more pkgdown stuff [skip ci]

mac-theobio · May 27, 2021 · 9e80643 · 9e80643
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -8,7 +8,9 @@ Authors@R: c(person("Ben","Bolker",email="[email protected]",role=c("aut","cre"
 		   person("Mike Li",role="aut"),
 		   person("Jonathan Dushoff",role="aut"),
 		   person("Zach Levine", role="ctb"),
-		   person("Matthew So", role="ctb"))
+		   person("Matthew So", role="ctb"),
+		   person("Irena Papst", role="ctb")
+		   )
 Depends: R (>= 3.5.0)
 Imports: 
 	lattice, 

diff --git a/Makefile b/Makefile
@@ -148,6 +148,9 @@ pkgcheck:
 clean:
 	find . \( -name "\.#*" -o -name "*~" -o -name ".Rhistory" \) -exec rm {} \;
 
+site-update-lazy:
+	echo "pkgdown::build_site(lazy=TRUE)" | $(R) --slave
+
 site-update:
 	echo "pkgdown::build_site()" | $(R) --slave
 

diff --git a/README.md b/README.md
@@ -4,35 +4,41 @@
 [![R-CMD-check](https://github.com/bbolker/McMasterPandemic/workflows/R-CMD-check/badge.svg)](https://github.com/bbolker/McMasterPandemic/actions)
 <!-- badges: end -->
 
-Compartmental epidemic models for forecasting and analysis of infectious disease pandemics: contributions from Ben Bolker, Jonathan Dushoff, David Earn, Morgan Kain, Michael Li, Irena Papst (in alphabetical order). Feedback is welcome at the [issues list](https://github.com/bbolker/McMasterPandemic/issues), or e-mail us.
+Compartmental epidemic models for forecasting and analysis of infectious disease pandemics. Feedback is welcome at the [issues list](https://github.com/bbolker/McMasterPandemic/issues).
 
 ### Installation
 
 The repository contains an R package and various workflows/analyses. You can fork/clone the repository (from [here](https://github.com/bbolker/McMasterPandemic)) and install locally or use `remotes::install_github("bbolker/McMasterPandemic")` to install the package. You will need to first install the developer version of `bbmle` (`remotes::install_github("bbolker/bbmle")`) before installing `McMasterPandemic`.
 
+### Documentation 
+
+See the accompanying [pkgdown site](https://bbolker.github.io/McMasterPandemic).
+
+- Functions are under the `Reference` tab.
+- Vignettes (under construction!) are under `Articles`
+
 ### For developers
 
 * to re-install the package, including re-building and incorporating vignettes, use `make build`
-* If you modify function arguments, you should change the roxygen documentation accordingly. If you change the roxygen documentation, please use `make doc-update` to update the `.Rd` files.
-* **please test/check the package periodically** as you go (use `make pkgcheck` and `make pkgtest` from the shell or `devtools::check()` and `devtools::test()` from within R). (Tests are also run on [GitHub Actions](https://github.com/bbolker/McMasterPandemic/actions); if you want to skip CI testing, e.g. for a trivial commit, put `[skip ci]` somewhere in your commit message.) Please don't make a habit of pushing without testing.
-* Code that is used in the refactoring process should go in the top-level refactor folder. 
+* re-build the `pkgdown` site with `make site-update-lazy` (to rebuild just changed files) or `make site-update` (to be thorough) (or `pkgdown::build_site()`)
+* it's OK to push *small* changes to the master branch; use your own branch + pull request for anything non-trivial
+* If you modify function arguments, please update the roxygen documentation and use `make doc-update` (or `devtools::document`) to update the `.Rd` files.
+* **Check the package periodically** as you go (use `make pkgcheck` and `make pkgtest` from the shell or `devtools::check()` and `devtools::test()` from within R). (Tests are also run on [GitHub Actions](https://github.com/bbolker/McMasterPandemic/actions); if you want to skip CI testing, e.g. for a trivial commit, put `[skip ci]` somewhere in your commit message.) Don't push without checking.
+* Code that is used in the refactoring process should go in the top-level `refactor` folder. 
 * Slow tests are skipped by default; this process is controlled by the presence of a `MACPAN_TEST_LEVEL` environment (shell) variable. Many of the test files contain this code:
 ```r
 testLevel <- if (nzchar(s <- Sys.getenv("MACPAN_TEST_LEVEL"))) as.numeric(s) else 1
 ```
 which sets `testLevel` to a default value of 1 unless the environment variable is found. You can set this environment variable outside of your R session (e.g. via `export MACPAN_TEST_LEVEL=2` in  a bash shell), or via `Sys.setenv(MACPAN_TEST_LEVEL=2)` from within R. In principle this mechanism allows for a hierarchy of slowness; at present only 1 and >1 are distinguished.
 
-### Documentation 
-
-The [documentation](https://bbolker.github.io/McMasterPandemic) is a little bit scattered right now, working on cleaning it up and making it easily accessible.
+## Obsolete documentation
 
-In addition to the standard short descriptions of the functions (`help(package="McMasterPandemic")`), stuff can be found: 
+(Keeping links here for now)
 
 * in the vignettes (look at the source code in the [vignettes] directory or `vignette(<title>, package="McMasterPandemic")`)
     * `getting_started`
 	* `model`: design decisions and information for developers
 	* `calibration` (**very out of date**)
-	* `farr`: stuff on Farr's law and phenomenological curve-fitting (**very incomplete and likely to remain so for now**)
 	* `testing_flow`: incorporating testing dynamics (**ditto**)
 * `McMasterReport.Rnw`: this is a more or less up-to-date description of calibration to Ontario data
 * `ontario_calibration_report.html`: more technical and less up-to-date than the preceding document

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/ChangeLog.html b/docs/ChangeLog.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/TODO.html b/docs/TODO.html
diff --git a/docs/articles/calibration.html b/docs/articles/calibration.html
diff --git a/docs/articles/calibration_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/calibration_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo ([email protected]) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/model.html b/docs/articles/model.html
diff --git a/docs/articles/new_getting_started.html b/docs/articles/new_getting_started.html
diff --git a/docs/articles/testing_flow.html b/docs/articles/testing_flow.html
diff --git a/docs/authors.html b/docs/authors.html