Improve identifiability of non-stationary GP - #1396

Merged

sbfnk merged 46 commits into

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identifiable-non-stationary-gp

Jun 4, 2026

Commits on May 8, 2026

Improve identifiability of non-stationary GP

sbfnk-bot
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5d870b5
Widen default alpha to compensate for rescaled GP

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3d96f3f
Update documentation
epiforecasts-workflows[bot]
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f25229e
Widen default alpha further to match observed posterior

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e0455bc
Merge branch 'identifiable-non-stationary-gp' of github.com:epiforecasts/EpiNow2 into identifiable-non-stationary-gp
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08d5717
Update gp_opts.Rd for new alpha default
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965d38c
Update tests for new GP parameterisation

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e234216
Widen default alpha to Normal(0, 0.5) and document weak identification

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71112fd
Revert default alpha to Normal(0, 0.2)

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7a0326e

Commits on May 11, 2026

Strip PR back to centring-only

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7a3d957
Merge branch 'main' into identifiable-non-stationary-gp
sbfnk
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f00a6a7
address review: document new R0 interpretation under centred GP

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be45c1b
Merge branch 'identifiable-non-stationary-gp' of github.com:epiforecasts/EpiNow2 into identifiable-non-stationary-gp
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674ec6f
address review: warn on custom prior under centred GP

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0055390

Commits on May 20, 2026

Apply user prior on derived initial Rt under centred GP

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d5f9081
fix ci: provide empty init prior data items in simulate_infections

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3351aa5

Commits on May 29, 2026

Rename centred_gp_init_lpdf to gp_init_lpdf

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e5c24b5

Commits on Jun 3, 2026

Truncate normal prior at zero in gp_init_lpdf

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ed76d5a
Centre GP over observation window, not forecast tail

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68eef6e
Consolidate duplicate Model changes sections in NEWS.md

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e0dba4c
fix ci: pass n_centre argument to update_Rt in tests

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db69ec6
Document GP reparameterisation in vignette

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4a7ae9c
Match vignette math style for the GP Rt section

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e1b768c
Use ragged init dist params and bounds from the distribution

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68cc92f
Simplify natural-scale wording in GP vignette

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47e6859
Update documentation
epiforecasts-workflows[bot]
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328d6e2
Test the centring algebra, invariants and truncation directly

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ced99bf
Merge branch 'identifiable-non-stationary-gp' of github.com:epiforecasts/EpiNow2 into identifiable-non-stationary-gp
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ac9aaab
Inline init-prior dispatch using ~ T[lower, upper] like params_lp

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866e017
Factor init-prior dispatch into shared helpers

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94c65a0
Move init-prior dispatch into init_priors_lp

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72ece9b
fix ci: wrap make_init_priors call to keep under 80 chars

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63d2022
Frame GP centring via regression-intercept analogy in vignette

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f107376
Merge remote-tracking branch 'origin/main' into identifiable-non-stationary-gp
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47fa8d2
Link brms reference to its CRAN page

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26e7a0b
Make the intercept/slope analogy explicit in the GP vignette

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2d03561
fix ci: rename apply_prior_lp bound args to avoid stanc reserved keywords

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e59ec01
Merge remote-tracking branch 'origin/main' into identifiable-non-stationary-gp
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230a949

Commits on Jun 4, 2026

Cross-link estimate_infections section from GP vignette

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aff9ca7
Make GP vignette wording more accessible

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d9b7f98
Tighten GP vignette: notation, linking and layout

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9fd37a2
Simplify Jacobian framing in GP vignette

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7d18426
Collapse Jacobian discussion in GP vignette into a single transform

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6dade6e
Tighten GP vignette flow around the centring identity

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b9f6851
Display Jacobian formula on its own line in GP vignette

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19c89af
Restructure the centring derivation in the GP vignette

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1d46ab6