[1] "2025-04-29 21:47:23 MDT" [1] "1406" "140809" "d221" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/140809a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 85920 63 [1] 85920 [1] 85920 [1] "testing skipping spike filter" [1] 85920 [1] 85920 [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 21:47:27 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 0.858, ave o2scale2 = 0.773" [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 1 MR FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 MR FC 2 jog(s) with SP SD > 1000" [1] "25 MR delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.858, ave o2scale2 = 0.773" [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 1 RC FC 1 jog(s) with SP SD > 1000" [1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000" [1] "25 RC delta diff NA values ( most likely because WTDIFF > 1000 )" [1] "2025-04-29 21:47:28 MDT" [1] "Plotting 1-second data" [1] "2025-04-29 21:47:28 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-29 21:47:47 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-29 21:47:49 MDT" [1] "reading in recalculated plot titles" [1] "Removed 25 row(s) with NAs in them ( most likely because WTDIFF > 1000 )" [1] "TEMP: 1406 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-29 21:47:51 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 = -476.7" [1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.6" [1] "position 3 cylinder CC339490 description: LS CO2 = 404.23 O2 = -634.5" [1] "position 4 cylinder CC332564 description: LT CO2 = 394.09 O2 = -572.2" [1] "position 5 cylinder CA07554 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.473 co2off = 380.72 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 9.01 minutes" [1] "Average Cal: 8.73 minutes" [1] "Shortest Cal: 5.01 minutes" [1] "Longest Cal: 9.07 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 57 66 0.04012665 0.04638594 0.04395184 3 -20.88357 277.4179 3 4 67 76 0.04708134 0.05334112 0.05090677 3 37.51309 125.1346 4 3 77 86 0.05403652 0.06029618 0.05925283 3 17.73211 217.8806 6 4 353 362 0.24879456 0.25505440 0.25262014 2 37.29793 117.1332 7 2 363 368 0.25574997 0.25922731 0.25818404 2 -21.06703 281.3230 9 2 639 648 0.45753330 0.46379653 0.46135911 3 -21.10647 288.6700 10 4 649 658 0.46449201 0.47075130 0.46831718 3 37.23139 134.5150 11 5 659 668 0.47144688 0.47770608 0.47666274 NA 14.94828 199.1474 12 3 669 678 0.47840145 0.48466068 0.48361743 3 17.45805 219.9440 14 4 932 941 0.66621617 0.67247885 0.67004375 2 37.40273 138.7089 15 2 942 951 0.67317416 0.67943328 0.67699924 2 -20.99637 282.9059 17 2 1228 1237 0.87500443 0.88126739 0.87883219 3 -20.92284 280.5919 18 4 1238 1247 0.88196296 0.88823047 0.88579253 3 37.45481 134.6792 19 3 1248 1257 0.88893056 0.89522818 0.89417943 3 17.66558 211.5765 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 2 1.168706 1.301688 -0.0041105436 -2.0884099 0.011262317 5.9062105 3 1.168231 1.301199 0.0046934286 -4.0043867 0.014315755 15.2968992 4 1.168061 1.300992 0.0013014247 0.2350104 0.004984211 2.0687091 6 1.157002 1.288930 0.0027109138 7.6861916 0.009706832 23.6518934 7 1.158366 1.290437 -0.0050664771 3.2250925 0.007583648 4.2522203 9 1.163508 1.290976 -0.0087317311 -4.3132190 0.022090090 17.1018645 10 1.161043 1.288245 0.0036525481 -2.1257442 0.012090191 6.9045262 11 1.160218 1.287349 -0.0043049663 0.2192638 0.003049398 0.4793948 12 1.160637 1.287831 0.0008122072 -3.9838664 0.008608125 6.5450427 14 1.165107 1.292689 -0.0010418470 -0.6604175 0.004321347 3.7461331 15 1.164963 1.292539 -0.0003492689 -0.7865359 0.008159132 5.5413236 17 1.170690 1.298819 -0.0065460523 0.1853625 0.016335729 1.6594300 18 1.171239 1.299422 0.0052236677 0.3040124 0.013627908 4.4210169 19 1.171999 1.300274 -0.0020405837 -0.6205216 0.009242743 2.0592938 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 386.571 co2l1 = 0.473 co2l0 = 0.085" [1] "co2l0 = -141.08 co2l1 = 0.21" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "129 out of 865 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "736 out of 1228 1-min values rejected as stack air" [1] "0 out of 0 Line 1 1-min values rejected as stack air" [1] "736 out of 1228 Line 2 1-min values rejected as stack air" [1] "JGOFS data found" [1] "LOXY data found" [1] "making html"