Code

174 cmdstanr sample args#175

Code

Merged

dylanhmorris merged 63 commits intomainCDCgov/ww-inference-model:mainfrom 174-cmdstanr-sample-argsCDCgov/ww-inference-model:174-cmdstanr-sample-argsCopy head branch name to clipboardSep 27, 2024

+144-90

Commits

Commits on Sep 19, 2024

• add all non depracted cmdstanr::sample args to mcmc options

  kaitejohnson

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  65312a5

• set show messages to false in the test data mcmc options

  kaitejohnson

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• update test data

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• add documentation for refresh

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• update tests to expect all args to mcmc_options

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  4ae2e9d

• replace very verbose handling of passing cmdstanr::sample with a do.call

  kaitejohnson

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  7543c2b

• replace very verbose handling of passing cmdstanr::sample with a do.call

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  35754b5

• update docs

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  221304c

• fix test

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• try to suppress ESS warning

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• Update tests/testthat/test_ww_model.R

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  kaitejohnson

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  dylanhmorris

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• set fit_opts as an empty list

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• replace test with checkmate

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• Merge branch '174-cmdstanr-sample-args' of https://github.com/CDCgov/ww-inference-model into 174-cmdstanr-sample-args

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• add wrapper function to silence warnings on mcmc tests

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Commits on Sep 22, 2024

• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  5dc640c

• remove extra args from get mcmc options

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  2dba97b

• fix example and rerun documentation

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  3dc8b95

• add checkmates expect names to only allow cmdstanr$ sample args to be passed to fit opts

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  3c76895

• make get_mcmc_options an internal function

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  f7d7d39

• modify wwinference call to pass a list not function to fit_opts

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• fix call to get number of chains

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• update package data

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• modify language in vignette to no longer reference get_mcmc_options

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  47ec753

• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  388a81c

• update documentation

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  6e41735

• run precommit

  kaitejohnson

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  be2aaa3

• remove example for function thts not exported

  kaitejohnson

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  fc635a2

• fix test

  kaitejohnson

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  1932126

• modify test data and rerun

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  4af34d6

Commits on Sep 23, 2024

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

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• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  53f4772

• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  811c4f3

• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  fea1582

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  d02c83c

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

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  8aeddc0

• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  abac574

• Update R/wwinference.R

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  kaitejohnson

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  dylanhmorris

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  68db82c

• Update R/wwinference.R

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  dylanhmorris

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  5bff3df

• Update R/wwinference.R

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  dylanhmorris

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  77c7b73

• Update R/wwinference.R

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  dylanhmorris

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  1608f23

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  3bc1ac1

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  a255fc2

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  f202eb0

• export function and remove args that are already defaults

  kaitejohnson

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  c2c65a1

• fix tests

  kaitejohnson

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  f684518

• fix test, add formalArgs to imports

  kaitejohnson

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  c594a28

• remove parallel chains and set to default, document things

  kaitejohnson

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  d7d77e7

Commits on Sep 24, 2024

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  43571c1

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  718ebcf

• update docs

  kaitejohnson

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  606eff3

• run precommit and add new test

  kaitejohnson

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  becd549

• add reg exp to test

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  dc67274

• add setting mc cores to 4

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  d94d580

• add the chains back so that we use them in inits

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  b0ffc23

• update test data

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  d70c609

• Merge branch 'main' into 174-cmdstanr-sample-args

  dylanhmorris

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  acd0c4b

• remove methods formal args from package

  kaitejohnson

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  6d7a305

• Merge branch '174-cmdstanr-sample-args' of https://github.com/CDCgov/ww-inference-model into 174-cmdstanr-sample-args

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  committed
  492d793

Commits on Sep 25, 2024

• try updating testing data

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  ee27de0

Commits on Sep 26, 2024

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  a6e78b0

• Update R/wwinference.R

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  kaitejohnson

  and

  dylanhmorris

  authored
  1489d7c

• fix documentation

  kaitejohnson

  committed
  cfe8b0a