[1] "2025-04-29 16:47:22 MDT" [1] "1207" "120709" "d191" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120709a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85980 63 [1] 85980 [1] 85980 [1] "testing skipping spike filter" [1] 85980 [1] 85980 [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 16:47:26 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.753, ave o2scale2 = 0.759" [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] "190 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.753, ave o2scale2 = 0.759" [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] "190 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 16:47:27 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 16:47:27 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 16:47:49 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 16:47:51 MDT" [1] "reading in recalculated plot titles" [1] "Removed 190 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1241 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 16:48:06 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 = -450.3" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.96 O2 = -543.4" [1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.7" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2" [1] "position 5 cylinder CC339490 description: WT1 CO2 = 396.42 O2 = -582.4" [1] "position 6 cylinder CC339495 description: WT2 CO2 = 394.28 O2 = -550.8" [1] "Nominal linear calibrations:" [1] "co2scl = 0.968 co2off = 409.42 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 7.83 minutes" [1] "Shortest Cal: 4.04 minutes" [1] "Longest Cal: 9.08 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 8 [4,] 9 10 [5,] 11 12 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 3 2 17 26 0.01257642 0.01887891 0.01642714 3 -22.762766 122.063956 4 4 27 31 0.02308003 0.02588244 0.02518191 3 9.300354 -36.223597 5 3 32 41 0.02658249 0.03288348 0.03183307 3 -1.436859 26.994679 8 4 281 290 0.22136236 0.22762161 0.22518770 2 9.348844 -38.233809 9 2 291 297 0.22831716 0.23249010 0.23109928 2 -22.711675 116.593795 13 2 542 550 0.43001852 0.43558252 0.43349626 3 -22.727143 122.483814 14 4 551 557 0.43906007 0.44323264 0.44184159 3 9.335763 -37.202803 15 3 558 567 0.44392815 0.45018750 0.44914413 3 -1.404422 26.959030 18 4 797 806 0.63903576 0.64533197 0.64288311 2 9.391117 -36.264767 19 2 807 813 0.64603218 0.65232894 0.65092979 2 -22.664810 121.579976 22 2 1050 1059 0.84761209 0.85391036 0.85146038 2 -22.717016 124.792919 23 4 1060 1065 0.85740972 0.86090749 0.85985821 2 9.378625 -38.801857 24 5 1066 1075 0.86160764 0.86790486 0.86685502 NA -2.268062 9.749147 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 3 1.328961 1.317080 6.032857e-04 1.9650724 0.0025616832 4.9267535 4 1.329075 1.317184 4.646119e-04 0.2871116 0.0009064296 0.3209438 5 1.329377 1.317523 5.839309e-03 3.4372669 0.0145975303 4.6160575 8 1.330083 1.318231 8.604208e-04 0.6827659 0.0031332035 2.9196586 9 1.330181 1.318278 -4.275209e-03 1.9620541 0.0078662402 3.1810611 13 1.327595 1.315529 -9.581177e-05 0.3276971 0.0026052617 2.5666884 14 1.327707 1.315665 -9.922434e-04 2.3178307 0.0017305843 3.7699103 15 1.327904 1.315879 2.325437e-03 3.1009137 0.0075224923 4.2992560 18 1.330368 1.318404 -1.200032e-03 0.3230842 0.0040783944 1.9602304 19 1.330290 1.318282 -1.020223e-03 1.2167415 0.0039379504 2.3633565 22 1.326958 1.314740 -1.613707e-03 1.8757864 0.0051215962 5.1801939 23 1.326854 1.314623 -9.430360e-04 1.3570218 0.0012624381 3.0290384 24 1.326950 1.314717 -8.680914e-04 1.0612161 0.0006187184 2.2896751 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 396.283 co2l1 = 0.967 co2l0 = 0.012" [1] "co2l0 = -103.92 co2l1 = 0.224" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "339 out of 619 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "280 out of 1044 1-min values rejected as stack air" [1] "131 out of 600 Line 1 1-min values rejected as stack air" [1] "149 out of 444 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"