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shravanngoswamiishravanngoswamii
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converted diagrams to mermaid
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‎docs/make.jl‎

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@@ -8,6 +8,7 @@ using DynamicPPL: AbstractPPL
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# in the doctest as run in `test/runtests.jl`, and so we need to stay
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# consistent with that.
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using Distributions
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using DocumenterMermaid
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# Doctest setup
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DocMeta.setdocmeta!(DynamicPPL, :DocTestSetup, :(using DynamicPPL); recursive=true)

‎docs/src/internals/transformations.md‎

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@@ -41,10 +41,35 @@ But to ensure that we stay consistent with what the user expects, DynamicPPL.jl
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In the end, we'll end up with something that looks like this:
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```@raw html
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<div style="flex-direction: row; display: flex; justify-content: space-around; margin: 1em;">
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<img style="border-radius: 5px;" src="../../assets/images/transformations.dot.png" />
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</div>
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```mermaid
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%%{ init: { 'themeVariables': { 'lineColor': '#000000' } } }%%
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%%{ init: { 'flowchart': { 'curve': 'linear' } } }%%
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graph TD
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subgraph assume ["assume"]
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style assume fill:#ffffff,font-family:Courier
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A["x ~ Normal()"]:::boxStyle
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B["vn = <span style='color:#3B6EA8 !important;'>@varname</span>(x)<br>dist = Normal()<br>x, vi = ..."]:::boxStyle
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C["assume(vn, dist, vi)"]:::boxStyle
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D(["<span style='color:#3B6EA8 !important;'>if</span> istrans(vi, vn)"]):::boxStyle
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E["f = from_internal_transform(vi, vn, dist)"]:::boxStyle
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F["f = from_linked_internal_transform(vi, vn, dist)"]:::boxStyle
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G["x, logjac = with_logabsdet_jacobian(f, getindex_internal(vi, vn, dist))"]:::boxStyle
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H["<span style='color:#3B6EA8 !important;'>return</span> x, logpdf(dist, x) - logjac, vi"]:::boxStyle
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A -.->|<span style='color:#3B6EA8 ; background-color:#ffffff;'>@model</span>| B
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B -.->|<span style='color:#000000 ; background-color:#ffffff;'>tilde-pipeline</span>| C
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C --> D
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D -->|<span style='color:#97365B ; background-color:#ffffff;'>false</span>| E
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D -->|<span style='color:#97365B ; background-color:#ffffff;'>true</span>| F
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E --> G
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F --> G
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G --> H
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end
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classDef boxStyle fill:#ffffff,stroke:#000000,font-family:Courier,color:#000000
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linkStyle default stroke:#000000,stroke-width:1px,color:#000000
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```
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Below we'll see how this is done.
@@ -197,10 +222,27 @@ One might wonder why we need both `to_internal_transform` and `to_linked_interna
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That is, why can't we just do
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```@raw html
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<div style="flex-direction: row; display: flex; justify-content: space-around; margin: 1em;">
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<img style="border-radius: 5px;" src="../../assets/images/transformations-assume-without-istrans.dot.png" />
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</div>
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```mermaid
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%%{ init: { 'flowchart': { 'curve': 'linear' } } }%%
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%%{ init: { 'themeVariables': { 'lineColor': '#000000' } } }%%
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graph TD
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subgraph assume ["assume"]
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style assume fill:#ffffff,font-family:Courier
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A["assume(varinfo, <span style='color:#3B6EA8 !important;'>@varname</span>(x), Normal())"]:::boxStyle
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B["f = from_internal_transform(varinfo, varname, dist)"]:::boxStyle
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C["x, logjac = with_logabsdet_jacobian(f, assume_internal(varinfo, varname, dist))"]:::boxStyle
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D["<span style='color:#3B6EA8 !important;'>return</span> x, logpdf(dist, x) - logjac, varinfo"]:::dashedBox
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A --> B
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B --> C
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C --> D
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end
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classDef dashedBox fill:#ffffff,stroke:#000000,stroke-dasharray: 5 5,font-family:Courier,color:#000000
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classDef boxStyle fill:#ffffff,stroke:#000000,font-family:Courier,color:#000000
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linkStyle default stroke:#000000,stroke-width:1px,color:#000000
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```
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Unfortunately, this is not possible in general. Consider for example the following model:
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And so the earlier diagram becomes:
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```@raw html
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<div style="flex-direction: row; display: flex; justify-content: space-around; margin: 1em;">
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<img style="border-radius: 5px;" src="../../assets/images/transformations-assume.dot.png" />
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</div>
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```mermaid
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%%{ init: { 'flowchart': { 'curve': 'linear' } } }%%
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%%{ init: { 'themeVariables': { 'lineColor': '#000000' } } }%%
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graph TD
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subgraph assume ["assume"]
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style assume fill:#ffffff,font-family:Courier
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A["assume(varinfo, <span style='color:#3B6EA8 !important;'>@varname</span>(x), Normal())"]:::boxStyle
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B(["<span style='color:#3B6EA8 !important;'>if</span> istrans(varinfo, varname)"]):::boxStyle
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C["f = from_internal_transform(varinfo, varname, dist)"]:::boxStyle
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D["f = from_linked_internal_transform(varinfo, varname, dist)"]:::boxStyle
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E["x, logjac = with_logabsdet_jacobian(f, assume_internal(varinfo, varname, dist))"]:::boxStyle
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F["<span style='color:#3B6EA8 !important;'>return</span> x, logpdf(dist, x) - logjac, varinfo"]:::dashedBox
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A --> B
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B -->|<span style='color:#97365B ; background-color:#ffffff;'>false</span>| C
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B -->|<span style='color:#97365B ; background-color:#ffffff;'>true</span>| D
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C --> E
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D --> E
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E --> F
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end
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classDef dashedBox fill:#ffffff,stroke:#000000,stroke-dasharray: 5 5,font-family:Courier,color:#000000
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classDef boxStyle fill:#ffffff,stroke:#000000,font-family:Courier,color:#000000
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linkStyle default stroke:#000000,stroke-width:1px,color:#000000
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```
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!!! note
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For `getindex` we have the following diagram:
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```@raw html
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<div style="flex-direction: row; display: flex; justify-content: space-around; margin: 1em;">
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<img style="border-radius: 5px;" src="../../assets/images/transformations-getindex-with-dist.dot.png" />
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</div>
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```mermaid
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%%{ init: { 'flowchart': { 'curve': 'linear' } } }%%
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%%{ init: { 'themeVariables': { 'lineColor': '#000000' } } }%%
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graph TD
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subgraph getindex ["getindex"]
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style getindex fill:#ffffff,font-family:Courier
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A["x = getindex(varinfo, <span style='color:#3B6EA8 !important;'>@varname</span>(x), Normal())"]:::boxStyle
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B(["<span style='color:#3B6EA8 !important;'>if</span> istrans(varinfo, varname)"]):::boxStyle
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C["f = from_internal_transform(varinfo, varname, dist)"]:::boxStyle
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D["f = from_linked_internal_transform(varinfo, varname, dist)"]:::boxStyle
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E["<span style='color:#3B6EA8 !important;'>return</span> f(getindex_internal(varinfo, varname))"]:::dashedBox
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A --> B
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B -->|<span style='color:#97365B ; background-color:#ffffff;'>false</span>| C
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B -->|<span style='color:#97365B ; background-color:#ffffff;'>true</span>| D
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C --> E
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D --> E
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end
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classDef dashedBox fill:#ffffff,stroke:#000000,stroke-dasharray: 5 5,font-family:Courier,color:#000000
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classDef boxStyle fill:#ffffff,stroke:#000000,font-family:Courier,color:#000000
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linkStyle default stroke:#000000,stroke-width:1px,color:#000000
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```
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While if `dist` is not provided, we have:
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```@raw html
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<div style="flex-direction: row; display: flex; justify-content: space-around; margin: 1em;">
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<img style="border-radius: 5px;" src="../../assets/images/transformations-getindex-without-dist.dot.png" />
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</div>
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```mermaid
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%%{ init: { 'flowchart': { 'curve': 'linear' } } }%%
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%%{ init: { 'themeVariables': { 'lineColor': '#000000' } } }%%
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graph TD
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subgraph getindex ["getindex"]
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style getindex fill:#ffffff,font-family:Courier
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A["x = getindex(varinfo, <span style='color:#3B6EA8 !important;'>@varname</span>(x))"]:::boxStyle
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B(["<span style='color:#3B6EA8 !important;'>if</span> istrans(varinfo, varname)"]):::boxStyle
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C["f = from_internal_transform(varinfo, varname)"]:::boxStyle
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D["f = from_linked_internal_transform(varinfo, varname)"]:::boxStyle
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E["<span style='color:#3B6EA8 !important;'>return</span> f(getindex_internal(varinfo, varname))"]:::dashedBox
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A --> B
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B -->|<span style='color:#97365B ; background-color:#ffffff;'>false</span>| C
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B -->|<span style='color:#97365B ; background-color:#ffffff;'>true</span>| D
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C --> E
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D --> E
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end
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classDef dashedBox fill:#ffffff,stroke:#000000,stroke-dasharray: 5 5,font-family:Courier,color:#000000
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classDef boxStyle fill:#ffffff,stroke:#000000,font-family:Courier,color:#000000
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linkStyle default stroke:#000000,stroke-width:1px,color:#000000
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```
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Notice that `dist` is not present here, but otherwise the diagrams are the same.

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