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Branch: master
Commits on Jul 20, 2012
  1. Added README.md from develop branch

    Charles R. Hogg III authored
Commits on Jul 17, 2012
  1. Merge branch 'release-0.2-1'

    Charles R. Hogg III authored
  2. Trimmed and compressed: now 83% smaller!

    Charles R. Hogg III authored
  3. Merge branch 'release-0.2-0' into develop

    Charles R. Hogg III authored
    Conflicts:
    	.Rbuildignore
    	DESCRIPTION
    	inst/tests/test-Covariance.R
    	inst/tests/test-Dataset.R
  4. Merge branch 'release-0.2-0'

    Charles R. Hogg III authored
Commits on Jul 16, 2012
  1. Ready for initial submission to CRAN!

    Charles R. Hogg III authored
Commits on Jul 13, 2012
  1. Started adding flameSpeed demo

    Charles R. Hogg III authored
    steelStrain demo is just way too slow!
  2. Fix syntax error in R-dependency

    Charles R. Hogg III authored
    Boneheaded... needed a space before the number
  3. Added datasets from JAC paper

    Charles R. Hogg III authored
  4. Dependency bump to R >=2.14.0

    Charles R. Hogg III authored
    The package now thoroughly uses the new NAMESPACE-based approach.  Given
    that even Debian installs can easily obtain recent versions of R, I see
    no reason to cater to old versions.
  5. Innumerable changes to pass R CMD check

    Charles R. Hogg III authored
Commits on Jul 12, 2012
  1. Modified tests so Dataset passes

    Charles R. Hogg III authored
    The 'SameX' test apparently tested a feature which no longer exists.
    
    Also, I get warnings about being unable to find datasets when I run the
    tests, but the tests pass.  So I'm not sure what that's about...
  2. Setup infrastructure for unit testing

    Charles R. Hogg III authored
    I started copying some of my old unit tests.  But it's changed enough to
    make this a non-trivial task, so I'm deferring the rest until I can do
    it properly.
    
    Also, I augmented the steelStrain dataset to include exy and eyy columns
    in addition to exx column.
  3. Made script to reproduce steelStrain from raw data

    Charles R. Hogg III authored
    I want my data generation to be more reproducible and transparent, so I
    made a script that does what I want it to with the raw data for the
    steelStrain dataset.  It will be tracked in github, but the datafile
    will be excluded from the package build (it's 5.1 MB; that's too big).
  4. Setup infrastructure for unit testing

    Charles R. Hogg III authored
    Also, started copying some of my old unit tests.  But it's changed
    enough to make this a non-trivial task, so I'm deferring the rest until
    I can do it properly.
Commits on Jul 11, 2012
  1. Setup structure for unit tests

    Charles R. Hogg III authored
    Note: there is no reason to believe these tests will run, or that they
    are reasonably complete.
  2. Removed redundant 'gppois:::' qualifiers

    Charles R. Hogg III authored
    I was a little overzealous adding 'gppois:::' before each private
    method.  This appears to be unnecessary for code that is WITHIN the
    package.  (Code "outside" the package, such as the steelStrain.R demo,
    still needs this qualifier.)
  3. steelStrain demo: show TRUE datapoints in gap

    Charles R. Hogg III authored
  4. Use the "modern" approach for sd() on data.frame

    Charles R. Hogg III authored
  5. Fixed demo (removed syn-sugar for private methods)

    Charles R. Hogg III authored
    R.oo provides syntactic-sugar field access: e.g., instead of
      Method(this=object, ...)
    you can write
      object$Method(...)
    which is a more "object oriented" way of doing things.  Unfortunately,
    this seems to rely on the fully qualified method name, i.e.
      Method.class
    being exported to the namespace.  Private methods should *not* be
    exported to the namespace.  Hence, we can't use the "nice" way to access
    private methods.
  6. Fixed oversights in documentation

    Charles R. Hogg III authored
    - getVaryingParamNames: I had written roxygen comments, but I forgot to
      write "#'" instead of "#" so roxygen would actually see them
    - setParams.Covariance had been missing export and S3method tags; these
      are now added
  7. Made public R.oo play nice with NAMESPACE

    Charles R. Hogg III authored
    Apparently I need to export both the generic function and the fully
    qualified name for each class, or else the R.oo syntactic sugar won't
    work.  This commit doesn't represent a working state, because I need to
    fix the private files, but it should be OK for the public ones.
Commits on Jul 10, 2012
  1. Made documentation compatible with NAMESPACE

    Charles R. Hogg III authored
    - Added export statements for print and clone method
    - For now, I have to manually add the constructors to NAMESPACE, because
      they use R.oo instead of roxygen.
    - Gave in to the Collate message in the DESCRIPTION file, which the
      newer devtools generates
Commits on Jul 9, 2012
  1. Fixed: had double-counted .Model in docs

    Charles R. Hogg III authored
    I had written
    @S3method getLower.Model Model
    instead of
    @S3method getLower Model
    which is boneheaded.
  2. Changed documentation to use R 2.15

    Charles R. Hogg III authored
    Most .Rd files only changed the ordering of a few lines.
Commits on Jul 5, 2012
  1. steelStrain demo now plots best-fit surface

    Charles R. Hogg III authored
  2. Bumped version number to 0.2-0

    Charles R. Hogg III authored
  3. Merge branch 'strainDemo' into develop

    Charles R. Hogg III authored
  4. Fixed bug for Model$Train with bounds

    Charles R. Hogg III authored
    Bug: certain Models being trained would get stuck at the boundaries.
    Turns out, this was because 'optim' *ignores* the names on the 'lower'
    and 'upper' vectors, so boundaries weren't necessarily matched with the
    corresponding parameters.
    Fix: caused getLower and getUpper to omit values for constant
    parameters, in accordance with the behaviour of getParams.
  5. Merge branch 'develop' into strainDemo

    Charles R. Hogg III authored
  6. Expand bounds during training to prevent clamping

    Charles R. Hogg III authored
    The optimizer seems to be getting confused when parameter values get
    clamped.  I think I'll have better results if I just let L-BFGS-B take
    care of the boundaries.  Expand the Model's bounds ($lower and $upper)
    during training, then bring them back once we're done.
Commits on Jun 20, 2012
  1. Setup steel strain demo (but Train.Model buggy)

    Charles R. Hogg III authored
    First code relating to a demo for the package.  Made a demo directory
    and script.  Other changes include:
      Dataset.R:  Improved Plot2D function: you can now adjust the vertical
        scale, and it doesn't force you to clear the plot
      utils.R:  Made a "pause" function for the demo
      Covariance.R: Removed a useless line
    
    Model training is not working for aniso2D, but it works quite well for
    regular SE.  In particular, it always maximizes the sigma's (and the
    ell's are correspondingly too large).  I've verified that the parameter
    values from DEoptim have significantly higher LogML than the parameters
    where it's getting stuck.  Maybe it's some kind of boundary issue?
    Maybe try enlarging the Model's bounds, then shrinking them back down?
    L-BFGS-B really shouldn't propose outside the bounds, so we should still
    be OK...
Commits on Jun 16, 2012
  1. Added citation information

    Charles R. Hogg III authored
  2. Put rgl aspect ratio code in own function

    Charles R. Hogg III authored
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