[1] "2025-04-29 20:23:48 MDT" [1] "1401" "140128" "d028" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140128a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86160 63 [1] 86160 [1] 86160 [1] "testing skipping spike filter" [1] 86160 [1] 86160 [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 20:23:53 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.81, ave o2scale2 = 0.737" [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] "16 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.81, ave o2scale2 = 0.737" [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] "16 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:23:53 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:23:53 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:24:09 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:24:11 MDT" [1] "reading in recalculated plot titles" [1] "Removed 16 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1419 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:24:23 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 = -475.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.8" [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 = 0.458 co2off = 384.12 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.69 minutes" [1] "Shortest Cal: 6.01 minutes" [1] "Longest Cal: 9.03 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 jfcv1 2 2 176 185 0.1227278 0.1289869 0.1265527 3 -4.942109 307.6215 1.232221 3 4 186 195 0.1296829 0.1359422 0.1335079 3 55.007078 155.8768 1.232135 4 3 196 205 0.1366377 0.1428970 0.1418540 3 34.544281 242.3667 1.232257 6 4 475 484 0.3314200 0.3376794 0.3352449 2 55.087453 160.0384 1.233860 7 2 485 494 0.3383750 0.3446378 0.3422012 2 -5.142094 300.7690 1.234024 8 5 495 504 0.3453334 0.3515936 0.3505497 NA 30.154656 225.3214 1.234061 10 2 773 782 0.5403111 0.5465752 0.5441392 3 -5.217156 301.3780 1.235258 11 4 783 789 0.5472720 0.5514485 0.5500562 3 55.070575 154.9378 1.235307 12 3 790 799 0.5542338 0.5604972 0.5594532 3 34.521070 235.9116 1.235097 14 4 1066 1075 0.7492013 0.7554653 0.7530289 2 55.119828 160.8083 1.236680 15 2 1076 1085 0.7561617 0.7624259 0.7599895 2 -5.331992 299.7918 1.236777 17 2 1362 1370 0.9581608 0.9637330 0.9616439 3 -5.434527 301.8802 1.236181 18 4 1371 1379 0.9658220 0.9713938 0.9693054 3 55.137080 165.7373 1.235647 19 5 1380 1389 0.9720903 0.9783598 0.9773152 NA 29.697250 228.7386 1.235545 20 3 1390 1399 0.9790563 0.9853252 0.9842808 3 34.359609 244.4120 1.235493 jfcv2 co2slp o2slp co2sd o2sd 2 1.354866 -0.0058793218 2.62202197 0.015392439 7.186300 3 1.354777 0.0061279821 2.84976855 0.020282815 8.419352 4 1.354941 0.0005127133 -0.78040151 0.003796733 3.017920 6 1.356652 0.0013429499 2.18381917 0.010625827 6.754400 7 1.356807 -0.0065101642 0.86918458 0.016525278 6.310593 8 1.356825 -0.0414416286 3.28852196 0.029389126 4.477175 10 1.358199 0.0086769630 0.06414062 0.022645191 8.231306 11 1.358208 0.0098952119 1.86450861 0.015940649 3.119619 12 1.358062 0.0004536163 0.26737407 0.011871731 1.856687 14 1.359490 0.0032657983 3.98073924 0.010971745 10.212537 15 1.359615 -0.0022811165 3.63217075 0.007844928 9.319782 17 1.358730 -0.0003894199 1.84637043 0.010088531 5.021032 18 1.358387 -0.0014319073 3.13618644 0.005329961 10.805931 19 1.358178 -0.0381308411 -1.79209367 0.027046834 2.892737 20 1.358096 -0.0055351670 -0.20574309 0.014141258 3.446131 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.031 co2l1 = 0.458 co2l0 = 0.022" [1] "co2l0 = -149.37 co2l1 = 0.224" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "172 out of 335 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "163 out of 1217 1-min values rejected as stack air" [1] "163 out of 1217 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"