[1] "2025-04-29 19:54:35 MDT" [1] "1312" "131128" "d332" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/131128a.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 19:54:40 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.821, ave o2scale2 = 0.745" [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] "70 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.821, ave o2scale2 = 0.745" [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] "72 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 19:54:40 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 19:54:40 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 19:54:58 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 19:55:00 MDT" [1] "reading in recalculated plot titles" [1] "Removed 72 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1364 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 19:55:07 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 = -446.4" [1] "position 2 cylinder CB08911 description: MS CO2 = 405.33 O2 = -624.2" [1] "position 3 cylinder CB08905 description: LS CO2 = 394.98 O2 = -542.2" [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 = 0.444 co2off = 384.37 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.95 minutes" [1] "Shortest Cal: 8.01 minutes" [1] "Longest Cal: 9.03 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 9 [4,] 10 10 [5,] 11 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 157 166 0.1213926 0.1276523 0.1252181 3 -14.68479 296.9481 1.212156 3 4 167 176 0.1283477 0.1346131 0.1321745 3 31.82822 209.4537 1.212071 4 3 177 186 0.1353084 0.1415679 0.1405248 3 56.21068 123.1859 1.212063 6 4 447 456 0.3300883 0.3363486 0.3339146 2 31.93740 207.0048 1.214775 7 2 457 466 0.3370440 0.3433043 0.3408696 2 -14.31768 296.7413 1.215071 9 2 746 755 0.5389207 0.5451818 0.5427478 3 -15.08181 300.8387 1.219311 10 4 756 765 0.5458773 0.5521408 0.5497065 3 31.63367 212.8212 1.219425 11 5 766 775 0.5528361 0.5590961 0.5580527 NA 25.16628 177.6006 1.219617 12 3 776 785 0.5597916 0.5660512 0.5650077 3 56.10608 143.6066 1.219465 15 2 1026 1034 0.7545822 0.7608456 0.7582593 1 -15.65921 283.3755 1.224596 17 2 1302 1311 0.9563214 0.9625807 0.9601464 3 -15.93309 298.4736 1.227824 18 4 1312 1321 0.9632765 0.9695463 0.9671100 3 31.22348 200.6439 1.228021 19 3 1322 1331 0.9702420 0.9765023 0.9754590 3 55.88960 139.2712 1.228047 jfcv2 co2slp o2slp co2sd o2sd 2 1.335353 -0.0111306365 1.3375648 0.029416004 7.467226 3 1.335205 0.0029480994 -1.3393396 0.010672530 9.993319 4 1.335283 0.0024864904 0.6217264 0.008291255 1.300588 6 1.338212 -0.0017363473 -0.7573068 0.007225400 5.079421 7 1.338524 -0.0093007195 -0.2286675 0.026620251 4.585567 9 1.342743 -0.0038665018 0.8350711 0.010286249 5.392967 10 1.342847 0.0054572703 -2.5815591 0.014606397 10.775699 11 1.342909 -0.0519758735 -1.6313591 0.036813747 3.424844 12 1.342911 -0.0025645006 -2.3388450 0.007555801 3.570807 15 1.345678 0.0034385892 8.8035756 0.014936071 25.319192 17 1.351052 0.0052055261 0.4818251 0.015058477 8.363548 18 1.351202 0.0016355391 1.1283652 0.014421971 8.037889 19 1.351233 0.0002607771 1.1767522 0.004572816 4.466648 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 380.98 co2l1 = 0.438 co2l0 = 0.148" [1] "co2l0 = -141.87 co2l1 = 0.222" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "141 out of 415 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "274 out of 1185 1-min values rejected as stack air" [1] "274 out of 1185 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"