346 0.73250237 0.73006849 2 -4.805602 301.2842 17 2 1320 1329 0.92799190 0.93425110 0.93181685 3 -5.119711 296.4328 18 4 1330 1339 0.93494647 0.94120602 0.93877175 3 57.559594 153.6414 19 5 1340 1349 0.94190165 0.94816331 0.94711965 NA 30.937531 217.9867 20 3 1350 1359 0.94886007 0.95512043 0.95407704 3 36.093484 236.5726 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.245705 1.367497 0.0074360638 4.375882 0.019261822 11.638912 3 1.245761 1.367537 0.0032779308 1.033926 0.013849898 6.096717 4 1.245907 1.367679 -0.0023676236 -2.920029 0.007193355 4.591686 6 1.246212 1.368125 -0.0008690573 1.963063 0.010907433 6.237947 7 1.246264 1.368247 0.0030315594 1.919028 0.015853523 5.689192 8 1.246282 1.368262 -0.0428731436 -1.581715 0.030449786 2.137118 10 1.247696 1.369815 0.0038296619 2.953721 0.011944834 8.062164 11 1.247237 1.369301 0.0098332079 2.603857 0.024669073 8.430014 12 1.247148 1.369245 -0.0015109939 1.135254 0.007758492 2.063862 14 1.248905 1.370967 -0.0052819770 1.450522 0.014307060 6.772304 15 1.249053 1.371110 -0.0155426976 2.117648 0.038503289 5.303418 17 1.250634 1.372793 0.0022397995 4.112125 0.009270004 10.319508 18 1.250595 1.372772 0.0044336659 0.482960 0.016696577 3.015736 19 1.250579 1.372803 -0.0427341541 -2.203490 0.030273009 3.911602 20 1.250536 1.372790 -0.0004814432 3.406947 0.008631581 4.445792 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.591 co2l1 = 0.445 co2l0 = 0.013" [1] "co2l0 = -148.96 co2l1 = 0.226" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "76 out of 160 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "84 out of 1218 1-min values rejected as stack air" [1] "84 out of 1218 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"