[1] "2025-04-29 20:09:21 MDT" [1] "1401" "140103" "d003" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140103a.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 20:09:25 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] "49 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] "49 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-29 20:09:25 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 20:09:25 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 20:09:43 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 20:09:45 MDT" [1] "reading in recalculated plot titles" [1] "Removed 49 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1387 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 20:09:55 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 = -475.6" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.98 O2 = -542.1" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.21 O2 = -633.7" [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 = 0.431 co2off = 382.62 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.55 minutes" [1] "Shortest Cal: 5.01 minutes" [1] "Longest Cal: 9.02 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,] 7 9 [4,] 10 10 [5,] 11 14 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 2 2 115 124 0.08260648 0.08886687 0.08643204 3 -2.825305 306.4464 3 4 125 134 0.08956224 0.09582167 0.09338725 3 62.247664 157.8337 4 3 135 144 0.09651698 0.10277633 0.10173313 3 39.959562 240.9602 6 4 407 416 0.29130668 0.29756568 0.29513150 2 61.917492 153.6380 7 2 417 426 0.29826126 0.30452083 0.30208670 2 -2.697375 306.7646 8 5 427 436 0.30521644 0.31148330 0.31043717 NA 33.874562 227.0526 10 2 690 696 0.50208440 0.50625778 0.50486649 3 -2.712212 288.3338 11 4 697 702 0.50973495 0.51321288 0.51216942 3 61.556250 159.7357 12 3 703 711 0.51390856 0.52016788 0.51947227 3 39.566710 240.5619 14 4 973 982 0.70868287 0.71494213 0.71250809 1 61.273109 152.5209 17 2 1271 1280 0.91738244 0.92364540 0.92120933 3 -2.572961 299.8410 18 4 1281 1290 0.92434074 0.93060064 0.92816600 3 61.031891 160.9071 19 5 1291 1300 0.93129601 0.93755894 0.93651556 NA 33.382094 221.9506 20 3 1301 1310 0.93825440 0.94451505 0.94347187 3 39.257992 242.5542 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.255969 1.379365 -0.0066861493 3.7142059 0.017000014 13.184657 3 1.255816 1.379319 0.0126236770 -2.4838351 0.033443715 11.693299 4 1.255859 1.379445 -0.0033608736 -1.8239145 0.008996713 2.408645 6 1.254782 1.377952 -0.0013393476 0.5946323 0.008001425 10.141713 7 1.255045 1.378195 0.0035232964 1.4065976 0.008791356 12.934044 8 1.254940 1.378160 -0.0460354883 -0.8954493 0.032792077 2.762368 10 1.251795 1.374594 0.0067878544 6.6927436 0.011039223 14.055147 11 1.251800 1.374658 -0.0068764363 15.5381432 0.009011133 22.386036 12 1.251484 1.374386 -0.0001810755 4.9165284 0.002802672 4.925816 14 1.247617 1.370511 0.0024415131 0.4286804 0.010082348 6.510358 17 1.242243 1.365049 0.0043036763 1.3876660 0.011418477 9.070080 18 1.242059 1.364790 0.0064863188 1.4477543 0.025038581 4.151534 19 1.241936 1.364578 -0.0658360028 4.1144259 0.046624853 5.910157 20 1.241896 1.364631 -0.0042170199 1.0797047 0.011025510 1.431070 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 377.793 co2l1 = 0.43 co2l0 = -0.011" [1] "co2l0 = -149.82 co2l1 = 0.227" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "0 out of 0 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "0 out of 1188 1-min values rejected as stack air" [1] "0 out of 1188 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"