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Fix broken doctests (#92)
* Update ASCII rendering of dataset header * Update PosteriorStats doctests for changed example data * Increment patch number * Update timestamps for datasets * Update ASCII rendering of dataset header in ext * Point to new NCDatasets docs URL
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-56
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7 files changed

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‎Project.toml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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name = "InferenceObjects"
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uuid = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
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authors = ["Seth Axen <[email protected]> and contributors"]
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version = "0.4.8"
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version = "0.4.9"
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[deps]
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Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

‎docs/make.jl‎

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@@ -20,7 +20,7 @@ links = InterLinks(
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"https://juliamath.github.io/IntervalSets.jl/stable/",
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joinpath(@__DIR__, "inventories", "IntervalSets.toml"),
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),
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"NCDatasets" => "https://alexander-barth.github.io/NCDatasets.jl/stable/",
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"NCDatasets" => "https://juliageo.org/NCDatasets.jl/stable/",
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"PosteriorStats" => "https://julia.arviz.org/PosteriorStats/stable/",
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"MCMCDiagnosticTools" => "https://julia.arviz.org/MCMCDiagnosticTools/stable/",
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)

‎ext/InferenceObjectsPosteriorStatsExt/loo.jl‎

Lines changed: 3 additions & 3 deletions
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@@ -20,13 +20,13 @@ julia> idata = load_example_data("centered_eight");
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julia> loo(idata)
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PSISLOOResult with estimates
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elpd elpd_mcse p p_mcse
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-31 1.4 0.9 0.34
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-31 1.4 0.9 0.33
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and PSISResult with 500 draws, 4 chains, and 8 parameters
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Pareto shape (k) diagnostic values:
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Count Min. ESS
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(-Inf, 0.5] good 6 (75.0%) 135
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(0.5, 0.7] okay 2 (25.0%) 421
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(-Inf, 0.5] good 4 (50.0%) 270
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(0.5, 0.7] okay 4 (50.0%) 307
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```
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"""
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function PosteriorStats.loo(

‎ext/InferenceObjectsPosteriorStatsExt/loo_pit.jl‎

Lines changed: 18 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -26,19 +26,18 @@ julia> idata = load_example_data("centered_eight");
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julia> loo_result = loo(idata; var_name=:obs);
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julia> loo_pit(idata, loo_result.psis_result.log_weights; y_name=:obs)
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╭────────────────────────────────────────────╮
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│ 8-element DimArray{Float64, 1} loo_pit_obs │
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┌ 8-element DimArray{Float64, 1} loo_pit_obs ┐
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├────────────────────────────────────────────┴─────────────────────────── dims ┐
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↓ school Categorical{String} [Choate, Deerfield, …, St. Paul's, Mt. Hermon] Unordered
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└──────────────────────────────────────────────────────────────────────────────┘
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"Choate" 0.943511
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"Deerfield" 0.63797
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"Phillips Andover" 0.316697
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"Phillips Exeter" 0.582252
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"Hotchkiss" 0.295321
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"Lawrenceville" 0.403318
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"St. Paul's" 0.902508
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"Mt. Hermon" 0.655275
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"Choate" 0.942759
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"Deerfield" 0.641057
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"Phillips Andover" 0.32729
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"Phillips Exeter" 0.581451
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"Hotchkiss" 0.288523
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"Lawrenceville" 0.393741
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"St. Paul's" 0.886175
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"Mt. Hermon" 0.638821
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```
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"""
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function PosteriorStats.loo_pit(
@@ -86,19 +85,18 @@ julia> using ArviZExampleData, PosteriorStats
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julia> idata = load_example_data("centered_eight");
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julia> loo_pit(idata; y_name=:obs)
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╭────────────────────────────────────────────╮
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│ 8-element DimArray{Float64, 1} loo_pit_obs │
88+
┌ 8-element DimArray{Float64, 1} loo_pit_obs ┐
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├────────────────────────────────────────────┴─────────────────────────── dims ┐
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↓ school Categorical{String} [Choate, Deerfield, …, St. Paul's, Mt. Hermon] Unordered
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└──────────────────────────────────────────────────────────────────────────────┘
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"Choate" 0.943511
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"Deerfield" 0.63797
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"Phillips Andover" 0.316697
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"Phillips Exeter" 0.582252
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"Hotchkiss" 0.295321
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"Lawrenceville" 0.403318
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"St. Paul's" 0.902508
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"Mt. Hermon" 0.655275
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"Choate" 0.942759
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"Deerfield" 0.641057
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"Phillips Andover" 0.32729
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"Phillips Exeter" 0.581451
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"Hotchkiss" 0.288523
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"Lawrenceville" 0.393741
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"St. Paul's" 0.886175
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"Mt. Hermon" 0.638821
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```
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"""
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function PosteriorStats.loo_pit(

‎ext/InferenceObjectsPosteriorStatsExt/summarize.jl‎

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Original file line numberDiff line numberDiff line change
@@ -34,16 +34,16 @@ julia> data = load_example_data("centered_eight");
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julia> summarize(data)
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SummaryStats
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mean std hdi_3% hdi_97% mcse_mean mcse_std ess ⋯
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mu 4.5 3.5 -1.62 10.7 0.23 0.11 ⋯
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theta[Choate] 6.5 5.9 -4.56 17.1 0.30 0.29 ⋯
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theta[Deerfield] 5.0 4.9 -4.31 14.3 0.23 0.17 ⋯
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theta[Phillips Andover] 3.9 5.7 -7.77 13.7 0.23 0.28 ⋯
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theta[Phillips Exeter] 4.9 5.0 -4.49 14.7 0.26 0.17 ⋯
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theta[Hotchkiss] 3.7 5.0 -6.47 11.7 0.25 0.16 ⋯
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theta[Lawrenceville] 4.0 5.2 -7.04 12.2 0.22 0.22 ⋯
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theta[St. Paul's] 6.6 5.1 -3.09 16.3 0.30 0.19 ⋯
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theta[Mt. Hermon] 4.8 5.7 -5.86 16.0 0.26 0.25 ⋯
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tau 4.1 3.1 0.896 9.67 0.26 0.17 ⋯
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mu 4.2 3.3 -1.61 10.3 0.21 0.088 ⋯
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theta[Choate] 6.4 5.9 -3.68 17.9 0.25 0.20 ⋯
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theta[Deerfield] 5.0 4.9 -4.98 13.4 0.21 0.15 ⋯
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theta[Phillips Andover] 3.4 5.4 -7.54 12.9 0.23 0.17 ⋯
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theta[Phillips Exeter] 4.8 5.2 -5.11 14.1 0.21 0.21 ⋯
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theta[Hotchkiss] 3.5 4.8 -6.12 12.0 0.25 0.15 ⋯
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theta[Lawrenceville] 3.7 5.2 -6.50 12.7 0.22 0.21 ⋯
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theta[St. Paul's] 6.5 5.2 -2.67 16.9 0.22 0.15 ⋯
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theta[Mt. Hermon] 4.8 5.7 -5.97 15.4 0.24 0.23 ⋯
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tau 4.3 3.0 0.715 9.41 0.22 0.14 ⋯
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3 columns omitted
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```
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@@ -54,14 +54,14 @@ parameters:
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julia> summarize(data.posterior[(:theta,)], (:mean, :std) => mean_and_std, median, mad)
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SummaryStats
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mean std median mad
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theta[Choate] 6.46 5.87 6.08 4.64
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theta[Deerfield] 5.03 4.88 5.01 4.96
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theta[Phillips Andover] 3.94 5.69 4.23 4.67
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theta[Phillips Exeter] 4.87 5.01 5.02 4.82
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theta[Hotchkiss] 3.67 4.96 3.89 4.70
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theta[Lawrenceville] 3.97 5.19 4.14 4.64
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theta[St. Paul's] 6.58 5.11 6.07 4.47
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theta[Mt. Hermon] 4.77 5.74 4.71 4.95
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theta[Choate] 6.42 5.85 5.80 4.95
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theta[Deerfield] 4.95 4.91 5.02 4.68
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theta[Phillips Andover] 3.42 5.43 3.74 4.84
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theta[Phillips Exeter] 4.75 5.25 4.69 4.84
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theta[Hotchkiss] 3.45 4.78 3.62 4.55
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theta[Lawrenceville] 3.66 5.23 3.90 4.88
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theta[St. Paul's] 6.51 5.24 6.09 4.57
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theta[Mt. Hermon] 4.82 5.70 4.65 4.89
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```
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"""
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function PosteriorStats.summarize(

‎ext/InferenceObjectsPosteriorStatsExt/waic.jl‎

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@@ -20,7 +20,7 @@ julia> idata = load_example_data("centered_eight");
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julia> waic(idata)
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WAICResult with estimates
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elpd elpd_mcse p p_mcse
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-31 1.4 0.9 0.33
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-31 1.4 0.9 0.32
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```
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"""
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function PosteriorStats.waic(

‎src/inference_data.jl‎

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@@ -302,8 +302,7 @@ InferenceData with groups:
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> posterior
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julia> idata_cat1.posterior
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╭─────────────────╮
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│ 100×8×3 Dataset │
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┌ 100×8×3 Dataset ┐
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├─────────────────┴──────────────────────────────────── dims ┐
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↓ draw ,
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→ chain,
@@ -313,7 +312,7 @@ julia> idata_cat1.posterior
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:b eltype: Float64 dims: draw, chain size: 100×8
314313
├────────────────────────────────────────────────── metadata ┤
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Dict{String, Any} with 1 entry:
316-
"created_at" => "2024-03-11T14:10:48.434"
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"created_at" => "2025-02-04T10:49:16.704"
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```
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Alternatively, we can concatenate along a new `run` dimension, which will be created.
@@ -324,8 +323,7 @@ InferenceData with groups:
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> posterior
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julia> idata_cat2.posterior
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╭───────────────────╮
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│ 100×4×3×2 Dataset │
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┌ 100×4×3×2 Dataset ┐
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├───────────────────┴─────────────────────────────────── dims ┐
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↓ draw ,
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→ chain,
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:b eltype: Float64 dims: draw, chain, run size: 100×4×2
337335
├──────────────────────────────────────────────────────────── metadata ┤
338336
Dict{String, Any} with 1 entry:
339-
"created_at" => "2024-03-11T14:10:48.434"
337+
"created_at" => "2025-02-04T10:49:16.704"
340338
```
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We can also concatenate only a subset of groups and merge the rest, which is useful when
@@ -357,8 +355,7 @@ InferenceData with groups:
357355
> observed_data
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julia> idata_cat3.posterior
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╭───────────────────╮
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│ 100×4×3×2 Dataset │
358+
┌ 100×4×3×2 Dataset ┐
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├───────────────────┴─────────────────────────────────── dims ┐
363360
↓ draw ,
364361
→ chain,
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:b eltype: Float64 dims: draw, chain, run size: 100×4×2
370367
├──────────────────────────────────────────────────────────── metadata ┤
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Dict{String, Any} with 1 entry:
372-
"created_at" => "2024-03-11T14:10:48.434"
369+
"created_at" => "2025-02-04T10:49:16.704"
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374371
julia> idata_cat3.observed_data
375-
╭────────────────────╮
376-
│ 10-element Dataset │
372+
┌ 10-element Dataset ┐
377373
├────────────── dims ┤
378374
↓ y_dim_1
379375
├────────────────────┴─────────────── layers ┐
380376
:y eltype: Float64 dims: y_dim_1 size: 10
381377
├────────────────────────────────────────────┴ metadata ┐
382378
Dict{String, Any} with 1 entry:
383-
"created_at" => "2024-03-11T14:10:53.539"
379+
"created_at" => "2025-02-04T10:49:16.71"
384380
```
385381
"""
386382
function Base.cat(data::InferenceData, others::InferenceData...; groups=keys(data), dims)

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