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JSON and R dump format specs in reference manual

1

#### Summary: We should talk about our JSON and R dump formats accepted by CmdStan in the reference manual. #### Description: Note that our JSON format is different than the...

bob-carpenter

update issue templates

2

#### Summary: GitHub has changed issue templates. update https://github.com/stan-dev/docs/blob/master/.github/ISSUE_TEMPLATE.md ? #### Current Version: change this!!!!

mitzimorris

#### Summary: Make the notation consistent for covariance and correlation matrices. #### Description: From @andrewgelman: In section 5.5 of the reference manual, you label the cov matrix as Omega and...

bob-carpenter

Update https://mc-stan.org/docs/stan-users-guide/calling-the-algebraic-solver.html because it has algebra_solver_newton in the code examples but the function is solve_newton.

spinkney

In terms of naming arguments, inconsistencies in notation to iron out (little vs. big N for example in sizing, for example), etc. Originally posted by @bob-carpenter in https://github.com/stan-dev/docs/pull/678#pullrequestreview-1801159337, see additional...

WardBrian

Clarify that sampling statements vs. target += may not always preserve sampling behavior

5

[Section 7.4 of the Stan reference manual](https://mc-stan.org/docs/reference-manual/sampling-statements.html#log-probability-increment-vs.-sampling-statement) says that using the sampling statement `y ~ normal(mu, sigma)` and incrementing the target probability directly with `target += normal_lpdf(y | mu,sigma)` will...

jtassarotti

Minor fixes to beta function parameters and clarifying text for gamma distribution

2

#### Submission Checklist - [ ] Builds locally -- see below - [x ] New functions marked with `` `r since("VERSION")` `` - [x ] Declare copyright holder and open-source...

mikegilchrist

discuss propto with double vs. autodiff variables in User's Guide

2

#### Summary: In the *User's Guide* chapter on efficiency, we should discuss the tradeoff between evaluating `propto=true` with `double` and autodiff variables. #### Description: The issue is that * `propto=true`...

bob-carpenter

#### Summary: The description of the unit vector transform isn't accurate as written in the *Reference Manual* chapter on constraining transforms. There's no Jacobian determinant involved, just a density on...

bob-carpenter

Complex accessor vectorization

3

Complex accessors are vectorized but documentation just shows that the output is a `real`. https://mc-stan.org/docs/functions-reference/complex-constructors.html#complex-accessors

spinkney