All pull requests

Pull requests

• Bump actions/create-github-app-token from 3.2.0 to 3.3.0

  dependenciesgithub_actions
  #1618·dependabot[bot] opened Oct 19, 2026Bot·

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• fix: reject existing files as target_folder

  #1617·dannyward630 opened Oct 17, 2026·3 of 7 tasks·

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  1

• Update estimate_infections_workflow vignette

  documentation
  #1612·github-actions[bot] opened Oct 1, 2026Bot·

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• Update estimate_dist_workflow vignette

  documentation
  #1611·github-actions[bot] opened Oct 1, 2026Bot·

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• Update prior_choice_guide vignette

  documentation
  #1610·github-actions[bot] opened Oct 1, 2026Bot·

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• Update epinow vignette

  documentation
  #1609·github-actions[bot] opened Oct 1, 2026Bot·

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• Update EpiNow2 vignette

  documentation
  #1608·github-actions[bot] opened Oct 1, 2026Bot·

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• Update forecasting_multiple_data_streams vignette

  documentation
  #1607·github-actions[bot] opened Oct 1, 2026Bot·

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• Update estimate_infections_options vignette

  documentation
  #1606·github-actions[bot] opened Oct 1, 2026Bot·

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• Support pathfinder initialisation for NUTS sampling

  #1601·sbfnk-bot opened Sep 28, 2026Collaborator·

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  1

  4

• Fold secondary observation type into obs_opts()

  #1600·sbfnk-bot opened Sep 28, 2026Collaborator·

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  3

• Estimate the case (cohort) reproduction number

  #1599·sbfnk-bot opened Sep 28, 2026Collaborator·

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  1

  6

• Share the fitting step across the estimate_* functions

  llm-reviewed
  #1596·seabbs-bot opened Sep 25, 2026Collaborator·6 of 7 tasks·

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  1

  4

• Remove 1.9.0 deprecations and error on estimate_delay()

  llm-reviewed
  #1595·seabbs-bot opened Sep 25, 2026Collaborator·7 tasks done·

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  8

• Add tests for model wrapper inputs, helpers and preprocessing

  llm-reviewed
  #1590·seabbs-bot opened Sep 25, 2026Collaborator·6 of 7 tasks·

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  10

• Test epinow(), regional_epinow() and report helpers with a mocked fit

  llm-reviewed
  #1589·seabbs-bot opened Sep 25, 2026Collaborator·6 of 7 tasks·

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  6

• Add tests for summary, formatting and accessor functions

  llm-reviewed
  #1581·seabbs-bot opened Sep 25, 2026Collaborator·7 tasks done·

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  5

• Test backend dispatch, logging set up and as_forecast_sample() with mocks

  llm-reviewed
  #1578·seabbs-bot opened Sep 25, 2026Collaborator·5 of 7 tasks·

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  3

• Add tests for option constructors, delay checks and utility helpers

  llm-reviewed
  #1568·seabbs-bot opened Sep 25, 2026Collaborator·5 of 7 tasks·

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  6

• Add unit tests for untested Stan observation, secondary and Rt functions

  llm-reviewed
  #1566·seabbs-bot opened Sep 25, 2026Collaborator·5 of 7 tasks·

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  1

  5

• Choose HSGP boundary and basis functions from the lengthscale prior

  llm-reviewed
  #1562·seabbs-bot opened Sep 25, 2026Collaborator·6 of 7 tasks·

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  61

• Use custom reverse-mode adjoints for the delay convolution, renewal equation and R_to_r()

  llm-reviewed
  #1561·seabbs-bot opened Sep 25, 2026Collaborator·6 of 7 tasks·

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  24

• Follow up Stan review suggestions: delay prior weights, docs and naming

  llm-reviewed
  #1554·seabbs-bot opened Sep 25, 2026Collaborator·4 of 7 tasks·

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  4

• Drop constant truncation terms from parameter priors

  llm-reviewed
  #1553·seabbs-bot opened Sep 25, 2026Collaborator·4 of 7 tasks·

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  14

• Centre the lowest-frequency Gaussian process coefficient

  #1549·sbfnk-bot opened Sep 25, 2026Collaborator·

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  9