[1] "2025-04-29 22:14:56 MDT" [1] "1409" "141018" "d291" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141018a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 86280 63 [1] 86280 [1] 86280 [1] "testing skipping spike filter" [1] 86280 [1] 86280 [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 22:15:00 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.822, 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] "13 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.822, ave o2scale2 = 0.741" [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] "13 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 22:15:01 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 22:15:01 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 22:15:19 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 22:15:21 MDT" [1] "reading in recalculated plot titles" [1] "Removed 13 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1423 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 22:15:29 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CC339495 description: HS CO2 = 376.63 O2 = -477.1" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.4" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.8" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.48 co2off = 397.59 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.75 minutes" [1] "Shortest Cal: 6.01 minutes" [1] "Longest Cal: 9.02 minutes" [1] "Plotting calibration sds and slopes" [1] "cbind(calstart,calend)" calstart calend [1,] 1 4 [2,] 5 6 [3,] 7 9 [4,] 10 11 [5,] 13 15 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 53 62 0.03764751 0.04391088 0.04147664 3 -33.648453 286.1564 3 4 63 72 0.04460645 0.05086574 0.04843156 3 23.995633 147.0084 4 5 73 82 0.05156134 0.05782060 0.05677737 NA 2.536187 192.7045 5 3 83 92 0.05851623 0.06477558 0.06373239 3 4.495602 222.5422 7 4 350 356 0.24633336 0.25050657 0.24911567 2 24.079225 133.8237 8 2 357 365 0.25328828 0.25885608 0.25676922 2 -33.539143 301.0755 10 2 640 649 0.45504864 0.46131134 0.45887665 3 -33.411578 281.9605 11 4 650 659 0.46200694 0.46826620 0.46583216 3 24.220188 139.5463 12 3 660 669 0.46896181 0.47522474 0.47418172 3 4.701953 221.3406 14 4 940 949 0.66373727 0.66999997 0.66756436 2 24.416898 139.1501 15 2 950 959 0.67069549 0.67695486 0.67452038 2 -33.219594 288.2268 16 5 960 969 0.67765026 0.68391319 0.68286941 NA 2.441781 194.8602 18 2 1240 1249 0.87245486 0.87871432 0.87628007 3 -33.078094 289.7088 19 4 1250 1259 0.87940978 0.88566910 0.88323504 3 24.537406 137.9416 20 3 1260 1269 0.88636464 0.89262436 0.89158124 3 5.021898 223.7178 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.206620 1.338215 -0.001313579 -1.09937360 0.004507280 7.9217095 3 1.206431 1.338002 0.009950706 3.59034863 0.025123810 10.7550287 4 1.207284 1.338964 -0.002121729 0.29535553 0.001502602 0.4085158 5 1.207184 1.338864 -0.004751085 -2.09831783 0.011892278 3.4074459 7 1.209619 1.341753 -0.005822490 -5.73569436 0.009976594 16.3890512 8 1.209637 1.341729 -0.011012733 -2.98793947 0.028489529 22.5658833 10 1.215319 1.347910 -0.002720996 0.04629647 0.006810308 3.8953753 11 1.215435 1.348065 0.004875127 -1.38472978 0.014494842 4.8730336 12 1.215767 1.348433 0.002029319 1.26276475 0.010271632 1.6467424 14 1.221360 1.354803 0.002448850 0.23782131 0.007215817 2.4217860 15 1.221650 1.355148 -0.003960821 -1.94170798 0.013471448 5.1422875 16 1.221667 1.355680 -0.012292013 2.84991740 0.008706252 5.7739214 18 1.227250 1.361269 -0.002352046 0.39109285 0.007764675 3.9021756 19 1.227413 1.361355 0.004398617 0.15785183 0.015709948 4.4609817 20 1.227749 1.361672 0.003499906 4.82557766 0.009123406 8.8138467 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 392.637 co2l1 = 0.479 co2l0 = 0.081" [1] "co2l0 = -143.5 co2l1 = 0.213" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "38 out of 55 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "17 out of 1220 1-min values rejected as stack air" [1] "17 out of 1220 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"