[1] "2025-04-30 01:41:01 MDT" [1] "1609" "161012" "d286" [1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/161012a.hr" [1] "reading in hr file header" Read 27 items [1] "Parsing HR flags" [1] "Doing high rate calculations (mean, sd, slope, shape)" [1] 81540 63 [1] 81540 [1] 81540 [1] "testing skipping spike filter" [1] 81540 [1] 81540 [1] "recalculating jog averages" [1] "recalculating jog sds" [1] "recalculating jog slopes" [1] "Parsing MR flags" [1] "Calculating derived concentration values" [1] "2025-04-30 01:41:05 MDT" [1] "o2scaleopt = wt, ave o2scale1 = 1.019, ave o2scale2 = 0.838" [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] "23 MR delta diff NA values ( most likely because WTDIFF > 200 )" [1] "recalc: o2scaleopt = wt, ave o2scale1 = 1.019, ave o2scale2 = 0.838" [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] "23 RC delta diff NA values ( most likely because WTDIFF > 200 )" [1] "2025-04-30 01:41:05 MDT" [1] "Plotting 1-second data" [1] "2025-04-30 01:41:05 MDT" [1] "reading in high-rate plot titles" [1] "Plotting 1-minute data" [1] "2025-04-30 01:41:18 MDT" [1] "reading in medium-rate plot titles" [1] "Plotting recalculated 1-minute data" [1] "2025-04-30 01:41:20 MDT" [1] "reading in recalculated plot titles" [1] "Removed 23 row(s) with NAs in them ( most likely because WTDIFF > 200 )" [1] "TEMP: 1334 0 TRUE" [1] "Plotting O2 and CO2 concentration data" [1] "2025-04-30 01:41:24 MDT" [1] "Reading in cylinder log" Read 78 records [1] "Finding cylinder IDs" Read 536 records [1] "position 1 cylinder CB08910 description: HS CO2 = 384.67 O2 = -522.9" [1] "position 2 cylinder CA07671 description: MS CO2 = 393.3 O2 = -526.1" [1] "position 3 cylinder CB08911 description: LS CO2 = 406.18 O2 = -648.1" [1] "position 4 cylinder CB08905 description: LT CO2 = 404.34 O2 = -653.2" [1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA" [1] "position 6 cylinder CA07556 description: WT2 CO2 = NA O2 = NA" [1] "Nominal linear calibrations:" [1] "co2scl = 0.961 co2off = 410.84 o2scla = 1 o2offa = 0" [1] "Finding cal and sample periods" [1] "Plotting MR jog shapes" [1] "Median Cal: 8.46 minutes" [1] "Average Cal: 8.1 minutes" [1] "Shortest Cal: 4.24 minutes" [1] "Longest Cal: 8.7 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,] 6 8 [4,] 9 10 [5,] 11 13 [1] "calperiods" type posi pose timei timee timea grp co2sig o2sig 1 2 1 5 0.001959983 0.004905208 0.004168461 3 -32.104083 61.44098 2 4 6 14 0.005637095 0.011483999 0.009282279 3 -9.658563 -58.82455 3 3 15 23 0.012216146 0.018118171 0.017383623 3 -23.074161 80.58515 5 4 276 284 0.207337066 0.213216377 0.211001405 2 -9.787563 -58.35181 6 2 285 293 0.213966580 0.219834375 0.217636016 2 -32.237893 62.31717 8 2 553 560 0.416152054 0.421298437 0.419465186 3 -32.352208 62.43568 9 4 561 569 0.422035909 0.427946065 0.425734565 3 -9.910705 -55.59991 11 3 579 587 0.435294271 0.441139207 0.440412182 3 -23.338589 39.07209 13 4 826 834 0.623705816 0.629744821 0.627480109 2 -10.002179 -56.74991 14 2 835 843 0.630522888 0.636432234 0.634206605 2 -32.458241 59.67744 16 2 1105 1113 0.831889583 0.837725637 0.835536839 3 -32.564455 57.61044 17 4 1114 1122 0.838445197 0.844329572 0.842125703 3 -10.126143 -58.43364 18 3 1123 1131 0.845088947 0.850967679 0.850236613 3 -23.530205 43.81345 jfcv1 jfcv2 co2slp o2slp co2sd o2sd 1 0.9867746 1.198553 0.0007262513 -1.2045813 0.0009402737 1.317091 2 0.9866468 1.198493 0.0002155174 1.5461908 0.0029174850 7.473337 3 0.9865745 1.198391 0.0003001924 11.0660179 0.0036091350 14.192392 5 0.9839277 1.195904 -0.0001842299 2.4816125 0.0026797368 10.429024 6 0.9839701 1.195952 -0.0004772675 2.7015232 0.0051602843 7.051481 8 0.9815072 1.193391 -0.0033502799 -1.7043709 0.0067074663 5.627276 9 0.9812911 1.193168 0.0006927048 -2.7508169 0.0046352244 9.102881 11 0.9813185 1.193093 -0.0011278781 -5.7464874 0.0041762687 6.280871 13 0.9801801 1.191584 0.0006605360 -0.4803139 0.0024990698 5.126214 14 0.9800840 1.191469 -0.0052636393 2.6612044 0.0130504045 7.307457 16 0.9788161 1.190041 -0.0020232787 2.3935556 0.0080204584 7.015187 17 0.9787055 1.189878 0.0031018417 -2.7254808 0.0082450833 6.707329 18 0.9786416 1.189931 0.0013792590 2.8550189 0.0044358439 4.667378 [1] "Plotting calibration fits" [1] "Average calibration parameters:" [1] "co2l0 = 415.654 co2l1 = 0.958 co2l0 = 0.065" [1] "co2l0 = -104.07 co2l1 = 0.209" [1] "Plotting calibration parameters" [1] "Plotting calibration data" [1] "150 out of 858 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm" [1] "708 out of 1173 1-min values rejected as stack air" [1] "708 out of 1173 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] "making html"