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-    "markdown": "# Contributing {.unlisted .unnumbered}\n\n\n\n\n\nIf you plan to do anything beyond fixing a typo, the best thing you can do is to [open an issue](https://github.com/aml4td/website/issues) and discuss changes before you spend a lot of time doing them. \n\nIf you dont have a lot of experience with git or GitHub, take a look at the wonderful [_Happy Git and GitHub for the useR_](https://happygitwithr.com/). \n\nIf you want to contribute, some general advice is: \n\n - Only check in the source files (qmd, yml, bib, pre-made image files, etc). Don't commit the rendered files. \n - Keep the changes small in scope. If the overall change is larger, make a sequence of small pull requests. \n - The edits cannot include exact code that is under another license (i.e., don't just copy/paste from R sources, etc.)\n - Respect the existing code formatting/linting (as heterogeneous as it is). \n - Stick to using R for computations.  \n - Don't update software versions unless you have to. If you need to update or add something, use [renv](https://rstudio.github.io/renv/) (described below) to codify the software requirements.  \n - The [usethis](https://usethis.r-lib.org/) package has excellent tools for creating, updating, and managing pull requests. You should consider utilizing those features. \n\nA merged PR will make you appear in the contributor list (see below). It will, however, be considered a donation of your work to this project. You are still bound by the conditions of the license, meaning that you are **not considered an author, copyright holder, or owner** of the content once it has been merged in.\n\nYou will mostly work with the `*.qmd` files in the `chapters` directory. \n\nHere is a list of the elements in the repo: \n\n```\n├── DESCRIPTION          # Set package dependencies\n├── _cache               # Location of cached chunks  \n├── _extensions          # Created by quarto\n├── _freeze              # Created by quarto\n├── _publish.yml         # Publishing details\n├── _quarto.yml          # Most options\n├── website.Rproj        # Rstudio IDE file\n├── chapters             # qmd content files\n├── delimited            # csv versions of the data\n├── docs                 # Created by quarto\n├── figures              # Location for created image files \n├── includes             # tex, bib, and html files to include\n├── index.qmd            # Initial quarto file\n├── license.*            # License information\n├── premade              # Premade diagrams and other files\n├── renv                 # Version control for R packages\n├── renv.lock            # Version control for R packages\n├── R                    # Ancillary R files\n├── RData                # WIP RData results\n├── README.*             # Information\n└── tests                # testthat files to check some results\n```\n\n## Software\n\nRegarding R packages, the repository has a DESCRIPTION file as if it were an R package. This lets us specify precisely what packages and their versions should be installed. The packages listed in the imports field contain packages for modeling/analysis and packages used to make the website/book. \nSome basic system requirements are likely needed to install packages: Fortran, gdal, and others. \n\nThe main requirements are as follows.\n\n### Quarto\n\nQuarto is an open-source scientific and technical publishing system. [Quarto](https://quarto.org/docs/get-started/) version 1.4.521 is used to compile the website. \n\nWe also use a few Quarto extensions. These should be installed from the project's root directory via:\n\n```\nquarto add quarto-ext/fontawesome\nquarto add quarto-ext/fancy-text\nquarto add leovan/quarto-pseudocode\n```\n\n### R and renv\n\nR version 4.3.2 (2023-10-31) is what we are currently using. We suggest using [rig](https://github.com/r-lib/rig) to manage R versions. There are several IDEs that you can use. We've used RStudio (>= 2023.6.1.524). \n\nThe current strategy is to use the [renv](https://rstudio.github.io/renv/) (>= version 1.0.3) package to make this project more isolated, portable and reproducible. \n\nTo get package dependencies installed...\n\n<details>\n\nWhen you open the `website.Rproj` file, the renv package should be automatically installed/updated (if neded). For example: \n\n```\n# Bootstrapping renv 1.0.3 ---------------------------------------------------\n- Downloading renv ... OK\n- Installing renv  ... OK\n\nThe following package(s) will be installed:\n- BiocManager [1.30.22]\nThese packages will be installed into \"~/content/aml4td/renv/library/R-4.3/x86_64-apple-darwin20\".\n```\n\nif you try to compile the book, you probably get and error: \n\n```\n- One or more packages recorded in the lockfile are not installed.\n- Use `renv::status()` for more details.\n```\n\nYou can get more information using `renv::status()` but you can get them installed by first running `renv::activate()`. As an example: \n\n```\n> renv::activate()\n\nRestarting R session...\n\n- Project '~/content/aml4td' loaded. [renv 1.0.3]\n- One or more packages recorded in the lockfile are not installed.\n- Use `renv::status()` for more details.\n```\n\nSince we have package versions recorded in the lockfile, we can installed them using `renv::restore()`. Here is an example of that output: \n\n```\n> renv::restore() \nThe following package(s) will be updated:\n\n# Bioconductor ---------------------------------------------------------------\n- mixOmics         [* -> mixOmicsTeam/mixOmics]\n\n# CRAN -----------------------------------------------------------------------\n- BiocManager      [1.30.22 -> 1.30.21.1]\n- lattice          [0.21-9 -> 0.21-8]\n- Matrix           [1.6-1.1 -> 1.6-0]\n- nlme             [3.1-163 -> 3.1-162]\n- rpart            [4.1.21 -> 4.1.19]\n- survival         [3.5-7 -> 3.5-5]\n- abind            [* -> 1.4-5]\n\n<snip>\n\n- zip              [* -> 2.2.0]\n- zoo              [* -> 1.8-12]\n\n# GitHub ---------------------------------------------------------------------\n- BiocParallel     [* -> Bioconductor/BiocParallel@devel]\n- BiocVersion      [* -> Bioconductor/BiocVersion@devel]\n- modeldatatoo     [* -> tidymodels/modeldatatoo@HEAD]\n- parsnip          [* -> tidymodels/parsnip@HEAD]\n- usethis          [* -> r-lib/usethis@HEAD]\n\n# RSPM -----------------------------------------------------------------------\n- bslib            [* -> 0.5.1]\n- fansi            [* -> 1.0.5]\n- fontawesome      [* -> 0.5.2]\n- ggplot2          [* -> 3.4.4]\n- htmltools        [* -> 0.5.6.1]\n- withr            [* -> 2.5.1]\n\nDo you want to proceed? [Y/n]: y\n\n# Downloading packages -------------------------------------------------------\n- Downloading BiocManager from CRAN ...         OK [569 Kb in 0.19s]\n- Downloading nlme from CRAN ...                OK [828.7 Kb in 0.19s]\n- Downloading BH from CRAN ...                  OK [12.7 Mb in 0.4s]\n- Downloading BiocVersion from GitHub ...       OK [826 bytes in 0.37s]\n\n<snip>\n\n```\n\nDepending on whether you have to install packages from source, you may need to install some system dependencies and try again (I had to install `libgit2` the last time I did this). \n\nOnce you have everything installed, we recommend installing the underlying torch computational libraries. You can do this by loading the torch package A download will automatically begin if you need one. \n\n</details>\n\n\n## Contributor List\n\n\n\n",
+    "markdown": "# Contributing {.unlisted .unnumbered}\n\n\n\n\n\nIf you plan to do anything beyond fixing a typo, the best thing you can do is to [open an issue](https://github.com/aml4td/website/issues) and discuss changes before you spend a lot of time doing them. \n\nIf you don't have a lot of experience with git or GitHub, take a look at the wonderful [_Happy Git and GitHub for the useR_](https://happygitwithr.com/). \n\nIf you want to contribute, some general advice is: \n\n - Only check in the source files (qmd, yml, bib, pre-made image files, etc). Don't commit the rendered files. \n - Keep the changes small in scope. If the overall change is larger, make a sequence of small pull requests. \n - The edits cannot include exact code that is under another license (i.e., don't just copy/paste from R sources, etc.)\n - Respect the existing code formatting/linting (as heterogeneous as it is). \n - Stick to using R for computations.  \n - Don't update software versions unless you have to. If you need to update or add something, use [renv](https://rstudio.github.io/renv/) (described below) to codify the software requirements.  \n - The [usethis](https://usethis.r-lib.org/) package has excellent tools for creating, updating, and managing pull requests. You should consider utilizing those features. \n\nA merged PR will make you appear in the contributor list (see below). It will, however, be considered a donation of your work to this project. You are still bound by the conditions of the license, meaning that you are **not considered an author, copyright holder, or owner** of the content once it has been merged in.\n\nYou will mostly work with the `*.qmd` files in the `chapters` directory. \n\nHere is a list of the elements in the repo: \n\n```\n├── DESCRIPTION          # Set package dependencies\n├── _cache               # Location of cached chunks  \n├── _extensions          # Created by quarto\n├── _freeze              # Created by quarto\n├── _publish.yml         # Publishing details\n├── _quarto.yml          # Most options\n├── website.Rproj        # Rstudio IDE file\n├── chapters             # qmd content files\n├── delimited            # csv versions of the data\n├── docs                 # Created by quarto\n├── figures              # Location for created image files \n├── includes             # tex, bib, and html files to include\n├── index.qmd            # Initial quarto file\n├── license.*            # License information\n├── premade              # Premade diagrams and other files\n├── renv                 # Version control for R packages\n├── renv.lock            # Version control for R packages\n├── R                    # Ancillary R files\n├── RData                # WIP RData results\n├── README.*             # Information\n└── tests                # testthat files to check some results\n```\n\n## Software\n\nRegarding R packages, the repository has a DESCRIPTION file as if it were an R package. This lets us specify precisely what packages and their versions should be installed. The packages listed in the imports field contain packages for modeling/analysis and packages used to make the website/book. \nSome basic system requirements are likely needed to install packages: Fortran, gdal, and others. \n\nThe main requirements are as follows.\n\n### Quarto\n\nQuarto is an open-source scientific and technical publishing system. [Quarto](https://quarto.org/docs/get-started/) version 1.4.533 is used to compile the website. \n\nWe also use a few Quarto extensions. These should be installed from the project's root directory via:\n\n```\nquarto add quarto-ext/fontawesome\nquarto add quarto-ext/fancy-text\nquarto add leovan/quarto-pseudocode\n```\n\n### R and renv\n\nR version 4.3.2 (2023-10-31) is what we are currently using. We suggest using [rig](https://github.com/r-lib/rig) to manage R versions. There are several IDEs that you can use. We've used RStudio (>= 2023.6.1.524). \n\nThe current strategy is to use the [renv](https://rstudio.github.io/renv/) (>= version 1.0.3) package to make this project more isolated, portable and reproducible. \n\nTo get package dependencies installed...\n\n<details>\n\nWhen you open the `website.Rproj` file, the renv package should be automatically installed/updated (if neded). For example: \n\n```\n# Bootstrapping renv 1.0.3 ---------------------------------------------------\n- Downloading renv ... OK\n- Installing renv  ... OK\n\nThe following package(s) will be installed:\n- BiocManager [1.30.22]\nThese packages will be installed into \"~/content/aml4td/renv/library/R-4.3/x86_64-apple-darwin20\".\n```\n\nif you try to compile the book, you probably get and error: \n\n```\n- One or more packages recorded in the lockfile are not installed.\n- Use `renv::status()` for more details.\n```\n\nYou can get more information using `renv::status()` but you can get them installed by first running `renv::activate()`. As an example: \n\n```\n> renv::activate()\n\nRestarting R session...\n\n- Project '~/content/aml4td' loaded. [renv 1.0.3]\n- One or more packages recorded in the lockfile are not installed.\n- Use `renv::status()` for more details.\n```\n\nSince we have package versions recorded in the lockfile, we can installed them using `renv::restore()`. Here is an example of that output: \n\n```\n> renv::restore() \nThe following package(s) will be updated:\n\n# Bioconductor ---------------------------------------------------------------\n- mixOmics         [* -> mixOmicsTeam/mixOmics]\n\n# CRAN -----------------------------------------------------------------------\n- BiocManager      [1.30.22 -> 1.30.21.1]\n- lattice          [0.21-9 -> 0.21-8]\n- Matrix           [1.6-1.1 -> 1.6-0]\n- nlme             [3.1-163 -> 3.1-162]\n- rpart            [4.1.21 -> 4.1.19]\n- survival         [3.5-7 -> 3.5-5]\n- abind            [* -> 1.4-5]\n\n<snip>\n\n- zip              [* -> 2.2.0]\n- zoo              [* -> 1.8-12]\n\n# GitHub ---------------------------------------------------------------------\n- BiocParallel     [* -> Bioconductor/BiocParallel@devel]\n- BiocVersion      [* -> Bioconductor/BiocVersion@devel]\n- modeldatatoo     [* -> tidymodels/modeldatatoo@HEAD]\n- parsnip          [* -> tidymodels/parsnip@HEAD]\n- usethis          [* -> r-lib/usethis@HEAD]\n\n# RSPM -----------------------------------------------------------------------\n- bslib            [* -> 0.5.1]\n- fansi            [* -> 1.0.5]\n- fontawesome      [* -> 0.5.2]\n- ggplot2          [* -> 3.4.4]\n- htmltools        [* -> 0.5.6.1]\n- withr            [* -> 2.5.1]\n\nDo you want to proceed? [Y/n]: y\n\n# Downloading packages -------------------------------------------------------\n- Downloading BiocManager from CRAN ...         OK [569 Kb in 0.19s]\n- Downloading nlme from CRAN ...                OK [828.7 Kb in 0.19s]\n- Downloading BH from CRAN ...                  OK [12.7 Mb in 0.4s]\n- Downloading BiocVersion from GitHub ...       OK [826 bytes in 0.37s]\n\n<snip>\n\n```\n\nDepending on whether you have to install packages from source, you may need to install some system dependencies and try again (I had to install `libgit2` the last time I did this). \n\nOnce you have everything installed, we recommend installing the underlying torch computational libraries. You can do this by loading the torch package A download will automatically begin if you need one. \n\n</details>\n\n\n## Contributor List\n\n\n\n\n\nThe would like to thank users who have made a contribution to the project: [&#x0040;bmreiniger](https://github.com/bmreiniger), [&#x0040;coatless](https://github.com/coatless), [&#x0040;syclik](https://github.com/syclik), and [&#x0040;tomsing1](https://github.com/tomsing1).\n",
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