fix: update tooling book to epiprocess==0.9.0 and others (#12)

* bump epiprocess, epipredict, epidatr versions, update due to breaking changes
* bump versions on all dependencies, update renv.lock.
* replace both `pivot_quantiles` and `unnest` `pivot_wider` patterns to
  `pivot_quantiles_wider`
* fix some `epi_recipe` and `frosting` printing that doesn't play well with
  knitr now.
* update a few plots
* update for epiprocess R6 refactor
* remove references to R6 and mutation
* fix the authors section of DESCRIPTION
* integrate Rprofile with user Rprofile
* add a README file
* fix broken formatting in packages.bib
* get missing data for sliding-forecasters.qmd online instead of local files

Co-authored-by: Daniel McDonald <[email protected]>
Co-authored-by: Dmitry Shemetov <[email protected]>

Author: 3 people

.Rprofile

@@ -1 +1,7 @@
 source("renv/activate.R")
+
+# Check if user .Rprofile exists
+if (file.exists("~/.Rprofile")) {
+  # Source user .Rprofile
+  source("~/.Rprofile")
+}

DESCRIPTION

@@ -2,11 +2,12 @@ Package: delphitoolingbook
 Title: Delphi Tooling
 Version: 0.0.0.9999
 Authors@R: c(
-    person("Daniel", "McDonald", "J.", "[email protected]", role = c("cre", "aut"),
-    person("Logan", "Brooks", role = c("cre","aut"),
-    person("Rachel", "Lobay", role = "aut"))
-    person("Ryan", "Tibshirani", "J.", "[email protected]", role = "aut"),
-Description: 
+    person("Daniel", "McDonald", "J.", "[email protected]", role = c("cre", "aut")),
+    person("Logan", "Brooks", role = c("cre","aut")),
+    person("Rachel", "Lobay", role = "aut"),
+    person("Ryan", "Tibshirani", "J.", "[email protected]", role = "aut")
+    )
+Description:
   | This book is a longform introduction to analysing and forecasting epidemiological data.
 License: MIT + file LICENSE
 Imports:

README.md

@@ -42,3 +42,14 @@ options(
 
 ggplot2::theme_set(ggplot2::theme_bw())
 
+# Workaround for interleaved `cat`s and `message`s (from `cli`) getting
+# intercepted and not combined properly by `collapse: true`:
+with_messages_cat_to_stdout <- function(code) {
+  withCallingHandlers(
+    code,
+    message = function(m) {
+      cat(m$message)
+      tryInvokeRestart("muffleMessage")
+    }
+  )
+}