[1] "2025-04-29 20:00:49 MDT" [1] "1312" "131209" "d343" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/131209a.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 20:00:53 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.8, ave o2scale2 = 0.728" [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] "115 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.8, ave o2scale2 = 0.728" [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] "115 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:00:54 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:00:54 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:01:07 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:01:08 MDT" [1] "reading in recalculated plot titles" [1] "Removed 115 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1212 row(s) with low FLSP" [1] "TEMP: 109 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:01:15 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 = -446.3" [1] "position 2 cylinder CB08911 description: MS CO2 = 405.33 O2 = -624.1" [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 = 0.463 co2off = 377.34 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 8.02 minutes" [1] "Average Cal: 60.47 minutes" [1] "Shortest Cal: 3.01 minutes" [1] "Longest Cal: 299.54 minutes" [1] "Removed 2 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 6 [4,] 7 8 [5,] 9 9 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 9 0.07606597 0.08163035 0.07954379 3 -14.60686 301.8953 2 4 10 19 0.08232604 0.08858912 0.08615154 3 30.18333 209.0006 3 3 20 28 0.08928472 0.09484821 0.09415271 3 53.64013 134.7888 4 4 29 37 0.28476684 0.29033108 0.28824418 2 30.56155 212.1918 5 2 38 53 0.29102662 0.49903909 0.39557903 2 -14.34664 301.2495 6 4 54 63 0.49973435 0.50599745 0.50356224 1 30.31638 203.5321 8 4 70 78 0.70219155 0.70775926 0.70567271 2 30.55749 206.8897 9 2 79 96 0.70845477 0.91644123 0.82540362 2 -13.33944 305.4717 10 4 97 105 0.91713666 0.92270356 0.92061465 1 31.15698 212.3141 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 1.251712 1.376205 -0.0159183252 1.467796732 0.036106554 4.706313 2 1.251731 1.376180 -0.0001395451 0.063145220 0.006581711 3.119917 3 1.251830 1.376203 0.0034790135 -1.051114938 0.009430047 1.057691 4 1.252339 1.376733 0.0029995806 -0.626380998 0.007719819 9.177806 5 1.251973 1.376168 -0.0028879232 -0.006393708 0.444950658 4.536574 6 1.251698 1.375975 0.0016526308 -4.349971035 0.007594526 15.707532 8 1.251288 1.375404 0.0110281679 0.523766926 0.024964622 2.126538 9 1.250144 1.374192 0.0052026951 0.011188517 0.786242510 7.183744 10 1.249150 1.373108 0.0079830759 -1.221307096 0.019572173 3.751108 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 380.788 co2l1 = 0.463 co2l0 = 0.149" [1] "co2l0 = -141.17 co2l1 = 0.214" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "NO SAMPLE PERIODS" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"