[1] "2025-04-29 16:43:10 MDT"
[1] "1207"   "120703" "d185"  
[1] "reading in high rate data from /scr/sci/stephens/GO2DAT/DIRECT/120703a.hr"
[1] "reading in hr file header"
Read 27 items
[1] "Parsing HR flags"
[1] "Doing high rate calculations (mean, sd, slope, shape)"
[1] 85679    63
[1] 85679
[1] 85679
[1] "testing skipping spike filter"
[1] 85679
[1] 85679
[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 16:43:14 MDT"
[1] "o2scaleopt = wt, ave o2scale1 = 0.756, ave o2scale2 = 0.763"
[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] "492 MR delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "recalc: o2scaleopt = wt, ave o2scale1 = 0.756, ave o2scale2 = 0.763"
[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] "491 RC delta diff NA values ( most likely because WTDIFF > 200 )"
[1] "2025-04-29 16:43:14 MDT"
[1] "Plotting 1-second data"
[1] "2025-04-29 16:43:14 MDT"
[1] "reading in high-rate plot titles"
[1] "Plotting 1-minute data"
[1] "2025-04-29 16:43:24 MDT"
[1] "reading in medium-rate plot titles"
[1] "Plotting recalculated 1-minute data"
[1] "2025-04-29 16:43:25 MDT"
[1] "reading in recalculated plot titles"
[1] "Removed 491 row(s) with NAs in them ( most likely because WTDIFF > 200 )"
[1] "Removed 518 row(s) with low FLWTA"
[1] "TEMP: 416 0 TRUE"
[1] "Plotting O2 and CO2 concentration data"
[1] "2025-04-29 16:43:29 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 = -450.3"
[1] "position 2 cylinder CB08905 description: MS CO2 = 394.96 O2 = -543.4"
[1] "position 3 cylinder CB08911 description: LS CO2 = 405.32 O2 = -626.8"
[1] "position 4 cylinder CC332564 description: LT CO2 = 394.06 O2 = -572.2"
[1] "position 5 cylinder CC339490 description: WT1 CO2 = 396.42 O2 = -582.4"
[1] "position 6 cylinder CC339495 description: WT2 CO2 = 394.28 O2 = -550.7"
[1] "Nominal linear calibrations:"
[1] "co2scl = 0.967  co2off = 412.42 o2scla = 1  o2offa = 0"
[1] "Finding cal and sample periods"
[1] "Plotting MR jog shapes"
[1] "Median Cal: 4.65 minutes"
[1] "Average Cal: 4.33 minutes"
[1] "Shortest Cal: 1 minutes"
[1] "Longest Cal: 7.01 minutes"
[1] "Removed 2 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
5    4  181  188 0.7953461 0.8002143 0.7984758   2   8.587187 -43.53183
6    2  189  196 0.8036921 0.8085602 0.8068214   2 -23.448260 119.40903
     jfcv1    jfcv2        co2slp    o2slp       co2sd     o2sd
5 1.335538 1.324264 -0.0001354938 3.547378 0.001107503 6.960575
6 1.335408 1.324111 -0.0003370138 1.878660 0.001355208 5.077646
[1] "Plotting calibration fits"
[1] "Average calibration parameters:"
[1] "co2l0 = 397.01  co2l1 = 0.968 co2l0 = 0"
[1] "co2l0 = -103.02  co2l1 = 0.219"
[1] "Plotting calibration parameters"
[1] "Plotting calibration data"
[1] "3 out of 221 remaining 1-min values OK w abs(diffback+difffwd)/2 < 0.2 and difference from interpolated clean < 0.2 ppm"
[1] "218 out of 381 1-min values rejected as stack air"
[1] "2 out of 165 Line 1 1-min values rejected as stack air"
[1] "216 out of 216 Line 2 1-min values rejected as stack air"
[1] "untarring JGOFS directory for this cruise"
[1] "making html"