[1] "2025-04-29 22:46:21 MDT"
[1] "1501"   "141230" "d364"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/141230a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 47239    63
[1] 47239
[1] 47239
[1] "testing skipping spike filter"
[1] 47239
[1] 47239
[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 22:46:23 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.832, ave o2scale2 = 0.751"
[1] "Removing 1 MR FC 1 jog(s) with WT SD > 1000"
[1] "Removing 2 MR FC 2 jog(s) with WT SD > 1000"
[1] "Removing 2 MR FC 1 jog(s) with SP SD > 1000"
[1] "Removing 3 MR FC 2 jog(s) with SP SD > 1000"
[1] "115 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.832, ave o2scale2 = 0.751"
[1] "Removing 1 RC FC 1 jog(s) with WT SD > 1000"
[1] "Removing 3 RC FC 2 jog(s) with WT SD > 1000"
[1] "Removing 2 RC FC 1 jog(s) with SP SD > 1000"
[1] "Removing 2 RC FC 2 jog(s) with SP SD > 1000"
[1] "115 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 22:46:23 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 22:46:23 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 22:46:27 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 22:46:28 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 115 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 7 row(s) with low FLSP"
[1] "Removed 57 row(s) with variable TFCELL"
[1] "TEMP: 605 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 22:46:29 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 = -477.5"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.99 O2 = -541.3"
[1] "position 3 cylinder CC339490 description: LS CO2 = 404.24 O2 = -635.1"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.1 O2 = -572.2"
[1] "position 5 cylinder CB10100 description: WT1 CO2 = NA O2 = NA"
[1] "position 6 cylinder CB10023 description: WT2 CO2 = NA O2 = NA"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.941  co2off = 378.2 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 9.01 minutes"
[1] "Average Cal: 5.81 minutes"
[1] "Shortest Cal: 1 minutes"
[1] "Longest Cal: 9.02 minutes"
[1] "Removed 3 calibration row(s) with high SD"
[1] "Plotting calibration sds and slopes"
[1] "cbind(calstart,calend)"
     calstart calend
[1,]        1      2
[1] "calperiods"
  type posi pose     timei     timee     timea grp    co2sig    o2sig    jfcv1
3    4  200  209 0.5771530 0.5834158 0.5809811   2  15.02703 128.6620 1.201029
4    2  210  219 0.5841111 0.5903709 0.5879365   2 -14.37013 273.4159 1.201083
     jfcv2      co2slp    o2slp       co2sd      o2sd
3 1.329456 0.001864571 3.337532 0.006226922  9.585079
4 1.329588 0.002472209 3.706749 0.007643566 10.295196
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 390.124  co2l1 = 0.939 co2l0 = 0"
[1] "co2l0 = -142.04  co2l1 = 0.22"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "61 out of 85 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "24 out of 542 1-min values rejected as stack air"
[1] "24 out of 542 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"