[1] "2025-04-29 20:17:07 MDT" [1] "1401" "140117" "d017" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140117a.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 20:17:11 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.804, ave o2scale2 = 0.731" [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] "2 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.804, ave o2scale2 = 0.731" [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] "2 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:17:12 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:17:12 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:17:29 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:17:31 MDT" [1] "reading in recalculated plot titles" [1] "Removed 2 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1434 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:17:41 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 = -633.7" [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 = 0.445 co2off = 379.84 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 9.01 minutes" [1] "Shortest Cal: 9.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 2 [2,] 3 5 [3,] 6 7 [4,] 9 11 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 4 34 43 0.02413892 0.03040046 0.02796562 2 55.050812 160.4860 3 2 44 53 0.03109606 0.03735532 0.03492108 2 -6.597578 302.3353 5 2 334 343 0.23282760 0.23908762 0.23665336 3 -7.082617 300.5388 6 4 344 353 0.23978293 0.24604282 0.24360838 3 55.061281 167.0546 7 3 354 363 0.24673819 0.25299795 0.25195493 3 33.773234 242.6744 9 4 634 643 0.44162457 0.44788420 0.44544978 2 55.007742 161.6840 10 2 644 653 0.44857957 0.45483883 0.45240456 2 -7.113672 305.8705 11 5 654 663 0.45553443 0.46179366 0.46075048 NA 28.965687 225.3274 13 2 934 943 0.65031944 0.65657876 0.65414468 3 -7.093984 303.0043 14 4 944 953 0.65727431 0.66353414 0.66109965 3 55.006734 157.2169 15 3 954 963 0.66422931 0.67048929 0.66944550 3 33.743602 242.3448 17 4 1232 1241 0.85901644 0.86527789 0.86284279 2 54.985258 161.7944 18 2 1242 1251 0.86597341 0.87223319 0.86979912 2 -7.163305 306.2062 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.241728 1.365744 -0.0006500091 1.1512658 0.018080518 4.569561 3 1.241698 1.365662 0.0014308235 1.2825181 0.011562753 6.410121 5 1.242604 1.366585 -0.0003039643 3.5577787 0.009170352 9.614180 6 1.242587 1.366600 0.0027385743 4.0011761 0.015158648 12.046199 7 1.242684 1.366777 -0.0022357674 -0.1841147 0.006031146 1.328639 9 1.244142 1.368291 -0.0029260133 0.4164952 0.016637429 4.999961 10 1.244273 1.368457 -0.0032225683 4.4392973 0.010049529 12.135368 11 1.244279 1.368516 -0.0378245672 7.1185334 0.026781669 9.404435 13 1.244838 1.369126 0.0046473459 1.7958281 0.011863328 5.283411 14 1.244857 1.369116 0.0016365086 0.3562565 0.015140737 4.307029 15 1.244965 1.369235 -0.0033366379 -0.1609327 0.011243894 1.112046 17 1.244925 1.369189 0.0027808470 2.1686912 0.009766723 6.171528 18 1.244999 1.369263 0.0009648253 4.1622181 0.008954650 10.725890 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.756 co2l1 = 0.445 co2l0 = 0.044" [1] "co2l0 = -150 co2l1 = 0.225" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "165 out of 315 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "150 out of 1252 1-min values rejected as stack air" [1] "150 out of 1252 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"