[1] "2025-04-29 18:27:18 MDT"
[1] "1304"   "130415" "d105"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/130415a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 85362    63
[1] 85362
[1] 85362
[1] "testing skipping spike filter"
[1] 85362
[1] 85362
[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 18:27:23 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.764, ave o2scale2 = 0.766"
[1] "Removing 0 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 1 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] "216 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.764, ave o2scale2 = 0.766"
[1] "Removing 0 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 2 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 2 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 0 RC FC 2 jog(s) with SP SD > 1000"
[1] "218 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 18:27:23 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 18:27:23 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 18:27:32 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 18:27:33 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 218 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 675 row(s) with low FLWTA"
[1] "TEMP: 528 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 18:27:36 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 = -448.1"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.97 O2 = -542.7"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.33 O2 = -625.3"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.07 O2 = -572.2"
[1] "position 5 cylinder CB10023 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CA07554 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.351  co2off = 389.91 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.02 minutes"
[1] "Average Cal: 8.62 minutes"
[1] "Shortest Cal: 8.02 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      2
[2,]        3      4
[1] "calperiods"
  type posi pose     timei     timee     timea grp    co2sig     o2sig    jfcv1
2    4  245  253 0.7469872 0.7525544 0.7504677   2  59.51662  81.93357 1.326221
3    2  254  263 0.7539453 0.7602104 0.7577741   2 -30.55191 233.67425 1.325408
5    2  471  480 0.9557269 0.9619897 0.9595548   2 -28.65173 238.49575 1.320796
6    4  481  490 0.9626852 0.9689479 0.9665136   2  59.64284  83.92938 1.320642
     jfcv2       co2slp     o2slp       co2sd     o2sd
2 1.322447 -0.003190586 0.8886473 0.008879798 4.059407
3 1.321647 -0.014152244 2.0062276 0.038065966 6.100473
5 1.316576  0.035224833 1.5413326 0.087613185 4.490481
6 1.316412  0.008096117 1.3254643 0.020508299 3.562231
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 384.605  co2l1 = 0.348 co2l0 = 0"
[1] "co2l0 = -131.73  co2l1 = 0.234"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "64 out of 225 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "161 out of 465 1-min values rejected as stack air"
[1] "0 out of 0 Line 1 1-min values rejected as stack air"
[1] "161 out of 465 Line 2 1-min values rejected as stack air"
[1] "JGOFS data found"
[1] "LOXY data found"
[1] "making html"