Update Choco.jl #83
DominiqueMakowskiAnnotations
10 errors
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/Choco.md:138-156
```@example choco1
@model function model_choco(y)
p1 ~ Normal(0, 2)
μ0 ~ Normal(0, 1)
μ1 ~ Normal(0, 0.8)
ϕ0 ~ Normal(0, 1)
ϕ1 ~ Normal(0, 1.2)
for i in 1:length(y)
y[i] ~ Choco(logistic(p1), logistic(μ0), exp(ϕ0), logistic(μ1), exp(ϕ1))
end
end
fit_choco = model_choco(y)
posteriors = sample(fit_choco, NUTS(), 500)
# 95% CI
hpd(posteriors)
```
exception =
UndefVarError: `logpdf` not defined
Stacktrace:
[1] logpdf(d::OrderedBeta{Float64}, x::Float64)
@ SubjectiveScalesModels ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/OrderedBeta.jl:170
[2] logpdf(d::Distributions.LocationScale{Float64, Distributions.Continuous, OrderedBeta{Float64}}, x::Float64)
@ Distributions ~/.julia/packages/Distributions/ji8PW/src/univariate/locationscale.jl:133
[3] (::Distributions.var"#610#612"{Distributions.MixtureModel{Distributions.Univariate, Distributions.Continuous, Distributions.Distribution{Distributions.Univariate, Distributions.Continuous}, Distributions.Categorical{Float64, Vector{Float64}}}, Float64})(::Tuple{Int64, Float64})
@ Distributions ./essentials.jl:0
[4] MappingRF
@ ./reduce.jl:100 [inlined]
[5] FilteringRF
@ ./reduce.jl:112 [inlined]
[6] _foldl_impl(op::Base.FilteringRF{Distributions.var"#611#613", Base.MappingRF{Distributions.var"#610#612"{Distributions.MixtureModel{Distributions.Univariate, Distributions.Continuous, Distributions.Distribution{Distributions.Univariate, Distributions.Continuous}, Distributions.Categorical{Float64, Vector{Float64}}}, Float64}, Base.BottomRF{typeof(LogExpFunctions._logsumexp_onepass_op)}}}, init::Base._InitialValue, itr::Base.Iterators.Enumerate{Vector{Float64}})
@ Base ./reduce.jl:58
[7] foldl_impl
@ ./reduce.jl:48 [inlined]
[8] mapfoldl_impl
@ ./reduce.jl:44 [inlined]
[9] mapfoldl
@ ./reduce.jl:175 [inlined]
[10] mapreduce
@ ./reduce.jl:307 [inlined]
[11] reduce
@ ./reduce.jl:490 [inlined]
[12] _logsumexp_onepass_reduce
@ ~/.julia/packages/LogExpFunctions/X95j7/src/logsumexp.jl:81 [inlined]
[13] _logsumexp_onepass(X::Base.Generator{Base.Iterators.Filter{Distributions.var"#611#613", Base.Iterators.Enumerate{Vector{Float64}}}, Distributions.var"#610#612"{Distributions.MixtureModel{Distributions.Univariate, Distributions.Continuous, Distributions.Distribution{Distributions.Univariate, Distributions.Continuous}, Distributions.Categorical{Float64, Vector{Float64}}}, Float64}})
@ LogExpFunctions ~/.julia/packages/LogExpFunctions/X95j7/src/logsumexp.jl:63
[14] logsumexp
@ ~/.julia/packages/LogExpFunctions/X95j7/src/logsumexp.jl:15 [inlined]
[15] _mixlogpdf1
@ ~/.julia/packages/Distributions/ji8PW/src/mixtures/mixturemodel.jl:312 [inlined]
[16] logpdf
@ ~/.julia/packages/Distributions/ji8PW/src/mixtures/mixturemodel.jl:363 [inlined]
[17] logpdf
@ ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/Choco.jl:116 [inlined]
[18] loglikelihood
@ ~/.julia/packages/Distributions/ji8PW/src/univariates.jl:330 [inlined]
[19] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:266 [inlined]
[20] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:263 [inlined]
[21] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:158 [inlined]
[22] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:156 [inlined]
[23] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:151 [inlined]
[24] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/debug_utils.jl:370 [inlined]
[25] tilde_observe!!(context::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__choco1.model_choco), (:y,), (), (), Tuple{Vector{Float6
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/Choco.md:160-170
```@example choco1
# Make predictions
pred = predict(model_choco([missing for _ in 1:length(y)]), posteriors)
pred = Array(pred)
fig = hist(y, bins=beta_bins(30), color=:darkorange, normalization=:pdf)
for i in 1:size(pred, 1) # Iterate over each draw
hist!(pred[i, :], bins=beta_bins(30), color=(:dodgerblue, 0.005), normalization=:pdf)
end
fig
```
exception =
UndefVarError: `posteriors` not defined
Stacktrace:
[1] top-level scope
@ Choco.md:162
[2] eval
@ ./boot.jl:385 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/Choco.md:175-193
```@example choco1
posterior_mean = DataFrame(mean(posteriors))
# Format
results = DataFrame(
Parameter = posterior_mean.parameters,
Posterior_Mean = round.(posterior_mean.mean; digits=2),
Estimate = round.([
logistic(posterior_mean.mean[1]),
logistic(posterior_mean.mean[2]),
logistic(posterior_mean.mean[3]),
exp(posterior_mean.mean[4]),
exp(posterior_mean.mean[5])
]; digits=2),
Truth = [0.3, 0.7, 1, 0.3, 3]
)
results
```
exception =
UndefVarError: `posteriors` not defined
Stacktrace:
[1] top-level scope
@ Choco.md:176
[2] eval
@ ./boot.jl:385 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/Choco.md:372-391
```@example choco2
@model function model_choco(y)
p1 ~ Normal(0, 2)
μ0 ~ Normal(0, 1)
μ1 ~ Normal(0, 1)
ϕ0 ~ Normal(0, 1)
ϕ1 ~ Normal(0, 1)
# p_mid ~ Normal(-3, 1)
# ϕ_mid ~ truncated(Normal(5, 0.5); lower=0)
k0 ~ -Gamma(3, 3)
k1 ~ Gamma(3, 3)
for i in 1:length(y)
y[i] ~ Choco(logistic(p1), logistic(μ0), exp(ϕ0), logistic(μ1), exp(ϕ1), 0.0, 200, logistic(k0), logistic(k1))
end
end
fit_choco = model_choco(y)
posteriors = sample(fit_choco, NUTS(), 500)
```
exception =
UndefVarError: `logpdf` not defined
Stacktrace:
[1] logpdf(d::OrderedBeta{Float64}, x::Float64)
@ SubjectiveScalesModels ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/OrderedBeta.jl:170
[2] logpdf(d::Distributions.LocationScale{Float64, Distributions.Continuous, OrderedBeta{Float64}}, x::Float64)
@ Distributions ~/.julia/packages/Distributions/ji8PW/src/univariate/locationscale.jl:133
[3] (::Distributions.var"#610#612"{Distributions.MixtureModel{Distributions.Univariate, Distributions.Continuous, Distributions.Distribution{Distributions.Univariate, Distributions.Continuous}, Distributions.Categorical{Float64, Vector{Float64}}}, Float64})(::Tuple{Int64, Float64})
@ Distributions ./essentials.jl:0
[4] MappingRF
@ ./reduce.jl:100 [inlined]
[5] FilteringRF
@ ./reduce.jl:112 [inlined]
[6] _foldl_impl(op::Base.FilteringRF{Distributions.var"#611#613", Base.MappingRF{Distributions.var"#610#612"{Distributions.MixtureModel{Distributions.Univariate, Distributions.Continuous, Distributions.Distribution{Distributions.Univariate, Distributions.Continuous}, Distributions.Categorical{Float64, Vector{Float64}}}, Float64}, Base.BottomRF{typeof(LogExpFunctions._logsumexp_onepass_op)}}}, init::Base._InitialValue, itr::Base.Iterators.Enumerate{Vector{Float64}})
@ Base ./reduce.jl:58
[7] foldl_impl
@ ./reduce.jl:48 [inlined]
[8] mapfoldl_impl
@ ./reduce.jl:44 [inlined]
[9] mapfoldl
@ ./reduce.jl:175 [inlined]
[10] mapreduce
@ ./reduce.jl:307 [inlined]
[11] reduce
@ ./reduce.jl:490 [inlined]
[12] _logsumexp_onepass_reduce
@ ~/.julia/packages/LogExpFunctions/X95j7/src/logsumexp.jl:81 [inlined]
[13] _logsumexp_onepass(X::Base.Generator{Base.Iterators.Filter{Distributions.var"#611#613", Base.Iterators.Enumerate{Vector{Float64}}}, Distributions.var"#610#612"{Distributions.MixtureModel{Distributions.Univariate, Distributions.Continuous, Distributions.Distribution{Distributions.Univariate, Distributions.Continuous}, Distributions.Categorical{Float64, Vector{Float64}}}, Float64}})
@ LogExpFunctions ~/.julia/packages/LogExpFunctions/X95j7/src/logsumexp.jl:63
[14] logsumexp
@ ~/.julia/packages/LogExpFunctions/X95j7/src/logsumexp.jl:15 [inlined]
[15] _mixlogpdf1
@ ~/.julia/packages/Distributions/ji8PW/src/mixtures/mixturemodel.jl:312 [inlined]
[16] logpdf
@ ~/.julia/packages/Distributions/ji8PW/src/mixtures/mixturemodel.jl:363 [inlined]
[17] logpdf
@ ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/Choco.jl:116 [inlined]
[18] loglikelihood
@ ~/.julia/packages/Distributions/ji8PW/src/univariates.jl:330 [inlined]
[19] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:266 [inlined]
[20] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:263 [inlined]
[21] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:158 [inlined]
[22] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:156 [inlined]
[23] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:151 [inlined]
[24] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/debug_utils.jl:370 [inlined]
[25] tilde_observe!!(context::DynamicPPL.
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/Choco.md:396-406
```@example choco2
# Make predictions
pred = predict(model_choco([missing for _ in 1:length(y)]), posteriors)
pred = Array(pred)
fig = hist(y, bins=beta_bins(31), color=:darkblue, normalization=:pdf)
for i in 1:size(pred, 1) # Iterate over each draw
hist!(pred[i, :], bins=beta_bins(31), color=(:darkorange, 0.01), normalization=:pdf)
end
fig
```
exception =
UndefVarError: `posteriors` not defined
Stacktrace:
[1] top-level scope
@ Choco.md:398
[2] eval
@ ./boot.jl:385 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/OrderedBeta.md:137-152
```@example ordbeta1
@model function model_ordbeta(y)
# Priors
μ ~ Normal(0, 1)
ϕ ~ Normal(0, 1)
k0 ~ -Gamma(3, 3)
k1 ~ Gamma(3, 3)
# Inference
for i in 1:length(y)
y[i] ~ OrderedBeta(logistic(μ), exp(ϕ), logistic(k0), logistic(k1))
end
end
posteriors = sample(model_ordbeta(data), NUTS(), 1000);
```
exception =
UndefVarError: `logpdf` not defined
Stacktrace:
[1] logpdf(d::OrderedBeta{Float64}, x::Float64)
@ SubjectiveScalesModels ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/OrderedBeta.jl:170
[2] loglikelihood
@ ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/OrderedBeta.jl:179 [inlined]
[3] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:266 [inlined]
[4] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:263 [inlined]
[5] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:158 [inlined]
[6] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:156 [inlined]
[7] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:151 [inlined]
[8] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/debug_utils.jl:370 [inlined]
[9] tilde_observe!!(context::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta1.model_ordbeta), (:y,), (), (), Tuple{Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, DynamicPPL.SamplingContext{DynamicPPL.SampleFromPrior, DynamicPPL.DefaultContext, Random.TaskLocalRNG}}, right::OrderedBeta{Float64}, left::Float64, vi::DynamicPPL.UntypedVarInfo{DynamicPPL.Metadata{Dict{AbstractPPL.VarName, Int64}, Vector{Distributions.Distribution}, Vector{AbstractPPL.VarName}, Vector{Real}, Vector{Set{DynamicPPL.Selector}}}, Float64})
@ DynamicPPL ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:207
[10] tilde_observe!!(context::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta1.model_ordbeta), (:y,), (), (), Tuple{Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, DynamicPPL.SamplingContext{DynamicPPL.SampleFromPrior, DynamicPPL.DefaultContext, Random.TaskLocalRNG}}, right::OrderedBeta{Float64}, left::Float64, vname::AbstractPPL.VarName{:y, Accessors.IndexLens{Tuple{Int64}}}, vi::DynamicPPL.UntypedVarInfo{DynamicPPL.Metadata{Dict{AbstractPPL.VarName, Int64}, Vector{Distributions.Distribution}, Vector{AbstractPPL.VarName}, Vector{Real}, Vector{Set{DynamicPPL.Selector}}}, Float64})
@ DynamicPPL ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:194
[11] macro expansion
@ ~/.julia/packages/DynamicPPL/93t4P/src/compiler.jl:579 [inlined]
[12] model_ordbeta(__model__::DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta1.model_ordbeta), (:y,), (), (), Tuple{Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, __varinfo__::DynamicPPL.UntypedVarInfo{DynamicPPL.Metadata{Dict{AbstractPPL.VarName, Int64}, Vector{Distributions.Distribution}, Vector{AbstractPPL.VarName}, Vector{Real}, Vector{Set{DynamicPPL.Selector}}}, Float64}, __context__::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta1.model_ordbeta), (:y,), (), (), Tuple{Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, DynamicPPL.SamplingContext{DynamicPPL.SampleFromPrior, DynamicPPL.DefaultContext, Random.TaskLocalRNG}}, y::Vector{Float64})
@ Main.__atexample__named__ordbeta1 ./OrderedBeta.md:146
[13] _evaluate!!
@ ~/.julia/packages/DynamicPPL/93t4P/src/model.jl:973 [inlined]
[14] evaluate_threadunsafe!!
@ ~/.julia/packages/DynamicPPL/93t4P/src/model.jl:946 [inlined]
[15] check_model_and_trace(rng::Random.TaskLocalRNG, model::DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta1.model_ordbeta), (:y,), (), (), Tuple{Vector{Floa
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/OrderedBeta.md:154-163
```@example ordbeta1
means = DataFrame(mean(posteriors))
table = DataFrame(
Parameter = means.parameters,
PosteriorMean = means.mean,
Estimate = [logistic(means.mean[1]), exp(means.mean[2]), logistic(means.mean[3]), logistic(means.mean[4])],
TrueValue = [0.6, 2.5, 0.05, 0.9]
)
```
exception =
UndefVarError: `posteriors` not defined
Stacktrace:
[1] top-level scope
@ OrderedBeta.md:155
[2] eval
@ ./boot.jl:385 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
|
|
Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/OrderedBeta.md:235-256
```@example ordbeta2
@model function model_ordbeta(y, x)
μ_intercept ~ Normal(0, 3)
μ_x ~ Normal(0, 3)
ϕ ~ Normal(0, 3)
cutzero ~ Normal(-3, 3)
cutone ~ Normal(3, 3)
for i in 1:length(y)
μ = μ_intercept + μ_x * x[i]
y[i] ~ OrderedBeta(logistic(μ), exp(ϕ), logistic(cutzero), logistic(cutone))
end
end
fit = model_ordbeta(data.y, data.x)
posteriors = sample(fit, NUTS(), 1000)
# Mean posterior
mean(posteriors)
```
exception =
UndefVarError: `logpdf` not defined
Stacktrace:
[1] logpdf(d::OrderedBeta{Float64}, x::Float64)
@ SubjectiveScalesModels ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/OrderedBeta.jl:170
[2] loglikelihood
@ ~/work/SubjectiveScalesModels.jl/SubjectiveScalesModels.jl/src/OrderedBeta.jl:179 [inlined]
[3] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:266 [inlined]
[4] observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:263 [inlined]
[5] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:158 [inlined]
[6] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:156 [inlined]
[7] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:151 [inlined]
[8] tilde_observe
@ ~/.julia/packages/DynamicPPL/93t4P/src/debug_utils.jl:370 [inlined]
[9] tilde_observe!!(context::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta2.model_ordbeta), (:y, :x), (), (), Tuple{Vector{Float64}, Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, DynamicPPL.SamplingContext{DynamicPPL.SampleFromPrior, DynamicPPL.DefaultContext, Random.TaskLocalRNG}}, right::OrderedBeta{Float64}, left::Float64, vi::DynamicPPL.UntypedVarInfo{DynamicPPL.Metadata{Dict{AbstractPPL.VarName, Int64}, Vector{Distributions.Distribution}, Vector{AbstractPPL.VarName}, Vector{Real}, Vector{Set{DynamicPPL.Selector}}}, Float64})
@ DynamicPPL ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:207
[10] tilde_observe!!(context::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta2.model_ordbeta), (:y, :x), (), (), Tuple{Vector{Float64}, Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, DynamicPPL.SamplingContext{DynamicPPL.SampleFromPrior, DynamicPPL.DefaultContext, Random.TaskLocalRNG}}, right::OrderedBeta{Float64}, left::Float64, vname::AbstractPPL.VarName{:y, Accessors.IndexLens{Tuple{Int64}}}, vi::DynamicPPL.UntypedVarInfo{DynamicPPL.Metadata{Dict{AbstractPPL.VarName, Int64}, Vector{Distributions.Distribution}, Vector{AbstractPPL.VarName}, Vector{Real}, Vector{Set{DynamicPPL.Selector}}}, Float64})
@ DynamicPPL ~/.julia/packages/DynamicPPL/93t4P/src/context_implementations.jl:194
[11] macro expansion
@ ./OrderedBeta.md:246 [inlined]
[12] macro expansion
@ ~/.julia/packages/DynamicPPL/93t4P/src/compiler.jl:579 [inlined]
[13] model_ordbeta(__model__::DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta2.model_ordbeta), (:y, :x), (), (), Tuple{Vector{Float64}, Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, __varinfo__::DynamicPPL.UntypedVarInfo{DynamicPPL.Metadata{Dict{AbstractPPL.VarName, Int64}, Vector{Distributions.Distribution}, Vector{AbstractPPL.VarName}, Vector{Real}, Vector{Set{DynamicPPL.Selector}}}, Float64}, __context__::DynamicPPL.DebugUtils.DebugContext{DynamicPPL.Model{typeof(Main.__atexample__named__ordbeta2.model_ordbeta), (:y, :x), (), (), Tuple{Vector{Float64}, Vector{Float64}}, Tuple{}, DynamicPPL.DefaultContext}, DynamicPPL.SamplingContext{DynamicPPL.SampleFromPrior, DynamicPPL.DefaultContext, Random.TaskLocalRNG}}, y::Vector{Float64}, x::Vector{Float64})
@ Main.__atexample__named__ordbeta2 ./OrderedBeta.md:244
[14] _evaluate!!
@ ~/.julia/packages/DynamicPPL/93t4P/src/model.jl:973
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Documentation:
../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/OrderedBeta.md:266-277
```@example ordbeta2
# Make predictions
pred = predict(model_ordbeta([missing for _ in 1:length(data.y)], data.x), posteriors)
pred = Array(pred)
fig = hist(data.y, color=:forestgreen, normalization=:pdf, bins=beta_bins(20))
for i in 1:size(pred, 1) # Iterate over each draw
# density!(pred[i, :], color=(:black, 0), strokecolor=(:crimson, 0.05), strokewidth=1)
hist!(pred[i, :], color=(:crimson, 0.01), normalization=:pdf, bins=beta_bins(20))
end
fig
```
exception =
UndefVarError: `posteriors` not defined
Stacktrace:
[1] top-level scope
@ OrderedBeta.md:268
[2] eval
@ ./boot.jl:385 [inlined]
[3] #58
@ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
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Documentation
Process completed with exit code 1.
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