Merge pull request #5 from cmu-delphi/lcb/installation-updates

Update installation instructions, dependency lists

Author: brookslogan

DESCRIPTION

@@ -10,13 +10,18 @@ Description:
   | This book is a longform introduction to analysing and forecasting epidemiological data.
 License: MIT + file LICENSE
 Imports:
+    broom,
     epidatr,
     epidatasets,
     epipredict (>=0.0.5),
     epiprocess,
     modeldata,
+    performance,
+    poissonreg,
     outbreaks,
     ranger,
+    RcppRoll,
+    tidymodels,
     see,
     tidyverse,
     xgboost
@@ -25,6 +30,6 @@ Suggests:
     styler
 Remotes:
     cmu-delphi/epidatr,
+    cmu-delphi/epiprocess,
     cmu-delphi/epidatasets,
-    cmu-delphi/epiprocess@dev,
     cmu-delphi/epipredict

_freeze/index/execute-results/html.json

@@ -28,14 +28,23 @@ The following commands install the latest versions of the packages we use in thi
 
 # Install our packages from GitHub:
 pak::pkg_install("cmu-delphi/epidatr")
-pak::pkg_install("cmu-delphi/epiprocess@dev")
+pak::pkg_install("cmu-delphi/epiprocess")
 pak::pkg_install("cmu-delphi/epipredict")
-# Other data processing and example data packages we use in this book:
-pak::pkg_install("tidyverse")
-pak::pkg_install("modeldata")
+pak::pkg_install("cmu-delphi/epidatasets")
 # Other model-fitting packages we use in this book (via epipredict):
+pak::pkg_install("poissonreg")
 pak::pkg_install("ranger")
 pak::pkg_install("xgboost")
+# Other data processing, model evaluation, example data, and other packages we
+# use in this book:
+pak::pkg_install("RcppRoll")
+pak::pkg_install("tidyverse")
+pak::pkg_install("tidymodels")
+pak::pkg_install("broom")
+pak::pkg_install("performance")
+pak::pkg_install("modeldata")
+pak::pkg_install("see")
+pak::pkg_install("sessioninfo")
 ```
 
 Much of the data used for illustration can be loaded directly from [Delphi's Epidata API](https://cmu-delphi.github.io/delphi-epidata/) which is built and maintained by the Carnegie Mellon University [Delphi research group](https://delphi.cmu.edu/). We have tried to provide most of the data used in these examples in a separate package, `{epidatasets}`, but it can also be accessed using `{epidatr}`, an R interface to the API and the successor to [`{covidcast}`](https://cmu-delphi.github.io/covidcast/covidcastR/). These are also available from GitHub:
@@ -70,26 +79,54 @@ options(
 
 The above commands will give you the current versions of the packages used in
 this book. If you're having trouble reproducing some of the results, it may be
-due to package updates that took place after the book was last updated. You can
-try matching the package versions we used to build the book by one of the
-following methods. You may be required to obtain a [GitHub Personal Access
-Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)
-and store it in the environment variable `"GITHUB_PAT"`.
+due to package updates that took place after the book was last updated. To match
+the versions we used to generate this book, you can use the steps below.
 
-#### A: Download and use the `renv.lock`
+#### First: set up and store a GitHub PAT
+
+If you don't already have a GitHub PAT, you can use the following helper functions to create one:
+```{r}
+# Run this once:
+install.packages("usethis")
+usethis::create_github_token(
+           scopes = "public_repo",
+           description = "For public repo access"
+         )
+```
+This will open a web browser window allowing you to describe and customize
+settings of the PAT. Scroll to the bottom and click "Generate
+token".  You'll see a screen that has `ghp_<lots of letters and numbers>` with a green background; you can click the two-squares ("copy") icon to copy this `ghp_......` string to the clipboard.
+
+#### Either A: Download and use the `renv.lock`
 
 ```{r, eval = FALSE}
 # Run this once:
-install.packages("renv")
+install.packages(c("renv", "gitcreds"))
 download.file("https://raw.githubusercontent.com/cmu-delphi/delphi-tooling-book/main/renv.lock", "delphi-tooling-book.renv.lock")
-# Run this every session you'd like to use this set of versions:
+
+# Run this in a fresh session each time you'd like to use this set of versions.
+# Warning: don't save your GitHub PAT in a file you might share with others;
+# look into `gitcreds::gitcreds_set()` or `usethis::edit_r_environ()` instead.
+Sys.setenv("GITHUB_PAT" = "ghp_............")
 renv::use(lockfile = "delphi-tooling-book.renv.lock")
+# If you get 401 errors, you may need to regenerate your GitHub PAT or check if
+# `gitcreds::gitcreds_get()` is detecting an old PAT you have saved somewhere.
 ```
 
-#### B: Download the book and use its `.Rprofile`
+#### Or B: Download the book and use its `.Rprofile`
 
 1. Download the book [here](https://github.com/cmu-delphi/delphi-tooling-book/archive/refs/heads/main.zip) and unzip it.
-2. Launch R inside of the top-level directory; there should be a `.Rprofile` file there that takes care of loading the appropriate versions of all the packages used.
+2. One-time setup: launch R inside the delphi-tooling-book directory (to use its
+   `.Rprofile` file) and run
+
+```{r, eval = FALSE}
+# Warning: don't save your GitHub PAT in a file you might share with others;
+# look into `gitcreds::gitcreds_set()` or `usethis::edit_r_environ()` instead.
+Sys.setenv("GITHUB_PAT" = "ghp_............")
+renv::restore() # downloads the appropriate package versions
+```
+
+3. To use this set of versions: launch R inside the delphi-tooling-book directory.
 
 ### Other issues
 

_freeze/index/figure-html/unnamed-chunk-2-1.svg

@@ -3,16 +3,15 @@ @Manual{R-base
   author = {{R Core Team}},
   organization = {R Foundation for Statistical Computing},
   address = {Vienna, Austria},
-  year = {2023},
+  year = {2022},
   url = {https://www.R-project.org/},
 }
 
 @Manual{R-dplyr,
   title = {dplyr: A Grammar of Data Manipulation},
   author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
   year = {2023},
-  note = {R package version 1.1.2},
-  url = {https://CRAN.R-project.org/package=dplyr},
+  note = {https://dplyr.tidyverse.org},
 }
 
 @Manual{R-epidatasets,
@@ -49,80 +48,66 @@ @Manual{R-epiprocess
 @Manual{R-forcats,
   title = {forcats: Tools for Working with Categorical Variables (Factors)},
   author = {Hadley Wickham},
-  year = {2023},
-  note = {R package version 1.0.0},
+  year = {2021},
+  note = {R package version 0.5.1},
   url = {https://CRAN.R-project.org/package=forcats},
 }
 
 @Manual{R-ggplot2,
   title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
   author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
   year = {2023},
-  note = {R package version 3.4.2},
-  url = {https://CRAN.R-project.org/package=ggplot2},
-}
-
-@Manual{R-lubridate,
-  title = {lubridate: Make Dealing with Dates a Little Easier},
-  author = {Vitalie Spinu and Garrett Grolemund and Hadley Wickham},
-  year = {2023},
-  note = {R package version 1.9.2},
-  url = {https://CRAN.R-project.org/package=lubridate},
+  note = {https://ggplot2.tidyverse.org},
 }
 
 @Manual{R-parsnip,
   title = {parsnip: A Common API to Modeling and Analysis Functions},
   author = {Max Kuhn and Davis Vaughan},
   year = {2023},
-  note = {R package version 1.1.0},
-  url = {https://CRAN.R-project.org/package=parsnip},
+  note = {https://github.com/tidymodels/parsnip},
 }
 
 @Manual{R-purrr,
   title = {purrr: Functional Programming Tools},
   author = {Hadley Wickham and Lionel Henry},
   year = {2023},
-  note = {R package version 1.0.1},
-  url = {https://CRAN.R-project.org/package=purrr},
+  note = {https://purrr.tidyverse.org/},
 }
 
 @Manual{R-readr,
   title = {readr: Read Rectangular Text Data},
   author = {Hadley Wickham and Jim Hester and Jennifer Bryan},
-  year = {2023},
-  note = {R package version 2.1.4},
+  year = {2022},
+  note = {R package version 2.1.2},
   url = {https://CRAN.R-project.org/package=readr},
 }
 
 @Manual{R-stringr,
   title = {stringr: Simple, Consistent Wrappers for Common String Operations},
   author = {Hadley Wickham},
   year = {2022},
-  note = {R package version 1.5.0},
-  url = {https://CRAN.R-project.org/package=stringr},
+  note = {https://stringr.tidyverse.org},
 }
 
 @Manual{R-tibble,
   title = {tibble: Simple Data Frames},
   author = {Kirill Müller and Hadley Wickham},
   year = {2023},
-  note = {R package version 3.2.1},
-  url = {https://CRAN.R-project.org/package=tibble},
+  note = {https://tibble.tidyverse.org/},
 }
 
 @Manual{R-tidyr,
   title = {tidyr: Tidy Messy Data},
   author = {Hadley Wickham and Davis Vaughan and Maximilian Girlich},
   year = {2023},
-  note = {R package version 1.3.0},
-  url = {https://CRAN.R-project.org/package=tidyr},
+  note = {https://tidyr.tidyverse.org},
 }
 
 @Manual{R-tidyverse,
   title = {tidyverse: Easily Install and Load the Tidyverse},
   author = {Hadley Wickham},
-  year = {2023},
-  note = {R package version 2.0.0},
+  year = {2021},
+  note = {R package version 1.3.1},
   url = {https://CRAN.R-project.org/package=tidyverse},
 }
 
@@ -135,17 +120,6 @@ @Book{ggplot22016
   url = {https://ggplot2.tidyverse.org},
 }
 
-@Article{lubridate2011,
-  title = {Dates and Times Made Easy with {lubridate}},
-  author = {Garrett Grolemund and Hadley Wickham},
-  journal = {Journal of Statistical Software},
-  year = {2011},
-  volume = {40},
-  number = {3},
-  pages = {1--25},
-  url = {https://www.jstatsoft.org/v40/i03/},
-}
-
 @Article{tidyverse2019,
   title = {Welcome to the {tidyverse}},
   author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},