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Issue/870 affine xform clarification #872

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Submission Checklist

  • Builds locally
  • New functions marked with <<{ since VERSION }>>
  • Declare copyright holder and open-source license: see below

Summary

Minor clarifications to Reference Manual on affine transform, added example of Neal's funnel using affine xform to Stan User's Guide chapter on efficiency tuning.

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company): Columbia University

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

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@bob-carpenter bob-carpenter left a comment

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Was it intentional to update the submodule? I'm not 100% sure how that works.

The only major required change is for the model blocks---everything else is just style.

vector<multiplier=exp(y/2)>[9] x;
}
model {
y ~ std_normal(); // implies y ~ normal(0, 3)
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same issue as above.

transformed parameter.
sampled as independent standard normals, which is easy for Stan,
and then transformed into samples from the funnel.
When this reparameterization is used in Stan code, a comment indicating what the
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Although they are technically reparameterizations under the hood, I think we should stick to calling them transforms. The terminology is confusing if you have any suggestions---the problem is that with the affine transform there is no constraining or unconstraining. The domain and range of the transform function are the same---it's just a bijection over the whole real number line.

@WardBrian
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The submodule changes should not be committed here

@mitzimorris
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I don't know how or why the quarto-config was touched by this PR and I have spent the past hour trying to undo this.
@WardBrian - please advice.

@WardBrian
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Try

cd quarto-config
git fetch
git checkout 12e4c0771ba11de259bf9298dc9f56fc9dc3e0f0
cd .. && git add .

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@bob-carpenter bob-carpenter left a comment

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Just a couple minor tweaks.

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Is Stan's affine transform type <offset, multiplier> restricted to scalars?
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