rebuild website

.Rbuildignore

@@ -15,3 +15,4 @@
 ^_pkgdown\.yml$
 ^\.github$
 ^CRAN-SUBMISSION$
+.nojekyll

.gitignore

@@ -5,3 +5,5 @@
 DSAIDE.Rcheck/
 DSAIDE*.tar.gz
 DSAIDE*.tgz
+/doc/
+/Meta/

README.md

@@ -0,0 +1,104 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# DSAIDE <img src="man/figures/logo.png" align="right" alt="" width="120" />
+
+<!-- badges: start -->
+
+[![CRAN
+status](https://www.r-pkg.org/badges/version/DSAIDE)](https://cran.r-project.org/package=DSAIDE)
+[![CRAN
+checks](https://badges.cranchecks.info/worst/DSAIDE.svg)](https://cran.r-project.org/web/checks/check_results_DSAIDE.html)
+[![R-CMD-check](https://github.com/ahgroup/DSAIDE/workflows/R-CMD-check/badge.svg)](https://github.com/ahgroup/DSAIDE/actions)
+[![Coverage
+status](https://codecov.io/gh/ahgroup/DSAIDE/branch/master/graph/badge.svg?token=OGO3sVEcPD)](https://codecov.io/gh/ahgroup/DSAIDE)
+[![test-coverage](https://github.com/ahgroup/DSAIDE/workflows/test-coverage/badge.svg)](https://github.com/ahgroup/DSAIDE/actions)
+[![metacran monthly
+downloads](https://cranlogs.r-pkg.org/badges/DSAIDE)](https://cran.r-project.org/package=DSAIDE)
+[![metacran
+downloads](https://cranlogs.r-pkg.org/badges/grand-total/DSAIDE?color=ff69b4)](https://cran.r-project.org/package=DSAIDE)
+<!-- badges: end -->
+
+**DSAIDE - Dynamical Systems Approach to Infectious Disease Epidemiology
+(Ecology/Evolution).**
+
+## Description
+
+DSAIDE is an R package containing a set of simulation models (apps) that
+teach infectious disease epidemiology (ecology/evolution) from a
+dynamical systems modeling perspective.
+
+All models can be explored through a graphical user interface, no
+reading or writing code is required. Each app comes with documentation
+and instructions which teach important concepts of infectious disease
+epidemiology (ecology/evolution) and show how to use simulation models
+to understand such concepts.
+
+It is also possible to go beyond the graphical interface and directly
+access and modify all simulations to adapt them to your needs.
+
+## Getting Started
+
+While the main idea is to install the R package and use it locally, if
+you want to get a quick glimpse at the package to see if this package is
+for you, you can give it [a quick try online, without having to install
+it](https://shiny.ovpr.uga.edu/DSAIDE/). If you like what you see, you
+can install it and start using it with these 3 commands:
+
+    install.packages('DSAIDE')
+    library('DSAIDE')
+    dsaidemenu()
+
+For an introduction to the package, step-by-step instructions on getting
+started, and more information on the different ways you can use the
+package [see the *Get Started* tutorial
+(vignette)](https://ahgroup.github.io/DSAIDE/articles/DSAIDE.html).
+
+## Further information
+
+- The [package tutorial
+  (vignette)](https://ahgroup.github.io/DSAIDE/articles/DSAIDE.html)
+  contains detailed instructions on the different ways the package can
+  be used.
+- [I published a paper describing the
+  package](https://doi.org/10.1371/journal.pcbi.1005642). The package
+  has since been updated and changed, but the paper still describes the
+  overall idea and context well.  
+- I regularly teach two courses related to infectious diseases and
+  modeling. All materials for those courses [are freely available
+  online](https://andreashandel.github.io/IDEMAcourse/).
+- As part of these courses, [I wrote a freely available online
+  textbook](https://andreashandel.github.io/IDEMAbook/). It is not (and
+  probably never will be) finished, some chapters are fairly empty, but
+  some topics are covered in enough detail that I use it for teaching.
+- I have full solutions and quiz sheets for all of the **What to do**
+  tasks for each app. If you are an instructor using this package as
+  part of a class, email me if you are interested in having access to
+  the materials.
+- Contributions to the package are very welcome! If you want to take a
+  deeper look at the package, see [this Markdown
+  file](https://github.com/ahgroup/DSAIDE/blob/master/auxiliary/docsfordevelopers/documentation.md)
+  which provides further information on the details of the package
+  structure. I’d be excited to receive any contributions from
+  individuals who want to help improve the package. If you plan to
+  develop new apps, or make other substantial contributions, it might be
+  best to get in touch with me first.
+- A companion package to this one, called *Dynamical Systems Approaches
+  for Immune Response Modeling (DSAIRM)*, focuses on models for
+  analyzing with-host infection dynamics. It has the same structure as
+  DSAIDE. [See the DSAIRM site for more
+  information.](https://ahgroup.github.io/DSAIRM/)
+
+## Citation and Contributors
+
+If the package does in any way help you with your work such that it
+warrants citing it, please cite [this publication in PLoS Computational
+Biology](https://doi.org/10.1371/journal.pcbi.1005642).
+
+This R package is developed and maintained by [Andreas
+Handel](https://www.andreashandel.com/). A full list of contributors and
+a Bibtex entry for the citation [can be found
+here](https://ahgroup.github.io/DSAIDE/authors.html).
+
+This project was/is partially supported by NIH grants U19AI117891,
+U01AI150747, R01AI170116, R25AI147391 and R25GM089694.

doc/DSAIDE.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Andreas Handel" />
 
-<meta name="date" content="2023-08-24" />
+<meta name="date" content="2023-09-06" />
 
 <title>DSAIDE Package Tutorial</title>
 
@@ -363,7 +363,7 @@
 <h1 class="title toc-ignore">DSAIDE Package Tutorial</h1>
 <h4 class="author"><a href="http://handelgroup.uga.edu">Andreas
 Handel</a></h4>
-<h4 class="date">2023-08-24</h4>
+<h4 class="date">2023-09-06</h4>
 
 
 

docs/pkgdown.yml

@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   DSAIDE: DSAIDE.html
-last_built: 2023-08-24T13:09Z
+last_built: 2023-09-06T17:16Z
 urls:
   reference: https://ahgroup.github.io/DSAIDE/reference
   article: https://ahgroup.github.io/DSAIDE/articles