entry for wiener diffusion model#934
Conversation
|
Thanks, so much, @Franzi2114. If nobody else can get to this, I can review it some time over the next week. |
|
Perfec,t thanks @bob-carpenter! I was also in contact with @WardBrian before I did the PR. There are still three open points that I didn't manage to incorporate:
Please let me know when there occur more points that I should change. |
|
Hi @Franzi2114 -- I've just pushed a commit that addresses each of your comments, since they're mostly quarto-wrangling:
|
|
Pinging @bob-carpenter again -- I think the notifications for this got lost while you were away |
|
Thanks for pinging. I will review this week. |
bob-carpenter
left a comment
There was a problem hiding this comment.
Hi, Franzi:
I'm really sorry this is so many comments. Most of it's to try to get consistency with the rest of our documentation's formatting.
The most important comment is about the upper bounds for parameters that are missing from the examples.
If you'd rather not make the fixes yourself, I think I can go through and make almost all of them other than places where I had genuine questions.
|
Dear @bob-carpenter, I worked through all your comments and made several changes! Could you have another look at it? I also had some questions regarding your posts. I wrote them below your comments. I am afraid that I messed something up with the all.bib file. Can you fix this? |
|
There are also conflicts with character usage of unicode ~ when you try to build. Do all the docs build locally for you with the broken all.bib file and the stray unicode characters? It looks somehow like you dumped in an entirely conflicting bibtex file somehow. To fix, you just need to get rid of all the notes about conflicts that were autogenerated in I'll just go ahead and make the language changes and indicate what I did above. The main issue is that likelihoods are functions of parameters, not data, by construction. |
|
There are non-ASCII versions of stan-users-guide (feature/docs_for_wiener_lpdf_and_lcdf_unnorm)$ grep -rn $'\xe2\x88\xbc' *.qmd
wiener_diffusion_model.qmd:127: a ∼ normal(1, 1);
wiener_diffusion_model.qmd:128: w ∼ normal(0.5, 0.1);
wiener_diffusion_model.qmd:129: v ∼ normal(2, 3);
wiener_diffusion_model.qmd:130: t0 ∼ normal(0.435, 0.12);
wiener_diffusion_model.qmd:132: sv ∼ normal(1, 3);
wiener_diffusion_model.qmd:133: st0 ∼ normal(0.183, 0.09);
wiener_diffusion_model.qmd:134: sw ∼ beta(1, 3);
wiener_diffusion_model.qmd:384: y[i] ∼ wiener(a, t0, w, v, sv, sw, st0);
wiener_diffusion_model.qmd:388: y[i] ∼ wiener(a, t0, one_minus_w, neg_v, sv, sw, st0);I don't actually see any conflicts in the I went through and cut lines down to 80 characters. I also spaced out operators, etc. in code and tightened spaces to conform to our coding guidelines (appendix of user's guide). I also removed the "end" block and other comments on lines with braces and moved them down so the structure of the code is clearer. Italic words shouldn't be in formulas like |
|
I just went ahead and converted the figure to a .png and made that the default format for the web page. I just realized in doing a diff on the command line that the conflict with the .bib file is that it got Windows-style newlines. We strictly use Unix/Linux/Mac newlines. Windows should not have tried to innovate on the newline character! I switched it back using It all builds now and I checked the output in html and pdf and the images look right. Thanks for bearing with the long process here. It only took me an hour or so to put in the final patches. |
bob-carpenter
left a comment
There was a problem hiding this comment.
Looks good. Thanks for all the updates.
Summary
This PR adds a user's guide entry for the wiener diffusion model. It is linked to the PRs for the seven parameter diffusion model PDF and CDF functions
stan-dev/math#2822
stan-dev/math#3042
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):
Franziska Henrich
By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses: