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Reduce dependence on cmdstanr given it's suggested not required #362

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athowes opened this issue Oct 2, 2024 · 1 comment · Fixed by #424
Closed

Reduce dependence on cmdstanr given it's suggested not required #362

athowes opened this issue Oct 2, 2024 · 1 comment · Fixed by #424
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high Required for next release

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@athowes
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athowes commented Oct 2, 2024

I think make a new issue for handling this with my preference being to stop being opinionated about the backend in the core package. We can talk about doing so (and how to) in the vignettes. The minimal version is we use rstan everywhere and put a comment about preferring cmdstanr in the FAQ

Originally posted by @seabbs in #356 (comment)
@athowes athowes added the high Required for next release label Oct 2, 2024
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athowes commented Oct 2, 2024 •
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This plan seems fine to me.

When I've previously tried to migrate to rstan in tests it has thrown fails. So that will probably have to be tackled if we want to move to using rstan in tests.

@athowes athowes mentioned this issue Nov 6, 2024
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@athowes athowes linked a pull request Nov 7, 2024 that will close this issue
Issue #362: Reduce dependence on cmdstanr #424
Merged
9 tasks
@athowes athowes self-assigned this Nov 13, 2024
seabbs added a commit that referenced this issue Nov 14, 2024
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
4afb056 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
@athowes athowes mentioned this issue Nov 14, 2024
Closed
seabbs added a commit that referenced this issue Jan 10, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
266b4be 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 729e385075e181a2c7d9a716e776ac504d08a658 [formerly 70e78c0742b69012eb57ad58c5d92e39d25c45ad]
Former-commit-id: 38ff128853245a2fba7acdbe49951aabc476647e
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
cd928a6 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 4afb056
Former-commit-id: 764790be7d4ec49bce89e458a96556e91a472cb2
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
bfe0d21 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 4afb056
Former-commit-id: 764790be7d4ec49bce89e458a96556e91a472cb2
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
32c2660 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 4afb056
Former-commit-id: 764790be7d4ec49bce89e458a96556e91a472cb2
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
9fc612e 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 729e385075e181a2c7d9a716e776ac504d08a658 [formerly 70e78c0742b69012eb57ad58c5d92e39d25c45ad]
Former-commit-id: 38ff128853245a2fba7acdbe49951aabc476647e
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
5a89ac2 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 729e385075e181a2c7d9a716e776ac504d08a658 [formerly 70e78c0742b69012eb57ad58c5d92e39d25c45ad]
Former-commit-id: 38ff128853245a2fba7acdbe49951aabc476647e
Former-commit-id: 9fc612e
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
5472a2e 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 4afb056
Former-commit-id: 764790be7d4ec49bce89e458a96556e91a472cb2
Former-commit-id: 0de625c0e819bd977b6691ec528c385cbbd34615 [formerly 32c2660]
Former-commit-id: 67be8349533318a2c020276788ccdfe2dd84e106
seabbs added a commit that referenced this issue Jan 21, 2025
@athowes @seabbs
Issue #362: Reduce dependence on cmdstanr (#424)
975f3ad 
* Switch default to rstan rather than cmdstanr

* Import BH

* Use match.arg as suggested by @jamesmbaazam

* Add RcppEigen to Suggests

* Change backend to cmdstanr in approximate inference vignette

* Use cmdstanr for Laplace test

* Remove erroneous output_dir arg

* drop backend entirely as an arg

* remove cmdstanr using vignettes from cran check

* update cmdstan install instructions

* update epidist docs

* update approx-inference vignette to make it clear we are using cmdstanr and not rstan

* switch ebola vignette over to cmdstanr

* update test fit returns

* update more fit uses in test

* fix helper function

* bring silence to laplace

* fix epidist

* get tests passing

* fix CRAN check

* use fewer cores

* drop additional deps

* drop duplicate prepping

* try and use linking with instead of imports

* Update vignettes/epidist.Rmd

Co-authored-by: Adam Howes <[email protected]>

* Update tests/testthat/test-int-latent_individual.R

Co-authored-by: Adam Howes <[email protected]>

* Update inst/generate_examples.R

Co-authored-by: Adam Howes <[email protected]>

---------

Co-authored-by: Sam <[email protected]>
Former-commit-id: 4afb056
Former-commit-id: 764790be7d4ec49bce89e458a96556e91a472cb2
Former-commit-id: 0de625c0e819bd977b6691ec528c385cbbd34615 [formerly 32c2660]
Former-commit-id: 67be8349533318a2c020276788ccdfe2dd84e106
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Issue #362: Reduce dependence on cmdstanr epinowcast/epidist
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