Code

Issue 757: Vectorise GP stan code#742

Code

Merged

seabbs merged 107 commits intomainepiforecasts/EpiNow2:mainfrom vectorise-spectral-densityepiforecasts/EpiNow2:vectorise-spectral-densityCopy head branch name to clipboardAug 29, 2024

+606-220

Commits

Commits on Aug 9, 2024

• refactor gps along approach used by aki

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• add some skeleton unit tests

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• update model

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• update data chunk

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• add r interface code

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• add some R side tests where missing for gp related code

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Commits on Aug 12, 2024

• get tests passing

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• fix tests for create_gp_data

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• fix tests

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• update docs

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• fix tests warnings to error for uncommon mattern orders

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• remove spurious plots

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• update EpiNow2 vignette

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• review kkernals

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• update and test

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• correct scaling of L

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Commits on Aug 13, 2024

• rescale lengthscale

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• change adapt-delta default to 0.9

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• expand inits for GP as causing issues as to close to 1/0

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• get rid of normalisation and use unormalised lpdf where possible (equiv)

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• widen optimisation sweep to include delay weight default

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• non-center random walk

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• tune prior specification

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• tune dispersion prior

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• tune phi

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• update vignette

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• get rid of rw change

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• revert Rt

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• catch update_rt

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• add news

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• revert vignette changes

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• fix gp_opts tests

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• fix create tests

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Commits on Aug 14, 2024

• update gp tests

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• skip tests as required on windows

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• fix linting

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• constrain delay uncertainty

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• correct gp stan tests

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• fix GP test

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• put the deprecition warning behind a gate

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• refactor gps along approach used by aki

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  e338331

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• add some skeleton unit tests

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  9297afd

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• update model

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  8dec848

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• update data chunk

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  b503e82

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• add r interface code

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• add some R side tests where missing for gp related code

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  3cfc9aa

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• get tests passing

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• fix tests for create_gp_data

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• fix tests

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• update docs

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• fix tests warnings to error for uncommon mattern orders

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  282de44

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• update EpiNow2 vignette

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  d333a81

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• review kkernals

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  9e990ce

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• update and test

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  afc2520

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• correct scaling of L

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• rescale lengthscale

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• change adapt-delta default to 0.9

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• expand inits for GP as causing issues as to close to 1/0

  seabbs

  committed
  c0d0dbb

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• get rid of normalisation and use unormalised lpdf where possible (equiv)

  seabbs

  committed
  3ff3cb9

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• widen optimisation sweep to include delay weight default

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  committed
  9dba492

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• non-center random walk

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  committed
  7c16cd6

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• tune prior specification

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• tune dispersion prior

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• tune phi

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• update vignette

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• get rid of rw change

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• revert Rt

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• catch update_rt

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• add news

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• revert vignette changes

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• fix gp_opts tests

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• fix create tests

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• update gp tests

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• skip tests as required on windows

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• fix linting

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• constrain delay uncertainty

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• correct gp stan tests

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• fix GP test

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• put the deprecition warning behind a gate

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• fix linting

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• Update NEWS.md

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Commits on Aug 15, 2024

• merge

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• add linear kernel support

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• add docs and newa

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• integration tests and minor issues

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• fixes for periodic kernel dimension differences

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Commits on Aug 19, 2024

• drop linear kernel support

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• lint space

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• catch outstanding linear tests

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• catch stan tests

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Commits on Aug 20, 2024

• make the eecdf in convolve test less random

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Commits on Aug 27, 2024

• Update R/create.R

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• Merge branch 'main' into vectorise-spectral-density

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Commits on Aug 28, 2024

• Update NEWS.md

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• Update create.R - remove out of date gp type 3 check

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• Update opts.R - remove linear kernel references

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• Update R/opts.R

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• Update opts.R - fix review suggestions

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• Update opts.R - remove linear reference

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• Update estimate_infections.stan

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• Update tests/testthat/test-create_gp_data.R

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• Update NEWS.md

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• Update opts.R

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• Document

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• Merge branch 'main' into vectorise-spectral-density

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• Merge branch 'main' into vectorise-spectral-density

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• Merge branch 'main' into vectorise-spectral-density

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