[1] "2025-04-29 20:23:21 MDT" [1] "1401" "140127" "d027" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140127a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85978 63 [1] 85978 [1] 85978 [1] "testing skipping spike filter" [1] 85978 [1] 85978 [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 20:23:25 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.815, ave o2scale2 = 0.741" [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] "54 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.815, ave o2scale2 = 0.741" [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] "56 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:23:25 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:23:25 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:23:35 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:23:37 MDT" [1] "reading in recalculated plot titles" [1] "Removed 56 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1375 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:23:44 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 = 0.462 co2off = 365.77 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.37 minutes" [1] "Shortest Cal: 2 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,] 7 9 [4,] 10 10 [5,] 12 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 2 241 250 0.1814271 0.1876867 0.1852526 3 -4.630305 305.3026 1.224982 3 4 251 260 0.1883821 0.1946455 0.1922094 3 54.822336 158.8396 1.224827 4 3 261 270 0.1953408 0.2016007 0.2005573 3 34.536336 235.6504 1.224862 6 4 536 545 0.3901255 0.3963901 0.3939552 2 54.918289 156.4111 1.225710 7 2 546 555 0.3970857 0.4033519 0.4009135 2 -4.747172 301.2222 1.225942 8 5 556 565 0.4040475 0.4103067 0.4092634 NA 30.240094 226.8308 1.225980 10 2 836 845 0.5988479 0.6051068 0.6026729 3 -5.397062 300.2383 1.228229 11 4 846 855 0.6058027 0.6120615 0.6096276 3 54.985625 164.2765 1.228238 12 3 856 865 0.6127571 0.6190169 0.6179738 3 34.398617 240.8198 1.228379 15 4 975 982 0.7205484 0.7254165 0.7236777 1 55.058094 172.5520 1.229361 16 5 983 992 0.7261119 0.7323715 0.7313281 NA 29.992906 226.8056 1.229569 18 4 1252 1261 0.9139699 0.9202293 0.9177950 2 55.011008 162.2299 1.230832 19 2 1262 1271 0.9209248 0.9271841 0.9247499 2 -5.121953 306.2589 1.231086 jfcv2 co2slp o2slp co2sd o2sd 2 1.347010 0.0005697015 1.5126852 0.008404030 5.497722 3 1.346879 0.0050249740 1.6289073 0.018737762 4.333332 4 1.346837 0.0018325668 8.0318642 0.005072569 14.127435 6 1.347587 0.0035720113 1.1534268 0.010579838 5.131699 7 1.347846 0.0017380470 0.1404079 0.006326739 2.709549 8 1.347888 -0.0331322795 2.8424953 0.023467106 3.849209 10 1.350205 0.0218206862 2.7449419 0.054220676 7.973215 11 1.350250 -0.0003976810 2.4464160 0.019112975 7.244806 12 1.350336 -0.0021537643 -6.0465643 0.008525529 8.341485 15 1.351692 -0.0048158031 3.2919953 0.009591154 10.159791 16 1.351937 -0.0322614194 2.4733009 0.022848388 4.493047 18 1.353354 0.0019113669 0.8061868 0.005110218 2.873546 19 1.353575 -0.0012035858 -3.6535878 0.005283350 10.585736 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 378.94 co2l1 = 0.46 co2l0 = 0.02" [1] "co2l0 = -149.81 co2l1 = 0.225" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "107 out of 310 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "203 out of 1177 1-min values rejected as stack air" [1] "203 out of 1177 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"