[1] "2025-04-29 20:28:02 MDT" [1] "1401" "140203" "d034" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140203a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85920 63 [1] 85920 [1] 85920 [1] "testing skipping spike filter" [1] 85920 [1] 85920 [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 20:28:06 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.806, ave o2scale2 = 0.734" [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] "25 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.806, ave o2scale2 = 0.734" [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] "25 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:28:07 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:28:07 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:28:22 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:28:24 MDT" [1] "reading in recalculated plot titles" [1] "Removed 25 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1406 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:28:32 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 = -475.8" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.22 O2 = -633.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 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 = 0.45 co2off = 374.41 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.06 minutes" [1] "Average Cal: 8.96 minutes" [1] "Shortest Cal: 8.08 minutes" [1] "Longest Cal: 9.08 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 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig jfcv1 2 4 237 246 0.1753966 0.1816558 0.1792217 2 55.910133 163.0991 1.239263 3 2 247 256 0.1823512 0.1886111 0.1861766 2 -5.655828 302.4499 1.239315 5 2 536 544 0.3843768 0.3906538 0.3881595 3 -5.530607 298.1190 1.239584 6 4 545 554 0.3913532 0.3976597 0.3952101 3 55.857352 139.3049 1.239121 7 3 555 563 0.3990579 0.4046672 0.4039664 3 34.830402 241.7153 1.239469 9 4 826 835 0.5928553 0.5991499 0.5967010 2 55.810859 158.9205 1.240026 10 2 836 845 0.5998497 0.6061439 0.6036965 2 -5.616078 308.3855 1.240271 11 5 846 855 0.6068437 0.6131356 0.6120870 NA 30.555313 220.7309 1.240635 13 2 1123 1132 0.8012894 0.8075857 0.8051363 3 -4.594508 299.5258 1.241828 14 4 1133 1142 0.8082856 0.8145797 0.8121318 3 55.915828 164.7891 1.241834 15 3 1143 1152 0.8152790 0.8215729 0.8205236 3 35.250039 243.0307 1.241871 jfcv2 co2slp o2slp co2sd o2sd 2 1.362269 -0.0004673296 0.3960301 0.00342627 6.359999 3 1.362326 -0.0049401234 3.5502292 0.01392798 9.245563 5 1.362291 -0.0060582829 3.9758068 0.02577622 17.534349 6 1.361642 0.0058946180 3.8623123 0.02069353 16.974802 7 1.362008 -0.0046538688 -3.1213614 0.01032965 5.592031 9 1.362874 0.0102423714 1.5342792 0.02709358 6.555116 10 1.363180 0.0044982798 1.9708250 0.01580005 7.221982 11 1.363611 -0.0306717993 4.5083216 0.02183192 6.068548 13 1.364946 -0.0052463028 1.2844475 0.01641698 8.231925 14 1.364935 0.0043143887 0.4382836 0.01631802 10.947659 15 1.365004 -0.0034754714 3.7416385 0.01113758 5.787797 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.051 co2l1 = 0.451 co2l0 = 0.023" [1] "co2l0 = -148.18 co2l1 = 0.219" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "171 out of 305 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "134 out of 1251 1-min values rejected as stack air" [1] "134 out of 1251 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"