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Reorganise user guide section (#578)
* Don't let julia-actions delete cache * Reorganise user guide * Allow different workflows/PRs to share cached Julia environment * Merge _quarto.yml and _metadata.yml * Reorganise tutorials section * Fix colon in title * Fix aliases * Fix more aliases * Tidy up navigation bar
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‎.github/workflows/preview.yml‎

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group: docs
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permissions:
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actions: write
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contents: write
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pull-requests: write
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- name: Load Julia packages from cache
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uses: julia-actions/cache@v2
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with:
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cache-name: julia-cache;${{ hashFiles('**/Manifest.toml') }}
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delete-old-caches: false
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# Note: needs resolve() to fix #518
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- name: Instantiate Julia environment

‎_quarto.yml‎

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background: "#073c44"
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foreground: "#ffffff"
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left:
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- href: tutorials/docs-00-getting-started/
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- href: getting-started/
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text: Get Started
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- href: tutorials/00-introduction/
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- href: tutorials/coin-flipping/
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text: Tutorials
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- href: https://turinglang.org/library/
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text: Libraries
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- text: documentation
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collapse-level: 1
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contents:
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- section: "Users"
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# href: tutorials/index.qmd, This page will be added later so keep this line commented
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contents:
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- tutorials/docs-00-getting-started/index.qmd
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- tutorials/docs-12-using-turing-guide/index.qmd
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- getting-started/index.qmd
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- core-functionality/index.qmd
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- section: "Usage Tips"
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collapse-level: 1
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contents:
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- tutorials/docs-10-using-turing-autodiff/index.qmd
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- tutorials/usage-custom-distribution/index.qmd
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- tutorials/usage-probability-interface/index.qmd
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- tutorials/usage-modifying-logprob/index.qmd
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- tutorials/usage-generated-quantities/index.qmd
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- tutorials/docs-17-mode-estimation/index.qmd
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- tutorials/docs-13-using-turing-performance-tips/index.qmd
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- tutorials/docs-15-using-turing-sampler-viz/index.qmd
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- tutorials/docs-11-using-turing-dynamichmc/index.qmd
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- tutorials/docs-16-using-turing-external-samplers/index.qmd
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- section: "Tutorials"
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contents:
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- tutorials/00-introduction/index.qmd
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- text: Gaussian Mixture Models
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href: tutorials/01-gaussian-mixture-model/index.qmd
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- tutorials/02-logistic-regression/index.qmd
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- tutorials/03-bayesian-neural-network/index.qmd
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- text: Hidden Markov Models
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href: tutorials/04-hidden-markov-model/index.qmd
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- tutorials/05-linear-regression/index.qmd
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- text: Infinite Mixture Model
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href: tutorials/06-infinite-mixture-model/index.qmd
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- tutorials/07-poisson-regression/index.qmd
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- text: Multinomial Logistic Regression
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href: tutorials/08-multinomial-logistic-regression/index.qmd
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- text: Variational Inference
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href: tutorials/09-variational-inference/index.qmd
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- text: "Bayesian Differential Equations"
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href: tutorials/10-bayesian-differential-equations/index.qmd
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- text: "Probabilistic PCA"
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href: tutorials/11-probabilistic-pca/index.qmd
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- tutorials/13-seasonal-time-series/index.qmd
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- text: "Introduction to Gaussian Processes"
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href: tutorials/15-gaussian-processes/index.qmd
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- text: "Gaussian Process Latent Variable Models"
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href: tutorials/12-gplvm/index.qmd
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- section: "Usage Tips"
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collapse-level: 1
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contents:
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- usage/automatic-differentiation/index.qmd
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- usage/custom-distribution/index.qmd
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- usage/probability-interface/index.qmd
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- usage/modifying-logprob/index.qmd
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- usage/generated-quantities/index.qmd
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- usage/mode-estimation/index.qmd
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- usage/performance-tips/index.qmd
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- usage/sampler-visualisation/index.qmd
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- usage/dynamichmc/index.qmd
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- usage/external-samplers/index.qmd
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- section: "Tutorials"
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contents:
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- tutorials/coin-flipping/index.qmd
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- tutorials/gaussian-mixture-models/index.qmd
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- tutorials/bayesian-logistic-regression/index.qmd
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- tutorials/bayesian-neural-networks/index.qmd
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- tutorials/hidden-markov-models/index.qmd
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- tutorials/bayesian-linear-regression/index.qmd
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- tutorials/infinite-mixture-models/index.qmd
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- tutorials/bayesian-poisson-regression/index.qmd
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- tutorials/multinomial-logistic-regression/index.qmd
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- tutorials/variational-inference/index.qmd
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- tutorials/bayesian-differential-equations/index.qmd
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- tutorials/probabilistic-pca/index.qmd
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- tutorials/bayesian-time-series-analysis/index.qmd
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- tutorials/gaussian-processes-introduction/index.qmd
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- tutorials/gaussian-process-latent-variable-models/index.qmd
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- section: "Developers"
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contents:
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light: cosmo
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dark: [cosmo, theming/theme-dark.scss]
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css: theming/styles.css
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toc: true
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smooth-scroll: true
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code-overflow: wrap
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output-block-background: true
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toc: true
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toc-title: "Table of Contents"
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code-fold: false
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code-overflow: scroll
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execute:
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echo: true
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output: true
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freeze: auto
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include-in-header:
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- text: |
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<style>
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a {
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text-decoration: none;
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}
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a:hover {
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text-decoration: underline;
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}
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</style>
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# These variables can be used in any qmd files, e.g. for links:
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# the [Getting Started page]({{< meta get-started >}})

‎tutorials/docs-12-using-turing-guide/index.qmd‎ renamed to ‎core-functionality/index.qmd‎

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---
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title: "Core Functionality"
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engine: julia
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aliases:
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- ../tutorials/docs-12-using-turing-guide/index.html
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---
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```{julia}

‎tutorials/docs-00-getting-started/index.qmd‎ renamed to ‎getting-started/index.qmd‎

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title: Getting Started
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engine: julia
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aliases:
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- ../../
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- ../tutorials/docs-00-getting-started/index.html
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- ../index.html
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---
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```{julia}

‎tutorials/_metadata.yml‎

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This file was deleted.

‎tutorials/10-bayesian-differential-equations/index.qmd‎ renamed to ‎tutorials/bayesian-differential-equations/index.qmd‎

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---
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title: Bayesian Estimation of Differential Equations
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title: Bayesian Differential Equations
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engine: julia
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aliases:
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- ../10-bayesian-differential-equations/index.html
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---
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```{julia}

‎tutorials/05-linear-regression/index.qmd‎ renamed to ‎tutorials/bayesian-linear-regression/index.qmd‎

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---
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title: Linear Regression
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title: Bayesian Linear Regression
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engine: julia
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aliases:
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- ../05-linear-regression/index.html
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---
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```{julia}

‎tutorials/02-logistic-regression/index.qmd‎ renamed to ‎tutorials/bayesian-logistic-regression/index.qmd‎

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title: Bayesian Logistic Regression
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aliases:
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- ../02-logistic-regression/index.html
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---
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```{julia}
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The above shows that with a threshold of 0.07, we correctly predict a respectable portion of the defaults, and correctly identify most non-defaults. This is fairly sensitive to a choice of threshold, and you may wish to experiment with it.
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This tutorial has demonstrated how to use Turing to perform Bayesian logistic regression.
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This tutorial has demonstrated how to use Turing to perform Bayesian logistic regression.

‎tutorials/03-bayesian-neural-network/index.qmd‎ renamed to ‎tutorials/bayesian-neural-networks/index.qmd‎

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title: Bayesian Neural Networks
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engine: julia
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aliases:
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- ../03-bayesian-neural-network/index.html
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---
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```{julia}

‎tutorials/07-poisson-regression/index.qmd‎ renamed to ‎tutorials/bayesian-poisson-regression/index.qmd‎

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title: Bayesian Poisson Regression
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engine: julia
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aliases:
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- ../07-poisson-regression/index.html
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---
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```{julia}

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