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Pointpriors #663

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Sep 30, 2024
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d05124c
implement pointwise_logpriors
bgctw Sep 16, 2024
4f46102
implement varwise_logpriors
bgctw Sep 17, 2024
c6653b9
remove pointwise_logpriors
bgctw Sep 17, 2024
216d50c
revert dot_assume to not explicitly resolve components of sum
bgctw Sep 17, 2024
fd8d3b2
docstring varwise_logpriores
bgctw Sep 18, 2024
5842656
integrate pointwise_loglikelihoods and varwise_logpriors by pointwise…
bgctw Sep 19, 2024
18beb57
record single prior components
bgctw Sep 21, 2024
d9945d7
forward dot_tilde_assume to tilde_assume for Multivariate
bgctw Sep 22, 2024
656a757
avoid recording prior components on leaf-prior-context
bgctw Sep 24, 2024
7aa9ebe
undeprecate pointwise_loglikelihoods and implement pointwise_prior_lo…
bgctw Sep 24, 2024
2f67c5b
drop vi instead of re-compute vi
bgctw Sep 24, 2024
9dfb9ed
include docstrings of pointwise_logdensities
bgctw Sep 24, 2024
c1939e0
Update src/pointwise_logdensities.jl remove commented code
bgctw Sep 25, 2024
790be1d
Update src/pointwise_logdensities.jl remove commented code
bgctw Sep 25, 2024
426df38
Update test/pointwise_logdensities.jl rename m to model
bgctw Sep 25, 2024
c32bf3b
Update test/pointwise_logdensities.jl remove unused code
bgctw Sep 25, 2024
6213249
Update test/pointwise_logdensities.jl rename m to model
bgctw Sep 25, 2024
3551b38
Update test/pointwise_logdensities.jl rename m to model
bgctw Sep 25, 2024
95c892b
Update src/test_utils.jl remove old code
bgctw Sep 25, 2024
a7a7e70
rename m to model
bgctw Sep 25, 2024
1653aba
JuliaFormatter
bgctw Sep 25, 2024
e4f0a1d
Merge branch 'pointpriors' of github.com:bgctw/DynamicPPL.jl into poi…
bgctw Sep 25, 2024
a99eab4
Update test/runtests.jl remove interactive code
bgctw Sep 26, 2024
64ce63a
remove demo_dot_assume_matrix_dot_observe_matrix2 testcase
bgctw Sep 26, 2024
456115c
ignore local interactive development code
bgctw Sep 26, 2024
222529a
ignore temporary directory holding local interactive development code
bgctw Sep 26, 2024
17b251a
Apply suggestions from code review: clean up comments and Imports
bgctw Sep 26, 2024
7e990f0
Apply suggestions from code review: change test of applying to chains…
bgctw Sep 26, 2024
8706f68
fix test on names in likelihood components
bgctw Sep 26, 2024
073a325
try to fix testset pointwise_logdensities chain
bgctw Sep 26, 2024
23e1711
Update test/pointwise_logdensities.jl
torfjelde Sep 26, 2024
34ae4f8
Update .gitignore
torfjelde Sep 26, 2024
1f251d1
Merge branch 'master' into pointpriors
torfjelde Sep 26, 2024
777624a
Formtating
torfjelde Sep 26, 2024
4864e60
Fixed tests
torfjelde Sep 26, 2024
4d3b0c0
Updated docs for `pointwise_logdensities` + made it a doctest not
torfjelde Sep 27, 2024
e54fa4e
Bump patch version
torfjelde Sep 27, 2024
bcd82a9
Remove blank line from `@model` in doctest to see if that fixes the
torfjelde Sep 27, 2024
cff0941
Added doctest filter to handle the `;;]` at the end of lines for matr…
torfjelde Sep 29, 2024
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@
.DS_Store
Manifest.toml
**.~undo-tree~
/tmp
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6 changes: 5 additions & 1 deletion docs/src/api.md
Original file line number Diff line number Diff line change
Expand Up @@ -124,10 +124,14 @@ Return values of the model function for a collection of samples can be obtained
generated_quantities
```

For a chain of samples, one can compute the pointwise log-likelihoods of each observed random variable with [`pointwise_loglikelihoods`](@ref).
For a chain of samples, one can compute the pointwise log-likelihoods of each observed random variable with [`pointwise_loglikelihoods`](@ref). Similarly, the log-densities of the priors using
[`pointwise_prior_logdensities`](@ref) or both, i.e. all variables, using
[`pointwise_logdensities`](@ref).

```@docs
pointwise_logdensities
pointwise_loglikelihoods
pointwise_prior_logdensities
```

For converting a chain into a format that can more easily be fed into a `Model` again, for example using `condition`, you can use [`value_iterator_from_chain`](@ref).
Expand Down
4 changes: 3 additions & 1 deletion src/DynamicPPL.jl
Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,8 @@ export AbstractVarInfo,
# Convenience functions
logprior,
logjoint,
pointwise_prior_logdensities,
pointwise_logdensities,
pointwise_loglikelihoods,
condition,
decondition,
Expand Down Expand Up @@ -181,7 +183,7 @@ include("varinfo.jl")
include("simple_varinfo.jl")
include("context_implementations.jl")
include("compiler.jl")
include("loglikelihoods.jl")
include("pointwise_logdensities.jl")
include("submodel_macro.jl")
include("test_utils.jl")
include("transforming.jl")
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257 changes: 0 additions & 257 deletions src/loglikelihoods.jl

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