diff --git a/.Rprofile b/.Rprofile
new file mode 100644
index 0000000..81b960f
--- /dev/null
+++ b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/.github/workflows/test-targets-workflow.yml b/.github/workflows/test-targets-workflow.yml
new file mode 100644
index 0000000..a69feac
--- /dev/null
+++ b/.github/workflows/test-targets-workflow.yml
@@ -0,0 +1,47 @@
+name: test targets workflow
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+    # branches:
+    #   - '*'
+
+jobs:
+  test-targets-workflow:
+    runs-on: ubuntu-latest
+    container: rocker/tidyverse:4.3.3
+    env:
+      GIT_CRYPT_KEY64: ${{ secrets.GIT_CRYPT_KEY64 }}
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Install system dependencies
+        run: |
+          apt-get update && apt-get install -y --no-install-recommends \
+          libxt6 libglpk-dev
+          
+      - name: Trust git repo
+        run: |
+          git config --global --add safe.directory /__w/ihtm-targets-template/ihtm-targets-template
+          
+      - name: Install packages from renv.lock (with cache)
+        if: ${{ !env.ACT }}  
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          cache-version: 2
+
+      - name: Install packages from renv.lock (local, no cache)
+        if: ${{ env.ACT }}  
+        run: |
+          renv::restore()
+        shell: Rscript {0}
+        
+      - name: Run workflow
+        run: |
+          targets::tar_make()
+        shell: Rscript {0}
+        
+        
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..1207843
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+_targets
+docs
diff --git a/R/.gitkeep b/R/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 0000000..57c81d6
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,34 @@
+#' 
+#' Collect all targets and lists of targets in the environment
+#' 
+#' 
+all_targets <- function(env = parent.env(environment()), 
+                        type = "tar_target", 
+                        add_list_names = TRUE) {
+  
+  ## Function to determine if an object is a type (a target), 
+  ## or a list on only that type
+  rfn <- function(obj) 
+    inherits(obj, type) || (is.list(obj) && all(vapply(obj, rfn, logical(1))))
+  
+  ## Get the names of everything in the environment 
+  ## (e.g. sourced in the _targets.R file)
+  objs <- ls(env)
+  
+  out <- list()
+  for (o in objs) {
+    obj <- get(o, envir = env)      ## Get each top-level object in turn
+    if (rfn(obj)) {                 ## For targets and lists of targets
+      out[[length(out) + 1]] <- obj ## Add them to the output
+      
+      ## If the object is a list of targets, add a vector of the target names 
+      ## to the environment So that one can call `tar_make(list_name)` to make 
+      ## all the targets in that list
+      if (add_list_names && is.list(obj)) {
+        target_names <- vapply(obj, \(x) x$settings$name, character(1))
+        assign(o, target_names, envir = env)
+      }
+    }
+  }
+  return(out)
+}
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 0000000..856e68d
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,74 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+# A template R workflow for general data analysis
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+This repository is a template for a [`docker`](https://www.docker.com/get-started)-containerised, [`{targets}`](https://docs.ropensci.org/targets/)-based, [`{renv}`](https://rstudio.github.io/renv/articles/renv.html)-enabled [`R`](https://cran.r-project.org/) workflow for general data analysis.
+
+## About the Project
+
+
+
+## Repository Structure
+
+The project repository is structured as follows:
+
+```
+sc-policy-review
+    |-- .github/
+      |-- workflows/
+    |-- data/
+    |-- data-raw/
+    |-- outputs/
+    |-- R/
+    |-- reports
+    |-- renv
+      |-- library/
+      |-- activate.R
+    |-- renv.lock
+    |-- .Rprofile
+    |-- packages.R
+    |-- _targets.R
+```
+
+* `.github` contains project testing and automated deployment of outputs workflows via continuous integration and continuous deployment (CI/CD) using Github Actions.
+
+* `data/` contains intermediate and final data outputs produced by the workflow.
+
+* `data-raw/` contains raw datasets, usually either downloaded from source or added manually, that are used in the project. This directory is empty given that the raw datasets used in this project are restricted and are only distributed to eligible members of the project. This directory is kept here to maintain reproducibility of project directory structure and ensure that the workflow runs as expected. Those who are collaborating on this project and who have permissions to use the raw datasets should include their copies of the raw dataset into this directory in their local versions of this repository.
+
+* `outputs/` contains compiled reports and figures produced by the workflow.
+
+* `R/` contains functions developed/created specifically for use in this workflow.
+
+* `reports/` contains literate code for R Markdown reports rendered in the workflow.
+
+* `renv/` contains `renv` package specific files and directories used by the package for maintaining R package dependencies within the project. The directory `renv/library`, is a library that contains all packages currently used by the project. This directory, and all files and sub-directories within it, are all generated and managed by the `renv` package. Users should not change/edit these manually.
+
+* `renv.lock` file is the `renv` lockfile which records enough metadata about every package used in this project that it can be re-installed on a new machine. This file is generated by the `renv` package and should not be changed/edited manually.
+
+* `.Rprofile` file is a project R profile generated when initiating `renv` for the first time. This file is run automatically every time R is run within this project, and `renv` uses it to configure the R session to use the `renv` project library.
+
+* `packages.R` file lists out all R package dependencies required by the workflow.
+
+* `_targets.R` file defines the steps in the workflow's data ingest, data processing, data analysis, and reporting pipeline.
+
+## Reproducibility
+
+### R package dependencies
+
+This project was built using `R 4.3.3`. This project uses the `renv` framework to record R package dependencies and versions. Packages and versions used are recorded in `renv.lock` and code used to manage dependencies is in `renv/` and other files in the root project directory. On starting an R session in the working directory, run `renv::restore()` to install R package dependencies.
+
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..f496410
--- /dev/null
+++ b/README.md
@@ -0,0 +1,96 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# A template R workflow for general data analysis
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+This repository is a template for a
+[`docker`](https://www.docker.com/get-started)-containerised,
+[`{targets}`](https://docs.ropensci.org/targets/)-based,
+[`{renv}`](https://rstudio.github.io/renv/articles/renv.html)-enabled
+[`R`](https://cran.r-project.org/) workflow for general data analysis.
+
+## About the Project
+
+## Repository Structure
+
+The project repository is structured as follows:
+
+    sc-policy-review
+        |-- .github/
+          |-- workflows/
+        |-- data/
+        |-- data-raw/
+        |-- outputs/
+        |-- R/
+        |-- reports
+        |-- renv
+          |-- library/
+          |-- activate.R
+        |-- renv.lock
+        |-- .Rprofile
+        |-- packages.R
+        |-- _targets.R
+
+- `.github` contains project testing and automated deployment of outputs
+  workflows via continuous integration and continuous deployment (CI/CD)
+  using Github Actions.
+
+- `data/` contains intermediate and final data outputs produced by the
+  workflow.
+
+- `data-raw/` contains raw datasets, usually either downloaded from
+  source or added manually, that are used in the project. This directory
+  is empty given that the raw datasets used in this project are
+  restricted and are only distributed to eligible members of the
+  project. This directory is kept here to maintain reproducibility of
+  project directory structure and ensure that the workflow runs as
+  expected. Those who are collaborating on this project and who have
+  permissions to use the raw datasets should include their copies of the
+  raw dataset into this directory in their local versions of this
+  repository.
+
+- `outputs/` contains compiled reports and figures produced by the
+  workflow.
+
+- `R/` contains functions developed/created specifically for use in this
+  workflow.
+
+- `reports/` contains literate code for R Markdown reports rendered in
+  the workflow.
+
+- `renv/` contains `renv` package specific files and directories used by
+  the package for maintaining R package dependencies within the project.
+  The directory `renv/library`, is a library that contains all packages
+  currently used by the project. This directory, and all files and
+  sub-directories within it, are all generated and managed by the `renv`
+  package. Users should not change/edit these manually.
+
+- `renv.lock` file is the `renv` lockfile which records enough metadata
+  about every package used in this project that it can be re-installed
+  on a new machine. This file is generated by the `renv` package and
+  should not be changed/edited manually.
+
+- `.Rprofile` file is a project R profile generated when initiating
+  `renv` for the first time. This file is run automatically every time R
+  is run within this project, and `renv` uses it to configure the R
+  session to use the `renv` project library.
+
+- `packages.R` file lists out all R package dependencies required by the
+  workflow.
+
+- `_targets.R` file defines the steps in the workflow’s data ingest,
+  data processing, data analysis, and reporting pipeline.
+
+## Reproducibility
+
+### R package dependencies
+
+This project was built using `R 4.3.3`. This project uses the `renv`
+framework to record R package dependencies and versions. Packages and
+versions used are recorded in `renv.lock` and code used to manage
+dependencies is in `renv/` and other files in the root project
+directory. On starting an R session in the working directory, run
+`renv::restore()` to install R package dependencies.
diff --git a/_targets.R b/_targets.R
new file mode 100644
index 0000000..1f6c145
--- /dev/null
+++ b/_targets.R
@@ -0,0 +1,50 @@
+################################################################################
+#
+# General Targets Workflow
+#
+################################################################################
+
+## Load libraries and custom functions -----------------------------------------
+suppressPackageStartupMessages(source("packages.R"))
+for (f in list.files(here::here("R"), full.names = TRUE)) source (f)
+
+## Create targets and list targets objects -------------------------------------
+
+### Data targets
+data_targets <- tar_plan(
+  
+)
+
+
+### Processing targets
+processing_targets <- tar_plan(
+  
+)
+
+
+### Analysis targets
+analysis_targets <- tar_plan(
+  
+)
+
+
+### Output targets
+output_targets <- tar_plan(
+  
+)
+
+
+### Reporting targets
+report_targets <- tar_plan(
+  
+)
+
+
+### Deploy targets
+deploy_targets <- tar_plan(
+  
+)
+
+
+## List targets
+all_targets()
diff --git a/data/.gitkeep b/data/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/ihtm-targets-template.Rproj b/ihtm-targets-template.Rproj
new file mode 100644
index 0000000..8e3c2eb
--- /dev/null
+++ b/ihtm-targets-template.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
diff --git a/outputs/.gitkeep b/outputs/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/packages.R b/packages.R
new file mode 100644
index 0000000..d63b0f0
--- /dev/null
+++ b/packages.R
@@ -0,0 +1,16 @@
+################################################################################
+#
+# Load packages required for standard workflows
+#
+################################################################################
+
+library(targets)
+library(tarchetypes)
+library(here)
+library(rmarkdown)
+library(knitr)
+library(kableExtra)
+library(dplyr)
+library(tidyr)
+library(openxlsx)
+library(ggplot2)
\ No newline at end of file
diff --git a/renv.lock b/renv.lock
new file mode 100644
index 0000000..e7eb20b
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,1235 @@
+{
+  "R": {
+    "Version": "4.3.1",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
+    "MASS": {
+      "Package": "MASS",
+      "Version": "7.3-60",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "a56a6365b3fa73293ea8d084be0d9bb0"
+    },
+    "Matrix": {
+      "Package": "Matrix",
+      "Version": "1.6-1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "grid",
+        "lattice",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "1a00d4828f33a9d690806e98bd17150c"
+    },
+    "R6": {
+      "Package": "R6",
+      "Version": "2.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
+    "RColorBrewer": {
+      "Package": "RColorBrewer",
+      "Version": "1.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
+    },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.11",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods",
+        "utils"
+      ],
+      "Hash": "ae6cbbe1492f4de79c45fce06f967ce8"
+    },
+    "askpass": {
+      "Package": "askpass",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "sys"
+      ],
+      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
+    },
+    "backports": {
+      "Package": "backports",
+      "Version": "1.4.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "c39fbec8a30d23e721980b8afb31984c"
+    },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+    },
+    "base64url": {
+      "Package": "base64url",
+      "Version": "1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "backports"
+      ],
+      "Hash": "0c54cf3a08cc0e550fbd64ad33166143"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.5.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.0.8",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "c35768291560ce302c0a6589f92e837d"
+    },
+    "callr": {
+      "Package": "callr",
+      "Version": "3.7.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "processx",
+        "utils"
+      ],
+      "Hash": "9b2191ede20fa29828139b9900922e51"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "89e6d8219950eac806ae0c489052048a"
+    },
+    "codetools": {
+      "Package": "codetools",
+      "Version": "0.2-19",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "c089a619a7fae175d149d89164f8c7d8"
+    },
+    "colorspace": {
+      "Package": "colorspace",
+      "Version": "2.1-0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats"
+      ],
+      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
+    },
+    "cpp11": {
+      "Package": "cpp11",
+      "Version": "0.4.6",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "707fae4bbf73697ec8d85f9d7076c061"
+    },
+    "curl": {
+      "Package": "curl",
+      "Version": "5.0.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "511bacbfa153a15251166b463b4da4f9"
+    },
+    "data.table": {
+      "Package": "data.table",
+      "Version": "1.14.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "b4c06e554f33344e044ccd7fdca750a9"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.33",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d"
+    },
+    "dplyr": {
+      "Package": "dplyr",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "generics",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pillar",
+        "rlang",
+        "tibble",
+        "tidyselect",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949"
+    },
+    "ellipsis": {
+      "Package": "ellipsis",
+      "Version": "0.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "rlang"
+      ],
+      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "0.21",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "d59f3b464e8da1aef82dc04b588b8dfb"
+    },
+    "fansi": {
+      "Package": "fansi",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "utils"
+      ],
+      "Hash": "1d9e7ad3c8312a192dea7d3db0274fde"
+    },
+    "farver": {
+      "Package": "farver",
+      "Version": "2.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "8106d78941f34855c440ddb946b8f7a5"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
+    },
+    "furrr": {
+      "Package": "furrr",
+      "Version": "0.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "future",
+        "globals",
+        "lifecycle",
+        "purrr",
+        "rlang",
+        "vctrs"
+      ],
+      "Hash": "da7a4c32196cb2262a41dd5a25d486ff"
+    },
+    "future": {
+      "Package": "future",
+      "Version": "1.33.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "digest",
+        "globals",
+        "listenv",
+        "parallel",
+        "parallelly",
+        "utils"
+      ],
+      "Hash": "8e92c7bc53e91b9bb1faf9a6ef0e8514"
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+      "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
+    },
+    "webshot": {
+      "Package": "webshot",
+      "Version": "0.5.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "callr",
+        "jsonlite",
+        "magrittr"
+      ],
+      "Hash": "16858ee1aba97f902d24049d4a44ef16"
+    },
+    "withr": {
+      "Package": "withr",
+      "Version": "2.5.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.40",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "stats",
+        "tools"
+      ],
+      "Hash": "be07d23211245fc7d4209f54c4e4ffc8"
+    },
+    "xml2": {
+      "Package": "xml2",
+      "Version": "1.3.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "6c40e5cfcc6aefd88110666e18c31f40"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+    },
+    "zip": {
+      "Package": "zip",
+      "Version": "2.3.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "d98c94dacb7e0efcf83b0a133a705504"
+    }
+  }
+}
diff --git a/renv/.gitignore b/renv/.gitignore
new file mode 100644
index 0000000..22a0d01
--- /dev/null
+++ b/renv/.gitignore
@@ -0,0 +1,7 @@
+sandbox/
+library/
+local/
+cellar/
+lock/
+python/
+staging/
diff --git a/renv/activate.R b/renv/activate.R
new file mode 100644
index 0000000..cb5401f
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,1180 @@
+
+local({
+
+  # the requested version of renv
+  version <- "1.0.3"
+  attr(version, "sha") <- NULL
+
+  # the project directory
+  project <- getwd()
+
+  # use start-up diagnostics if enabled
+  diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+  if (diagnostics) {
+    start <- Sys.time()
+    profile <- tempfile("renv-startup-", fileext = ".Rprof")
+    utils::Rprof(profile)
+    on.exit({
+      utils::Rprof(NULL)
+      elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+      writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+      writeLines(sprintf("- Profile: %s", profile))
+      print(utils::summaryRprof(profile))
+    }, add = TRUE)
+  }
+
+  # figure out whether the autoloader is enabled
+  enabled <- local({
+
+    # first, check config option
+    override <- getOption("renv.config.autoloader.enabled")
+    if (!is.null(override))
+      return(override)
+
+    # next, check environment variables
+    # TODO: prefer using the configuration one in the future
+    envvars <- c(
+      "RENV_CONFIG_AUTOLOADER_ENABLED",
+      "RENV_AUTOLOADER_ENABLED",
+      "RENV_ACTIVATE_PROJECT"
+    )
+
+    for (envvar in envvars) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(tolower(envval) %in% c("true", "t", "1"))
+    }
+
+    # enable by default
+    TRUE
+
+  })
+
+  if (!enabled)
+    return(FALSE)
+
+  # avoid recursion
+  if (identical(getOption("renv.autoloader.running"), TRUE)) {
+    warning("ignoring recursive attempt to run renv autoloader")
+    return(invisible(TRUE))
+  }
+
+  # signal that we're loading renv during R startup
+  options(renv.autoloader.running = TRUE)
+  on.exit(options(renv.autoloader.running = NULL), add = TRUE)
+
+  # signal that we've consented to use renv
+  options(renv.consent = TRUE)
+
+  # load the 'utils' package eagerly -- this ensures that renv shims, which
+  # mask 'utils' packages, will come first on the search path
+  library(utils, lib.loc = .Library)
+
+  # unload renv if it's already been loaded
+  if ("renv" %in% loadedNamespaces())
+    unloadNamespace("renv")
+
+  # load bootstrap tools   
+  `%||%` <- function(x, y) {
+    if (is.null(x)) y else x
+  }
+  
+  catf <- function(fmt, ..., appendLF = TRUE) {
+  
+    quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+    if (quiet)
+      return(invisible())
+  
+    msg <- sprintf(fmt, ...)
+    cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+  
+    invisible(msg)
+  
+  }
+  
+  header <- function(label,
+                     ...,
+                     prefix = "#",
+                     suffix = "-",
+                     n = min(getOption("width"), 78))
+  {
+    label <- sprintf(label, ...)
+    n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+    if (n <= 0)
+      return(paste(prefix, label))
+  
+    tail <- paste(rep.int(suffix, n), collapse = "")
+    paste0(prefix, " ", label, " ", tail)
+  
+  }
+  
+  startswith <- function(string, prefix) {
+    substring(string, 1, nchar(prefix)) == prefix
+  }
+  
+  bootstrap <- function(version, library) {
+  
+    friendly <- renv_bootstrap_version_friendly(version)
+    section <- header(sprintf("Bootstrapping renv %s", friendly))
+    catf(section)
+  
+    # attempt to download renv
+    catf("- Downloading renv ... ", appendLF = FALSE)
+    withCallingHandlers(
+      tarball <- renv_bootstrap_download(version),
+      error = function(err) {
+        catf("FAILED")
+        stop("failed to download:\n", conditionMessage(err))
+      }
+    )
+    catf("OK")
+    on.exit(unlink(tarball), add = TRUE)
+  
+    # now attempt to install
+    catf("- Installing renv  ... ", appendLF = FALSE)
+    withCallingHandlers(
+      status <- renv_bootstrap_install(version, tarball, library),
+      error = function(err) {
+        catf("FAILED")
+        stop("failed to install:\n", conditionMessage(err))
+      }
+    )
+    catf("OK")
+  
+    # add empty line to break up bootstrapping from normal output
+    catf("")
+  
+    return(invisible())
+  }
+  
+  renv_bootstrap_tests_running <- function() {
+    getOption("renv.tests.running", default = FALSE)
+  }
+  
+  renv_bootstrap_repos <- function() {
+  
+    # get CRAN repository
+    cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+  
+    # check for repos override
+    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+    if (!is.na(repos)) {
+  
+      # check for RSPM; if set, use a fallback repository for renv
+      rspm <- Sys.getenv("RSPM", unset = NA)
+      if (identical(rspm, repos))
+        repos <- c(RSPM = rspm, CRAN = cran)
+  
+      return(repos)
+  
+    }
+  
+    # check for lockfile repositories
+    repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+    if (!inherits(repos, "error") && length(repos))
+      return(repos)
+  
+    # retrieve current repos
+    repos <- getOption("repos")
+  
+    # ensure @CRAN@ entries are resolved
+    repos[repos == "@CRAN@"] <- cran
+  
+    # add in renv.bootstrap.repos if set
+    default <- c(FALLBACK = "https://cloud.r-project.org")
+    extra <- getOption("renv.bootstrap.repos", default = default)
+    repos <- c(repos, extra)
+  
+    # remove duplicates that might've snuck in
+    dupes <- duplicated(repos) | duplicated(names(repos))
+    repos[!dupes]
+  
+  }
+  
+  renv_bootstrap_repos_lockfile <- function() {
+  
+    lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
+    if (!file.exists(lockpath))
+      return(NULL)
+  
+    lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
+    if (inherits(lockfile, "error")) {
+      warning(lockfile)
+      return(NULL)
+    }
+  
+    repos <- lockfile$R$Repositories
+    if (length(repos) == 0)
+      return(NULL)
+  
+    keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+    vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+    names(vals) <- keys
+  
+    return(vals)
+  
+  }
+  
+  renv_bootstrap_download <- function(version) {
+  
+    sha <- attr(version, "sha", exact = TRUE)
+  
+    methods <- if (!is.null(sha)) {
+  
+      # attempting to bootstrap a development version of renv
+      c(
+        function() renv_bootstrap_download_tarball(sha),
+        function() renv_bootstrap_download_github(sha)
+      )
+  
+    } else {
+  
+      # attempting to bootstrap a release version of renv
+      c(
+        function() renv_bootstrap_download_tarball(version),
+        function() renv_bootstrap_download_cran_latest(version),
+        function() renv_bootstrap_download_cran_archive(version)
+      )
+  
+    }
+  
+    for (method in methods) {
+      path <- tryCatch(method(), error = identity)
+      if (is.character(path) && file.exists(path))
+        return(path)
+    }
+  
+    stop("All download methods failed")
+  
+  }
+  
+  renv_bootstrap_download_impl <- function(url, destfile) {
+  
+    mode <- "wb"
+  
+    # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+    fixup <-
+      Sys.info()[["sysname"]] == "Windows" &&
+      substring(url, 1L, 5L) == "file:"
+  
+    if (fixup)
+      mode <- "w+b"
+  
+    args <- list(
+      url      = url,
+      destfile = destfile,
+      mode     = mode,
+      quiet    = TRUE
+    )
+  
+    if ("headers" %in% names(formals(utils::download.file)))
+      args$headers <- renv_bootstrap_download_custom_headers(url)
+  
+    do.call(utils::download.file, args)
+  
+  }
+  
+  renv_bootstrap_download_custom_headers <- function(url) {
+  
+    headers <- getOption("renv.download.headers")
+    if (is.null(headers))
+      return(character())
+  
+    if (!is.function(headers))
+      stopf("'renv.download.headers' is not a function")
+  
+    headers <- headers(url)
+    if (length(headers) == 0L)
+      return(character())
+  
+    if (is.list(headers))
+      headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
+  
+    ok <-
+      is.character(headers) &&
+      is.character(names(headers)) &&
+      all(nzchar(names(headers)))
+  
+    if (!ok)
+      stop("invocation of 'renv.download.headers' did not return a named character vector")
+  
+    headers
+  
+  }
+  
+  renv_bootstrap_download_cran_latest <- function(version) {
+  
+    spec <- renv_bootstrap_download_cran_latest_find(version)
+    type  <- spec$type
+    repos <- spec$repos
+  
+    baseurl <- utils::contrib.url(repos = repos, type = type)
+    ext <- if (identical(type, "source"))
+      ".tar.gz"
+    else if (Sys.info()[["sysname"]] == "Windows")
+      ".zip"
+    else
+      ".tgz"
+    name <- sprintf("renv_%s%s", version, ext)
+    url <- paste(baseurl, name, sep = "/")
+  
+    destfile <- file.path(tempdir(), name)
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (inherits(status, "condition"))
+      return(FALSE)
+  
+    # report success and return
+    destfile
+  
+  }
+  
+  renv_bootstrap_download_cran_latest_find <- function(version) {
+  
+    # check whether binaries are supported on this system
+    binary <-
+      getOption("renv.bootstrap.binary", default = TRUE) &&
+      !identical(.Platform$pkgType, "source") &&
+      !identical(getOption("pkgType"), "source") &&
+      Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+  
+    types <- c(if (binary) "binary", "source")
+  
+    # iterate over types + repositories
+    for (type in types) {
+      for (repos in renv_bootstrap_repos()) {
+  
+        # retrieve package database
+        db <- tryCatch(
+          as.data.frame(
+            utils::available.packages(type = type, repos = repos),
+            stringsAsFactors = FALSE
+          ),
+          error = identity
+        )
+  
+        if (inherits(db, "error"))
+          next
+  
+        # check for compatible entry
+        entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+        if (nrow(entry) == 0)
+          next
+  
+        # found it; return spec to caller
+        spec <- list(entry = entry, type = type, repos = repos)
+        return(spec)
+  
+      }
+    }
+  
+    # if we got here, we failed to find renv
+    fmt <- "renv %s is not available from your declared package repositories"
+    stop(sprintf(fmt, version))
+  
+  }
+  
+  renv_bootstrap_download_cran_archive <- function(version) {
+  
+    name <- sprintf("renv_%s.tar.gz", version)
+    repos <- renv_bootstrap_repos()
+    urls <- file.path(repos, "src/contrib/Archive/renv", name)
+    destfile <- file.path(tempdir(), name)
+  
+    for (url in urls) {
+  
+      status <- tryCatch(
+        renv_bootstrap_download_impl(url, destfile),
+        condition = identity
+      )
+  
+      if (identical(status, 0L))
+        return(destfile)
+  
+    }
+  
+    return(FALSE)
+  
+  }
+  
+  renv_bootstrap_download_tarball <- function(version) {
+  
+    # if the user has provided the path to a tarball via
+    # an environment variable, then use it
+    tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
+    if (is.na(tarball))
+      return()
+  
+    # allow directories
+    if (dir.exists(tarball)) {
+      name <- sprintf("renv_%s.tar.gz", version)
+      tarball <- file.path(tarball, name)
+    }
+  
+    # bail if it doesn't exist
+    if (!file.exists(tarball)) {
+  
+      # let the user know we weren't able to honour their request
+      fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
+      msg <- sprintf(fmt, tarball)
+      warning(msg)
+  
+      # bail
+      return()
+  
+    }
+  
+    catf("- Using local tarball '%s'.", tarball)
+    tarball
+  
+  }
+  
+  renv_bootstrap_download_github <- function(version) {
+  
+    enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+    if (!identical(enabled, "TRUE"))
+      return(FALSE)
+  
+    # prepare download options
+    pat <- Sys.getenv("GITHUB_PAT")
+    if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+      fmt <- "--location --fail --header \"Authorization: token %s\""
+      extra <- sprintf(fmt, pat)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "curl", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
+      fmt <- "--header=\"Authorization: token %s\""
+      extra <- sprintf(fmt, pat)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "wget", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    }
+  
+    url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+    name <- sprintf("renv_%s.tar.gz", version)
+    destfile <- file.path(tempdir(), name)
+  
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (!identical(status, 0L))
+      return(FALSE)
+  
+    renv_bootstrap_download_augment(destfile)
+  
+    return(destfile)
+  
+  }
+  
+  # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+  # can use renv::install() to fully capture metadata.
+  renv_bootstrap_download_augment <- function(destfile) {
+    sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+    if (is.null(sha)) {
+      return()
+    }
+  
+    # Untar
+    tempdir <- tempfile("renv-github-")
+    on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+    untar(destfile, exdir = tempdir)
+    pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+  
+    # Modify description
+    desc_path <- file.path(pkgdir, "DESCRIPTION")
+    desc_lines <- readLines(desc_path)
+    remotes_fields <- c(
+      "RemoteType: github",
+      "RemoteHost: api.github.com",
+      "RemoteRepo: renv",
+      "RemoteUsername: rstudio",
+      "RemotePkgRef: rstudio/renv",
+      paste("RemoteRef: ", sha),
+      paste("RemoteSha: ", sha)
+    )
+    writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+  
+    # Re-tar
+    local({
+      old <- setwd(tempdir)
+      on.exit(setwd(old), add = TRUE)
+  
+      tar(destfile, compression = "gzip")
+    })
+    invisible()
+  }
+  
+  # Extract the commit hash from a git archive. Git archives include the SHA1
+  # hash as the comment field of the tarball pax extended header
+  # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+  # For GitHub archives this should be the first header after the default one
+  # (512 byte) header.
+  renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+  
+    # open the bundle for reading
+    # We use gzcon for everything because (from ?gzcon)
+    # > Reading from a connection which does not supply a 'gzip' magic
+    # > header is equivalent to reading from the original connection
+    conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+    on.exit(close(conn))
+  
+    # The default pax header is 512 bytes long and the first pax extended header
+    # with the comment should be 51 bytes long
+    # `52 comment=` (11 chars) + 40 byte SHA1 hash
+    len <- 0x200 + 0x33
+    res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+  
+    if (grepl("^52 comment=", res)) {
+      sub("52 comment=", "", res)
+    } else {
+      NULL
+    }
+  }
+  
+  renv_bootstrap_install <- function(version, tarball, library) {
+  
+    # attempt to install it into project library
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+    output <- renv_bootstrap_install_impl(library, tarball)
+  
+    # check for successful install
+    status <- attr(output, "status")
+    if (is.null(status) || identical(status, 0L))
+      return(status)
+  
+    # an error occurred; report it
+    header <- "installation of renv failed"
+    lines <- paste(rep.int("=", nchar(header)), collapse = "")
+    text <- paste(c(header, lines, output), collapse = "\n")
+    stop(text)
+  
+  }
+  
+  renv_bootstrap_install_impl <- function(library, tarball) {
+  
+    # invoke using system2 so we can capture and report output
+    bin <- R.home("bin")
+    exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+    R <- file.path(bin, exe)
+  
+    args <- c(
+      "--vanilla", "CMD", "INSTALL", "--no-multiarch",
+      "-l", shQuote(path.expand(library)),
+      shQuote(path.expand(tarball))
+    )
+  
+    system2(R, args, stdout = TRUE, stderr = TRUE)
+  
+  }
+  
+  renv_bootstrap_platform_prefix <- function() {
+  
+    # construct version prefix
+    version <- paste(R.version$major, R.version$minor, sep = ".")
+    prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+  
+    # include SVN revision for development versions of R
+    # (to avoid sharing platform-specific artefacts with released versions of R)
+    devel <-
+      identical(R.version[["status"]],   "Under development (unstable)") ||
+      identical(R.version[["nickname"]], "Unsuffered Consequences")
+  
+    if (devel)
+      prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+  
+    # build list of path components
+    components <- c(prefix, R.version$platform)
+  
+    # include prefix if provided by user
+    prefix <- renv_bootstrap_platform_prefix_impl()
+    if (!is.na(prefix) && nzchar(prefix))
+      components <- c(prefix, components)
+  
+    # build prefix
+    paste(components, collapse = "/")
+  
+  }
+  
+  renv_bootstrap_platform_prefix_impl <- function() {
+  
+    # if an explicit prefix has been supplied, use it
+    prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
+    if (!is.na(prefix))
+      return(prefix)
+  
+    # if the user has requested an automatic prefix, generate it
+    auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (auto %in% c("TRUE", "True", "true", "1"))
+      return(renv_bootstrap_platform_prefix_auto())
+  
+    # empty string on failure
+    ""
+  
+  }
+  
+  renv_bootstrap_platform_prefix_auto <- function() {
+  
+    prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
+    if (inherits(prefix, "error") || prefix %in% "unknown") {
+  
+      msg <- paste(
+        "failed to infer current operating system",
+        "please file a bug report at https://github.com/rstudio/renv/issues",
+        sep = "; "
+      )
+  
+      warning(msg)
+  
+    }
+  
+    prefix
+  
+  }
+  
+  renv_bootstrap_platform_os <- function() {
+  
+    sysinfo <- Sys.info()
+    sysname <- sysinfo[["sysname"]]
+  
+    # handle Windows + macOS up front
+    if (sysname == "Windows")
+      return("windows")
+    else if (sysname == "Darwin")
+      return("macos")
+  
+    # check for os-release files
+    for (file in c("/etc/os-release", "/usr/lib/os-release"))
+      if (file.exists(file))
+        return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
+  
+    # check for redhat-release files
+    if (file.exists("/etc/redhat-release"))
+      return(renv_bootstrap_platform_os_via_redhat_release())
+  
+    "unknown"
+  
+  }
+  
+  renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
+  
+    # read /etc/os-release
+    release <- utils::read.table(
+      file             = file,
+      sep              = "=",
+      quote            = c("\"", "'"),
+      col.names        = c("Key", "Value"),
+      comment.char     = "#",
+      stringsAsFactors = FALSE
+    )
+  
+    vars <- as.list(release$Value)
+    names(vars) <- release$Key
+  
+    # get os name
+    os <- tolower(sysinfo[["sysname"]])
+  
+    # read id
+    id <- "unknown"
+    for (field in c("ID", "ID_LIKE")) {
+      if (field %in% names(vars) && nzchar(vars[[field]])) {
+        id <- vars[[field]]
+        break
+      }
+    }
+  
+    # read version
+    version <- "unknown"
+    for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
+      if (field %in% names(vars) && nzchar(vars[[field]])) {
+        version <- vars[[field]]
+        break
+      }
+    }
+  
+    # join together
+    paste(c(os, id, version), collapse = "-")
+  
+  }
+  
+  renv_bootstrap_platform_os_via_redhat_release <- function() {
+  
+    # read /etc/redhat-release
+    contents <- readLines("/etc/redhat-release", warn = FALSE)
+  
+    # infer id
+    id <- if (grepl("centos", contents, ignore.case = TRUE))
+      "centos"
+    else if (grepl("redhat", contents, ignore.case = TRUE))
+      "redhat"
+    else
+      "unknown"
+  
+    # try to find a version component (very hacky)
+    version <- "unknown"
+  
+    parts <- strsplit(contents, "[[:space:]]")[[1L]]
+    for (part in parts) {
+  
+      nv <- tryCatch(numeric_version(part), error = identity)
+      if (inherits(nv, "error"))
+        next
+  
+      version <- nv[1, 1]
+      break
+  
+    }
+  
+    paste(c("linux", id, version), collapse = "-")
+  
+  }
+  
+  renv_bootstrap_library_root_name <- function(project) {
+  
+    # use project name as-is if requested
+    asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
+    if (asis)
+      return(basename(project))
+  
+    # otherwise, disambiguate based on project's path
+    id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+    paste(basename(project), id, sep = "-")
+  
+  }
+  
+  renv_bootstrap_library_root <- function(project) {
+  
+    prefix <- renv_bootstrap_profile_prefix()
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+    if (!is.na(path))
+      return(paste(c(path, prefix), collapse = "/"))
+  
+    path <- renv_bootstrap_library_root_impl(project)
+    if (!is.null(path)) {
+      name <- renv_bootstrap_library_root_name(project)
+      return(paste(c(path, prefix, name), collapse = "/"))
+    }
+  
+    renv_bootstrap_paths_renv("library", project = project)
+  
+  }
+  
+  renv_bootstrap_library_root_impl <- function(project) {
+  
+    root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+    if (!is.na(root))
+      return(root)
+  
+    type <- renv_bootstrap_project_type(project)
+    if (identical(type, "package")) {
+      userdir <- renv_bootstrap_user_dir()
+      return(file.path(userdir, "library"))
+    }
+  
+  }
+  
+  renv_bootstrap_validate_version <- function(version, description = NULL) {
+  
+    # resolve description file
+    #
+    # avoid passing lib.loc to `packageDescription()` below, since R will
+    # use the loaded version of the package by default anyhow. note that
+    # this function should only be called after 'renv' is loaded
+    # https://github.com/rstudio/renv/issues/1625
+    description <- description %||% packageDescription("renv")
+  
+    # check whether requested version 'version' matches loaded version of renv
+    sha <- attr(version, "sha", exact = TRUE)
+    valid <- if (!is.null(sha))
+      renv_bootstrap_validate_version_dev(sha, description)
+    else
+      renv_bootstrap_validate_version_release(version, description)
+  
+    if (valid)
+      return(TRUE)
+  
+    # the loaded version of renv doesn't match the requested version;
+    # give the user instructions on how to proceed
+    remote <- if (!is.null(description[["RemoteSha"]])) {
+      paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+    } else {
+      paste("renv", description[["Version"]], sep = "@")
+    }
+  
+    # display both loaded version + sha if available
+    friendly <- renv_bootstrap_version_friendly(
+      version = description[["Version"]],
+      sha     = description[["RemoteSha"]]
+    )
+  
+    fmt <- paste(
+      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
+      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
+      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
+      sep = "\n"
+    )
+    catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+  
+    FALSE
+  
+  }
+  
+  renv_bootstrap_validate_version_dev <- function(version, description) {
+    expected <- description[["RemoteSha"]]
+    is.character(expected) && startswith(expected, version)
+  }
+  
+  renv_bootstrap_validate_version_release <- function(version, description) {
+    expected <- description[["Version"]]
+    is.character(expected) && identical(expected, version)
+  }
+  
+  renv_bootstrap_hash_text <- function(text) {
+  
+    hashfile <- tempfile("renv-hash-")
+    on.exit(unlink(hashfile), add = TRUE)
+  
+    writeLines(text, con = hashfile)
+    tools::md5sum(hashfile)
+  
+  }
+  
+  renv_bootstrap_load <- function(project, libpath, version) {
+  
+    # try to load renv from the project library
+    if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+      return(FALSE)
+  
+    # warn if the version of renv loaded does not match
+    renv_bootstrap_validate_version(version)
+  
+    # execute renv load hooks, if any
+    hooks <- getHook("renv::autoload")
+    for (hook in hooks)
+      if (is.function(hook))
+        tryCatch(hook(), error = warnify)
+  
+    # load the project
+    renv::load(project)
+  
+    TRUE
+  
+  }
+  
+  renv_bootstrap_profile_load <- function(project) {
+  
+    # if RENV_PROFILE is already set, just use that
+    profile <- Sys.getenv("RENV_PROFILE", unset = NA)
+    if (!is.na(profile) && nzchar(profile))
+      return(profile)
+  
+    # check for a profile file (nothing to do if it doesn't exist)
+    path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
+    if (!file.exists(path))
+      return(NULL)
+  
+    # read the profile, and set it if it exists
+    contents <- readLines(path, warn = FALSE)
+    if (length(contents) == 0L)
+      return(NULL)
+  
+    # set RENV_PROFILE
+    profile <- contents[[1L]]
+    if (!profile %in% c("", "default"))
+      Sys.setenv(RENV_PROFILE = profile)
+  
+    profile
+  
+  }
+  
+  renv_bootstrap_profile_prefix <- function() {
+    profile <- renv_bootstrap_profile_get()
+    if (!is.null(profile))
+      return(file.path("profiles", profile, "renv"))
+  }
+  
+  renv_bootstrap_profile_get <- function() {
+    profile <- Sys.getenv("RENV_PROFILE", unset = "")
+    renv_bootstrap_profile_normalize(profile)
+  }
+  
+  renv_bootstrap_profile_set <- function(profile) {
+    profile <- renv_bootstrap_profile_normalize(profile)
+    if (is.null(profile))
+      Sys.unsetenv("RENV_PROFILE")
+    else
+      Sys.setenv(RENV_PROFILE = profile)
+  }
+  
+  renv_bootstrap_profile_normalize <- function(profile) {
+  
+    if (is.null(profile) || profile %in% c("", "default"))
+      return(NULL)
+  
+    profile
+  
+  }
+  
+  renv_bootstrap_path_absolute <- function(path) {
+  
+    substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
+      substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
+      substr(path, 2L, 3L) %in% c(":/", ":\\")
+    )
+  
+  }
+  
+  renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
+    renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
+    root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
+    prefix <- if (profile) renv_bootstrap_profile_prefix()
+    components <- c(root, renv, prefix, ...)
+    paste(components, collapse = "/")
+  }
+  
+  renv_bootstrap_project_type <- function(path) {
+  
+    descpath <- file.path(path, "DESCRIPTION")
+    if (!file.exists(descpath))
+      return("unknown")
+  
+    desc <- tryCatch(
+      read.dcf(descpath, all = TRUE),
+      error = identity
+    )
+  
+    if (inherits(desc, "error"))
+      return("unknown")
+  
+    type <- desc$Type
+    if (!is.null(type))
+      return(tolower(type))
+  
+    package <- desc$Package
+    if (!is.null(package))
+      return("package")
+  
+    "unknown"
+  
+  }
+  
+  renv_bootstrap_user_dir <- function() {
+    dir <- renv_bootstrap_user_dir_impl()
+    path.expand(chartr("\\", "/", dir))
+  }
+  
+  renv_bootstrap_user_dir_impl <- function() {
+  
+    # use local override if set
+    override <- getOption("renv.userdir.override")
+    if (!is.null(override))
+      return(override)
+  
+    # use R_user_dir if available
+    tools <- asNamespace("tools")
+    if (is.function(tools$R_user_dir))
+      return(tools$R_user_dir("renv", "cache"))
+  
+    # try using our own backfill for older versions of R
+    envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
+    for (envvar in envvars) {
+      root <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(root))
+        return(file.path(root, "R/renv"))
+    }
+  
+    # use platform-specific default fallbacks
+    if (Sys.info()[["sysname"]] == "Windows")
+      file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
+    else if (Sys.info()[["sysname"]] == "Darwin")
+      "~/Library/Caches/org.R-project.R/R/renv"
+    else
+      "~/.cache/R/renv"
+  
+  }
+  
+  renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+    sha <- sha %||% attr(version, "sha", exact = TRUE)
+    parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+    paste(parts, collapse = "")
+  }
+  
+  renv_bootstrap_exec <- function(project, libpath, version) {
+    if (!renv_bootstrap_load(project, libpath, version))
+      renv_bootstrap_run(version, libpath)
+  }
+  
+  renv_bootstrap_run <- function(version, libpath) {
+  
+    # perform bootstrap
+    bootstrap(version, libpath)
+  
+    # exit early if we're just testing bootstrap
+    if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+      return(TRUE)
+  
+    # try again to load
+    if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+      return(renv::load(project = getwd()))
+    }
+  
+    # failed to download or load renv; warn the user
+    msg <- c(
+      "Failed to find an renv installation: the project will not be loaded.",
+      "Use `renv::activate()` to re-initialize the project."
+    )
+  
+    warning(paste(msg, collapse = "\n"), call. = FALSE)
+  
+  }
+  
+  renv_json_read <- function(file = NULL, text = NULL) {
+  
+    jlerr <- NULL
+  
+    # if jsonlite is loaded, use that instead
+    if ("jsonlite" %in% loadedNamespaces()) {
+  
+      json <- catch(renv_json_read_jsonlite(file, text))
+      if (!inherits(json, "error"))
+        return(json)
+  
+      jlerr <- json
+  
+    }
+  
+    # otherwise, fall back to the default JSON reader
+    json <- catch(renv_json_read_default(file, text))
+    if (!inherits(json, "error"))
+      return(json)
+  
+    # report an error
+    if (!is.null(jlerr))
+      stop(jlerr)
+    else
+      stop(json)
+  
+  }
+  
+  renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+    text <- paste(text %||% read(file), collapse = "\n")
+    jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+  }
+  
+  renv_json_read_default <- function(file = NULL, text = NULL) {
+  
+    # find strings in the JSON
+    text <- paste(text %||% read(file), collapse = "\n")
+    pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
+    locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
+  
+    # if any are found, replace them with placeholders
+    replaced <- text
+    strings <- character()
+    replacements <- character()
+  
+    if (!identical(c(locs), -1L)) {
+  
+      # get the string values
+      starts <- locs
+      ends <- locs + attr(locs, "match.length") - 1L
+      strings <- substring(text, starts, ends)
+  
+      # only keep those requiring escaping
+      strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
+  
+      # compute replacements
+      replacements <- sprintf('"\032%i\032"', seq_along(strings))
+  
+      # replace the strings
+      mapply(function(string, replacement) {
+        replaced <<- sub(string, replacement, replaced, fixed = TRUE)
+      }, strings, replacements)
+  
+    }
+  
+    # transform the JSON into something the R parser understands
+    transformed <- replaced
+    transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
+    transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
+    transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
+    transformed <- gsub(":", "=", transformed, fixed = TRUE)
+    text <- paste(transformed, collapse = "\n")
+  
+    # parse it
+    json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
+  
+    # construct map between source strings, replaced strings
+    map <- as.character(parse(text = strings))
+    names(map) <- as.character(parse(text = replacements))
+  
+    # convert to list
+    map <- as.list(map)
+  
+    # remap strings in object
+    remapped <- renv_json_remap(json, map)
+  
+    # evaluate
+    eval(remapped, envir = baseenv())
+  
+  }
+  
+  renv_json_remap <- function(json, map) {
+  
+    # fix names
+    if (!is.null(names(json))) {
+      lhs <- match(names(json), names(map), nomatch = 0L)
+      rhs <- match(names(map), names(json), nomatch = 0L)
+      names(json)[rhs] <- map[lhs]
+    }
+  
+    # fix values
+    if (is.character(json))
+      return(map[[json]] %||% json)
+  
+    # handle true, false, null
+    if (is.name(json)) {
+      text <- as.character(json)
+      if (text == "true")
+        return(TRUE)
+      else if (text == "false")
+        return(FALSE)
+      else if (text == "null")
+        return(NULL)
+    }
+  
+    # recurse
+    if (is.recursive(json)) {
+      for (i in seq_along(json)) {
+        json[i] <- list(renv_json_remap(json[[i]], map))
+      }
+    }
+  
+    json
+  
+  }
+
+  # load the renv profile, if any
+  renv_bootstrap_profile_load(project)
+
+  # construct path to library root
+  root <- renv_bootstrap_library_root(project)
+
+  # construct library prefix for platform
+  prefix <- renv_bootstrap_platform_prefix()
+
+  # construct full libpath
+  libpath <- file.path(root, prefix)
+
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
+
+  invisible()
+
+})
diff --git a/renv/settings.dcf b/renv/settings.dcf
new file mode 100644
index 0000000..169d82f
--- /dev/null
+++ b/renv/settings.dcf
@@ -0,0 +1,10 @@
+bioconductor.version:
+external.libraries:
+ignored.packages:
+package.dependency.fields: Imports, Depends, LinkingTo
+r.version:
+snapshot.type: implicit
+use.cache: TRUE
+vcs.ignore.cellar: TRUE
+vcs.ignore.library: TRUE
+vcs.ignore.local: TRUE
diff --git a/renv/settings.json b/renv/settings.json
new file mode 100644
index 0000000..2472d63
--- /dev/null
+++ b/renv/settings.json
@@ -0,0 +1,19 @@
+{
+  "bioconductor.version": [],
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": [],
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}
diff --git a/reports/.gitkeep b/reports/.gitkeep
new file mode 100644
index 0000000..e69de29