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Climategate: hide the decline – codified

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Watts Up With That
Wednesday, November 25, 2009

WUWT blogging ally Ecotretas writes in to say that he has made a compendium of programming code segments that show comments by the programmer that suggest places where data may be corrected, modified, adjusted, or busted. Some the  HARRY_READ_ME comments are quite revealing. For those that don’t understand computer programming, don’t fret, the comments by the programmer tell the story quite well even if the code itself makes no sense to you.

Climategate: hide the decline – codified software bug

To say that the CRU code might be “buggy” would be…well I’ll just let CRU’s programmer tell you in his own words.

  • FOIA\documents\osborn-tree6\mann\oldprog\maps12.proFOIA\documents\osborn-tree6\mann\oldprog\maps15.proFOIA\documents\osborn-tree6\mann\oldprog\maps24.pro; Plots 24 yearly maps of calibrated (PCR-infilled or not) MXD reconstructions
    ; of growing season temperatures. Uses "corrected" MXD - but shouldn't usually
    ; plot past 1960 because these will be artificially adjusted to look closer to
    ; the real temperatures.
  • FOIA\documents\harris-tree\recon_esper.pro; Computes regressions on full, high and low pass Esper et al. (2002) series,
    ; anomalies against full NH temperatures and other series.
    ; CALIBRATES IT AGAINST THE LAND-ONLY TEMPERATURES NORTH OF 20 N
    ;
    ; Specify period over which to compute the regressions (stop in 1960 to avoid
    ; the decline
  • FOIA\documents\harris-tree\calibrate_nhrecon.pro;
    ; Specify period over which to compute the regressions (stop in 1960 to avoid
    ; the decline that affects tree-ring density records)
    ;
  • FOIA\documents\harris-tree\recon1.pro
    FOIA\documents\harris-tree\recon2.proFOIA\documents\harris-tree\recon_jones.pro;
    ; Specify period over which to compute the regressions (stop in 1940 to avoid
    ; the decline
    ;
  • FOIA\documents\HARRY_READ_ME.txt17. Inserted debug statements into anomdtb.f90, discovered that
    a sum-of-squared variable is becoming very, very negative! Key
    output from the debug statements:
    (..)
    forrtl: error (75): floating point exception
    IOT trap (core dumped)
    ..so the data value is unbfeasibly large, but why does the
    sum-of-squares parameter OpTotSq go negative?!!
  • FOIA\documents\HARRY_READ_ME.txt22. Right, time to stop pussyfooting around the niceties of Tim's labyrinthine software
    suites - let's have a go at producing CRU TS 3.0! since failing to do that will be the
    definitive failure of the entire project..
  • FOIA\documents\HARRY_READ_ME.txtgetting seriously fed up with the state of the Australian data. so many new stations have been
    introduced, so many false references.. so many changes that aren't documented.
    Every time a
    cloud forms I'm presented with a bewildering selection of similar-sounding sites, some with
    references, some with WMO codes, and some with both. And if I look up the station metadata with
    one of the local references, chances are the WMO code will be wrong (another station will have
    it) and the lat/lon will be wrong too.
  • FOIA\documents\HARRY_READ_ME.txtI am very sorry to report that the rest of the databases seem to be in nearly as poor a state as
    Australia was. There are hundreds if not thousands of pairs of dummy stations, one with no WMO
    and one with, usually overlapping and with the same station name and very similar coordinates. I
    know it could be old and new stations, but why such large overlaps if that's the case? Aarrggghhh!
    There truly is no end in sight.
  • FOIA\documents\HARRY_READ_ME.txt28. With huge reluctance, I have dived into 'anomdtb' - and already I have
    that familiar Twilight Zone sensation.
  • FOIA\documents\HARRY_READ_ME.txtWrote 'makedtr.for' to tackle the thorny problem of the tmin and tmax databases not
    being kept in step. Sounds familiar, if worrying. am I the first person to attempt
    to get the CRU databases in working order?!!
  • FOIA\documents\HARRY_READ_ME.txtWell, dtr2cld is not the world's most complicated program. Wheras cloudreg is, and I
    immediately found a mistake!
    Scanning forward to 1951 was done with a loop that, for
    completely unfathomable reasons, didn't include months! So we read 50 grids instead
    of 600!!!
    That may have had something to do with it. I also noticed, as I was correcting
    THAT, that I reopened the DTR and CLD data files when I should have been opening the
    bloody station files!!
  • FOIA\documents\HARRY_READ_ME.txtBack to the gridding. I am seriously worried that our flagship gridded data product is produced by
    Delaunay triangulation - apparently linear as well. As far as I can see, this renders the station
    counts totally meaningless
    . It also means that we cannot say exactly how the gridded data is arrived
    at from a statistical perspective - since we're using an off-the-shelf product that isn't documented
    sufficiently to say that. Why this wasn't coded up in Fortran I don't know - time pressures perhaps?
    Was too much effort expended on homogenisation, that there wasn't enough time to write a gridding
    procedure? Of course, it's too late for me to fix it too. Meh.
  • FOIA\documents\HARRY_READ_ME.txtHere, the expected 1990-2003 period is MISSING - so the correlations aren't so hot! Yet
    the WMO codes and station names /locations are identical (or close). What the hell is
    supposed to happen here? Oh yeah - there is no 'supposed', I can make it up. So I have :-)
  • FOIA\documents\HARRY_READ_ME.txtWell, it's been a real day of revelations, never mind the week. This morning I
    discovered that proper angular weighted interpolation was coded into the IDL
    routine, but that its use was discouraged because it was slow! Aaarrrgghh.
    There is even an option to tri-grid at 0.1 degree resolution and then 'rebin'
    to 720x360 - also deprecated! And now, just before midnight (so it counts!),
    having gone back to the tmin/tmax work, I've found that most if not all of the
    Australian bulletin stations have been unceremoniously dumped into the files
    without the briefest check for existing stations.
  • FOIA\documents\HARRY_READ_ME.txtAs we can see, even I'm cocking it up! Though recoverably. DTR, TMN and TMX need to be written as (i7.7)./code>
  • FOIA\documents\HARRY_READ_ME.txtOH FUCK THIS. It's Sunday evening, I've worked all weekend, and just when I thought it was done I'm
    hitting yet another problem that's based on the hopeless state of our databases. There is no uniform
    data integrity, it's just a catalogue of issues that continues to grow as they're found.
  • FOIA\documents\osborn-tree6\mann\mxdgrid2ascii.proprintf,1,’Osborn et al. (2004) gridded reconstruction of warm-season’
    printf,1,’(April-September) temperature anomalies (from the 1961-1990 mean).’
    printf,1,’Reconstruction is based on tree-ring density records.’
    printf,1
    printf,1,’NOTE: recent decline in tree-ring density has been ARTIFICIALLY
    printf,1,’REMOVED to facilitate calibration. THEREFORE, post-1960 values’
    printf,1,’will be much closer to observed temperatures then they should be,’
    printf,1,’which will incorrectly imply the reconstruction is more skilful’
    printf,1,’than it actually is. See Osborn et al. (2004).’
  • FOIA\documents\osborn-tree6\summer_modes\data4sweden.pro
    FOIA\documents\osborn-tree6\summer_modes\data4sweden.proprintf,1,'IMPORTANT NOTE:'
    printf,1,'The data after 1960 should not be used. The tree-ring density'
    printf,1,'records tend to show a decline after 1960 relative to the summer'
    printf,1,'temperature in many high-latitude locations. In this data set'
    printf,1,'this "decline" has been artificially removed in an ad-hoc way, and'
    printf,1,'this means that data after 1960 no longer represent tree-ring
    printf,1,'density variations, but have been modified to look more like the
    printf,1,'observed temperatures.'
  • FOIA\documents\osborn-tree6\combined_wavelet_col.pro;
    ; Remove missing data from start & end (end in 1960 due to decline)
    ;
    kl=where((yrmxd ge 1402) and (yrmxd le 1960),n)
    sst=prednh(kl)
  • FOIA\documents\osborn-tree6\mann\mxd_pcr_localtemp.pro; Tries to reconstruct Apr-Sep temperatures, on a box-by-box basis, from the
    ; EOFs of the MXD data set. This is PCR, although PCs are used as predictors
    ; but not as predictands. This PCR-infilling must be done for a number of
    ; periods, with different EOFs for each period (due to different spatial
    ; coverage). *BUT* don’t do special PCR for the modern period (post-1976),
    ; since they won’t be used due to the decline/correction problem.
    ; Certain boxes that appear to reconstruct well are “manually” removed because
    ; they are isolated and away from any trees.
  • FOIA\documents\osborn-tree6\briffa_sep98_d.pro;mknormal,yyy,timey,refperiod=[1881,1940]
    ;
    ; Apply a VERY ARTIFICAL correction for decline!!
    ;
    yrloc=[1400,findgen(19)*5.+1904]
    valadj=[0.,0.,0.,0.,0.,-0.1,-0.25,-0.3,0.,-0.1,0.3,0.8,1.2,1.7,2.5,2.6,2.6,$
    2.6,2.6,2.6]*0.75 ; fudge factor
    (...)
    ;
    ; APPLY ARTIFICIAL CORRECTION
    ;
    yearlyadj=interpol(valadj,yrloc,x)
    densall=densall+yearlyadj
  • FOIA\documents\osborn-tree6\summer_modes\pl_decline.pro;
    ; Plots density ‘decline’ as a time series of the difference between
    ; temperature and density averaged over the region north of 50N,
    ; and an associated pattern in the difference field.
    ; The difference data set is computed using only boxes and years with
    ; both temperature and density in them – i.e., the grid changes in time.
    ; The pattern is computed by correlating and regressing the *filtered*
    ; time series against the unfiltered (or filtered) difference data set.
    ;
    ;*** MUST ALTER FUNCT_DECLINE.PRO TO MATCH THE COORDINATES OF THE
    ; START OF THE DECLINE *** ALTER THIS EVERY TIME YOU CHANGE ANYTHING ***
  • FOIA\documents\osborn-tree6\mann\oldprog\maps12.pro;
    ; Plots 24 yearly maps of calibrated (PCR-infilled or not) MXD reconstructions
    ; of growing season temperatures. Uses “corrected” MXD – but shouldn’t usually
    ; plot past 1960 because these will be artificially adjusted to look closer to
    ; the real temperatures.
    ;
  • FOIA\documents\osborn-tree6\mann\oldprog\calibrate_correctmxd.pro; We have previously (calibrate_mxd.pro) calibrated the high-pass filtered
    ; MXD over 1911-1990, applied the calibration to unfiltered MXD data (which
    ; gives a zero mean over 1881-1960) after extending the calibration to boxes
    ; without temperature data (pl_calibmxd1.pro). We have identified and
    ; artificially removed (i.e. corrected) the decline in this calibrated
    ; data set. We now recalibrate this corrected calibrated dataset against
    ; the unfiltered 1911-1990 temperature data, and apply the same calibration
    ; to the corrected and uncorrected calibrated MXD data.
  • FOIA\documents\osborn-tree6\summer_modes\calibrate_correctmxd.pro; No need to verify the correct and uncorrected versions, since these
    ; should be identical prior to 1920 or 1930 or whenever the decline
    ; was corrected onwards from.
  • FOIA\documents\osborn-tree5\densplus188119602netcdf.pro; we know the file starts at yr 440, but we want nothing till 1400, so we
    ; can skill lines (1400-440)/10 + 1 header line
    ; we now want all lines (10 yr per line) from 1400 to 1980, which is
    ; (1980-1400)/10 + 1 lines
    (...)
    ; we know the file starts at yr 1070, but we want nothing till 1400, so we
    ; can skill lines (1400-1070)/10 + 1 header line
    ; we now want all lines (10 yr per line) from 1400 to 1991, which is
    ; (1990-1400)/10 + 1 lines (since 1991 is on line beginning 1990)
  • FOIA\documents\osborn-tree6\mann\oldprog\maps12.pro
    FOIA\documents\osborn-tree6\mann\oldprog\maps15.pro
    FOIA\documents\osborn-tree6\mann\oldprog\maps24.pro
    ; Plots 24 yearly maps of calibrated (PCR-infilled or not) MXD reconstructions
    ; of growing season temperatures. Uses "corrected" MXD - but shouldn't usually
    ; plot past 1960 because these will be artificially adjusted to look closer to
    ; the real temperatures.
  • FOIA\documents\harris-tree\recon_esper.pro
    ; Computes regressions on full, high and low pass Esper et al. (2002) series,
    ; anomalies against full NH temperatures and other series.
    ; CALIBRATES IT AGAINST THE LAND-ONLY TEMPERATURES NORTH OF 20 N
    ;
    ; Specify period over which to compute the regressions (stop in 1960 to avoid
    ; the decline
  • FOIA\documents\harris-tree\calibrate_nhrecon.pro
    ;
    ; Specify period over which to compute the regressions (stop in 1960 to avoid
    ; the decline that affects tree-ring density records)
    ;
  • FOIA\documents\harris-tree\recon1.pro
    FOIA\documents\harris-tree\recon2.proFOIA\documents\harris-tree\recon_jones.pro
    ;
    ; Specify period over which to compute the regressions (stop in 1940 to avoid
    ; the decline
    ;
  • FOIA\documents\HARRY_READ_ME.txt
    17. Inserted debug statements into anomdtb.f90, discovered that
    a sum-of-squared variable is becoming very, very negative! Key
    output from the debug statements:
    (..)
    forrtl: error (75): floating point exception
    IOT trap (core dumped)
    ..so the data value is unbfeasibly large, but why does the
    sum-of-squares parameter OpTotSq go negative?!!
  • FOIA\documents\HARRY_READ_ME.txt
    22. Right, time to stop pussyfooting around the niceties of Tim's labyrinthine software
    suites - let's have a go at producing CRU TS 3.0! since failing to do that will be the
    definitive failure of the entire project..
  • FOIA\documents\HARRY_READ_ME.txt
    getting seriously fed up with the state of the Australian data. so many new stations have been
    introduced, so many false references.. so many changes that aren't documented.
    Every time a
    cloud forms I'm presented with a bewildering selection of similar-sounding sites, some with
    references, some with WMO codes, and some with both. And if I look up the station metadata with
    one of the local references, chances are the WMO code will be wrong (another station will have
    it) and the lat/lon will be wrong too.
  • FOIA\documents\HARRY_READ_ME.txt
    I am very sorry to report that the rest of the databases seem to be in nearly as poor a state as
    Australia was. There are hundreds if not thousands of pairs of dummy stations, one with no WMO
    and one with, usually overlapping and with the same station name and very similar coordinates. I
    know it could be old and new stations, but why such large overlaps if that's the case? Aarrggghhh!
    There truly is no end in sight.
  • FOIA\documents\HARRY_READ_ME.txt
    28. With huge reluctance, I have dived into 'anomdtb' - and already I have
    that familiar Twilight Zone sensation.
  • FOIA\documents\HARRY_READ_ME.txt
    Wrote 'makedtr.for' to tackle the thorny problem of the tmin and tmax databases not
    being kept in step. Sounds familiar, if worrying. am I the first person to attempt
    to get the CRU databases in working order?!!
  • FOIA\documents\HARRY_READ_ME.txt
    Well, dtr2cld is not the world's most complicated program. Wheras cloudreg is, and I
    immediately found a mistake!
    Scanning forward to 1951 was done with a loop that, for
    completely unfathomable reasons, didn't include months! So we read 50 grids instead
    of 600!!!
    That may have had something to do with it. I also noticed, as I was correcting
    THAT, that I reopened the DTR and CLD data files when I should have been opening the
    bloody station files!!
  • FOIA\documents\HARRY_READ_ME.txt
    Back to the gridding. I am seriously worried that our flagship gridded data product is produced by
    Delaunay triangulation - apparently linear as well. As far as I can see, this renders the station
    counts totally meaningless
    . It also means that we cannot say exactly how the gridded data is arrived
    at from a statistical perspective - since we're using an off-the-shelf product that isn't documented
    sufficiently to say that. Why this wasn't coded up in Fortran I don't know - time pressures perhaps?
    Was too much effort expended on homogenisation, that there wasn't enough time to write a gridding
    procedure? Of course, it's too late for me to fix it too. Meh.
  • FOIA\documents\HARRY_READ_ME.txt
    Here, the expected 1990-2003 period is MISSING - so the correlations aren't so hot! Yet
    the WMO codes and station names /locations are identical (or close). What the hell is
    supposed to happen here? Oh yeah - there is no 'supposed', I can make it up. So I have :-)
  • FOIA\documents\HARRY_READ_ME.txt
    Well, it's been a real day of revelations, never mind the week. This morning I
    discovered that proper angular weighted interpolation was coded into the IDL
    routine, but that its use was discouraged because it was slow! Aaarrrgghh.
    There is even an option to tri-grid at 0.1 degree resolution and then 'rebin'
    to 720x360 - also deprecated! And now, just before midnight (so it counts!),
    having gone back to the tmin/tmax work, I've found that most if not all of the
    Australian bulletin stations have been unceremoniously dumped into the files
    without the briefest check for existing stations.
  • FOIA\documents\HARRY_READ_ME.txt
    As we can see, even I'm cocking it up! Though recoverably. DTR, TMN and TMX need to be written as (i7.7)./code>
  • FOIA\documents\HARRY_READ_ME.txt
    OH FUCK THIS. It's Sunday evening, I've worked all weekend, and just when I thought it was done I'm
    hitting yet another problem that's based on the hopeless state of our databases. There is no uniform
    data integrity, it's just a catalogue of issues that continues to grow as they're found.
  • FOIA\documents\osborn-tree6\mann\mxdgrid2ascii.pro
    printf,1,’Osborn et al. (2004) gridded reconstruction of warm-season’
    printf,1,’(April-September) temperature anomalies (from the 1961-1990 mean).’
    printf,1,’Reconstruction is based on tree-ring density records.’
    printf,1
    printf,1,’NOTE: recent decline in tree-ring density has been ARTIFICIALLY
    printf,1,’REMOVED to facilitate calibration. THEREFORE, post-1960 values’
    printf,1,’will be much closer to observed temperatures then they should be,’
    printf,1,’which will incorrectly imply the reconstruction is more skilful’
    printf,1,’than it actually is. See Osborn et al. (2004).’
  • FOIA\documents\osborn-tree6\summer_modes\data4sweden.pro
    FOIA\documents\osborn-tree6\summer_modes\data4sweden.pro
    printf,1,'IMPORTANT NOTE:'
    printf,1,'The data after 1960 should not be used. The tree-ring density'
    printf,1,'records tend to show a decline after 1960 relative to the summer'
    printf,1,'temperature in many high-latitude locations. In this data set'
    printf,1,'this "decline" has been artificially removed in an ad-hoc way, and'
    printf,1,'this means that data after 1960 no longer represent tree-ring
    printf,1,'density variations, but have been modified to look more like the
    printf,1,'observed temperatures.'
  • FOIA\documents\osborn-tree6\combined_wavelet_col.pro
    ;
    ; Remove missing data from start & end (end in 1960 due to decline)
    ;
    kl=where((yrmxd ge 1402) and (yrmxd le 1960),n)
    sst=prednh(kl)
  • FOIA\documents\osborn-tree6\mann\mxd_pcr_localtemp.pro
    ; Tries to reconstruct Apr-Sep temperatures, on a box-by-box basis, from the
    ; EOFs of the MXD data set. This is PCR, although PCs are used as predictors
    ; but not as predictands. This PCR-infilling must be done for a number of
    ; periods, with different EOFs for each period (due to different spatial
    ; coverage). *BUT* don’t do special PCR for the modern period (post-1976),
    ; since they won’t be used due to the decline/correction problem.
    ; Certain boxes that appear to reconstruct well are “manually” removed because
    ; they are isolated and away from any trees.
  • FOIA\documents\osborn-tree6\briffa_sep98_d.pro;mknormal,yyy,timey,refperiod=[1881,1940]
    ;
    ; Apply a VERY ARTIFICAL correction for decline!!
    ;
    yrloc=[1400,findgen(19)*5.+1904]
    valadj=[0.,0.,0.,0.,0.,-0.1,-0.25,-0.3,0.,-0.1,0.3,0.8,1.2,1.7,2.5,2.6,2.6,$
    2.6,2.6,2.6]*0.75 ; fudge factor
    (...)
    ;
    ; APPLY ARTIFICIAL CORRECTION
    ;
    yearlyadj=interpol(valadj,yrloc,x)
    densall=densall+yearlyadj
  • FOIA\documents\osborn-tree6\summer_modes\pl_decline.pro
    ;
    ; Plots density ‘decline’ as a time series of the difference between
    ; temperature and density averaged over the region north of 50N,
    ; and an associated pattern in the difference field.
    ; The difference data set is computed using only boxes and years with
    ; both temperature and density in them – i.e., the grid changes in time.
    ; The pattern is computed by correlating and regressing the *filtered*
    ; time series against the unfiltered (or filtered) difference data set.
    ;
    ;*** MUST ALTER FUNCT_DECLINE.PRO TO MATCH THE COORDINATES OF THE
    ; START OF THE DECLINE *** ALTER THIS EVERY TIME YOU CHANGE ANYTHING ***
  • FOIA\documents\osborn-tree6\mann\oldprog\maps12.pro
    ;
    ; Plots 24 yearly maps of calibrated (PCR-infilled or not) MXD reconstructions
    ; of growing season temperatures. Uses “corrected” MXD – but shouldn’t usually
    ; plot past 1960 because these will be artificially adjusted to look closer to
    ; the real temperatures.
    ;
  • FOIA\documents\osborn-tree6\mann\oldprog\calibrate_correctmxd.pro
    ; We have previously (calibrate_mxd.pro) calibrated the high-pass filtered
    ; MXD over 1911-1990, applied the calibration to unfiltered MXD data (which
    ; gives a zero mean over 1881-1960) after extending the calibration to boxes
    ; without temperature data (pl_calibmxd1.pro). We have identified and
    ; artificially removed (i.e. corrected) the decline in this calibrated
    ; data set. We now recalibrate this corrected calibrated dataset against
    ; the unfiltered 1911-1990 temperature data, and apply the same calibration
    ; to the corrected and uncorrected calibrated MXD data.
  • FOIA\documents\osborn-tree6\summer_modes\calibrate_correctmxd.pro
    ; No need to verify the correct and uncorrected versions, since these
    ; should be identical prior to 1920 or 1930 or whenever the decline
    ; was corrected onwards from.
  • FOIA\documents\osborn-tree5\densplus188119602netcdf.pro
    ; we know the file starts at yr 440, but we want nothing till 1400, so we
    ; can skill lines (1400-440)/10 + 1 header line
    ; we now want all lines (10 yr per line) from 1400 to 1980, which is
    ; (1980-1400)/10 + 1 lines
    (...)
    ; we know the file starts at yr 1070, but we want nothing till 1400, so we
    ; can skill lines (1400-1070)/10 + 1 header line
    ; we now want all lines (10 yr per line) from 1400 to 1991, which is
    ; (1990-1400)/10 + 1 lines (since 1991 is on line beginning 1990)

This article was posted: Wednesday, November 25, 2009 at 11:08 am





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