[1] "2025-04-29 19:12:39 MDT" [1] "1306" "130704" "d185" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130704a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86040 63 [1] 86040 [1] 86040 [1] "testing skipping spike filter" [1] 86040 [1] 86040 [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 19:12:44 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.773, ave o2scale2 = 0.715" [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] "26 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.773, ave o2scale2 = 0.716" [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] "26 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 19:12:44 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 19:12:44 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 19:13:04 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 19:13:05 MDT" [1] "reading in recalculated plot titles" [1] "Removed 26 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "Removed 1 row(s) with LiCO2A spikes in them" [1] "TEMP: 1405 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 19:13:23 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 = -447.5" [1] "position 2 cylinder CB08911 description: MS CO2 = 405.33 O2 = -624.9" [1] "position 3 cylinder CB08905 description: LS CO2 = 394.97 O2 = -542.5" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.08 O2 = -572.2" [1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10019 description: WT2 CO2 = 407.52 O2 = -753.5" [1] "Nominal linear calibrations:" [1] "co2scl = 0.31 co2off = 382.71 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.05 minutes" [1] "Average Cal: 8.9 minutes" [1] "Shortest Cal: 8.02 minutes" [1] "Longest Cal: 9.06 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 3 [2,] 4 5 [3,] 6 9 [4,] 10 11 [5,] 12 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 51 60 0.03647653 0.04273958 0.04030288 3 -14.64198 246.37522 3 4 61 69 0.04343513 0.04900234 0.04691402 3 51.67859 157.32335 4 3 70 78 0.05108909 0.05665628 0.05596070 3 86.27187 91.24081 6 4 349 357 0.24522983 0.25149297 0.24920553 2 51.38826 159.43628 7 2 358 367 0.25218837 0.25844740 0.25601330 2 -15.26394 247.62934 9 2 647 656 0.45429514 0.46057963 0.45813703 3 -15.53391 246.08012 10 4 657 666 0.46127778 0.46756201 0.46511783 3 51.39082 157.38436 11 5 667 676 0.46825987 0.47454404 0.47349715 NA 41.33600 140.59165 12 3 677 686 0.47524334 0.48152818 0.48048179 3 86.42074 85.98851 14 4 937 946 0.66306128 0.66934670 0.66690136 2 51.33502 159.22989 15 2 947 956 0.67004508 0.67632867 0.67388494 2 -15.76043 242.99659 17 2 1227 1236 0.87186924 0.87815978 0.87571250 3 -16.77397 248.82738 18 4 1237 1245 0.87885825 0.88514132 0.88304651 3 50.96306 158.62027 19 3 1246 1255 0.88583941 0.89212445 0.89107782 3 86.26160 83.12319 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.285035 1.388902 0.002602423 -0.7273769 0.015293043 3.279883 3 1.285073 1.388930 0.007536741 -0.2958014 0.019740565 2.271668 4 1.284522 1.388289 -0.002331299 -2.9033956 0.016386963 4.075806 6 1.286697 1.390573 0.009273337 1.0712927 0.024261069 7.650423 7 1.287108 1.390991 0.027015781 -0.7237308 0.066674273 3.720171 9 1.291395 1.395606 0.006272447 0.8655411 0.016875265 7.718068 10 1.291648 1.395870 0.009049670 1.3699422 0.025247556 3.847586 11 1.292151 1.396364 -0.044772407 3.8414652 0.031819805 6.401925 12 1.292316 1.396513 -0.003521399 3.0204358 0.009970349 4.192236 14 1.297203 1.401679 -0.003639094 -0.6663702 0.012474919 4.089604 15 1.297351 1.401845 -0.004488647 -1.3116948 0.014532424 4.852917 17 1.304246 1.409082 0.008344856 -1.6781070 0.024364100 4.502934 18 1.304144 1.408948 -0.005289972 -0.1567699 0.014780395 1.016507 19 1.304115 1.408977 -0.018239897 3.1243045 0.048392888 5.902089 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 379.129 co2l1 = 0.306 co2l0 = 0.091" [1] "co2l0 = -132.5 co2l1 = 0.228" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "10 out of 10 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "0 out of 1227 1-min values rejected as stack air" [1] "0 out of 1227 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"