build package website using pkgdown

Author: bastistician

.Rbuildignore

@@ -4,6 +4,9 @@
 
 ^data-raw$
 
+^docs$
+^_pkgdown.yml$
+
 Makefile$
 
 ^vignettes/.+_cache$

DESCRIPTION

@@ -16,7 +16,7 @@ Description: The Handbook of Infectious Disease Data Analysis ("HIDDA")
     'surveillance' and 'prophet',
     and an age-stratified analysis of norovirus counts in Berlin
     using the multivariate time-series model "hhh4" from 'surveillance'.
-URL: https://github.com/HIDDA/forecasting
+URL: https://HIDDA.github.io/forecasting, https://github.com/HIDDA/forecasting
 BugReports: https://github.com/HIDDA/forecasting/issues
 Depends: R (>= 3.2.0)
 Imports: grDevices, graphics, stats, utils, zoo, scoringRules (>= 0.9.4)

Makefile

@@ -1,7 +1,7 @@
 ################################################################################
 ## Useful rules to build, check and install an R source package
 ##
-## Copyright (C) 2012,2014-2017 Sebastian Meyer
+## Copyright (C) 2012,2014-2018 Sebastian Meyer
 ################################################################################
 
 ## define variable for R to enable 'make check R=R-devel'
@@ -43,5 +43,9 @@ check: build
 	_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=2 $R CMD check --as-cran --timings ${PKG}_${VERSION}.tar.gz
 	@$(check-report-warnings-in-examples)
 
+## pkgdown documentation
+docs:
+	$R --no-restore --no-save --no-init-file --slave -e "pkgdown::build_site()"
+
 ## almost all targets are "phony"
-.PHONY: document extra_vignettes build install check
+.PHONY: document extra_vignettes build install check docs

README.md

@@ -7,35 +7,37 @@ by Leonhard Held and Sebastian Meyer.
 The R package **HIDDA.forecasting** provides the data and code to
 reproduce results from the two applications presented in that chapter:
 
-1. Univariate forecasting of Swiss ILI counts,
-   available as `data("CHILI", package = "HIDDA.forecasting")`, using
+1. Univariate forecasting of
+   [Swiss ILI counts](https://HIDDA.github.io/forecasting/articles/CHILI.html)
+   using
 
     * [**forecast**](https://CRAN.R-project.org/package=forecast)`::arima()`
+      --> `vignette("CHILI_arima")`
 
     * [**glarma**](https://CRAN.R-project.org/package=glarma)`::glarma()`
+      --> `vignette("CHILI_glarma")`
 
     * [**surveillance**](https://CRAN.R-project.org/package=surveillance)`::hhh4()`
+      --> `vignette("CHILI_hhh4")`
 
     * [**prophet**](https://CRAN.R-project.org/package=prophet)`::prophet()`
+      --> `vignette("CHILI_prophet")`
 
-2. Age-stratified analysis of norovirus counts in Berlin, available from
-   [**hhh4contacts**](https://CRAN.R-project.org/package=hhh4contacts)`::noroBE()`,
-   using the multivariate time-series model `hhh4` from **surveillance**
+    * experimental [**kcde**](https://github.com/reichlab/kcde)`::kcde()`
+      --> `vignette("CHILI_kcde")`
 
+    * and [**MASS**](https://CRAN.R-project.org/package=MASS)`::fitdistr()` for naive reference forecasts
+      --> `vignette("CHILI_naive")`
 
-## Documentation
-
-The package contains several vignettes which document each of the methods
-applied in the book chapter. An online version of the documentation is
-available at
-
-<!-- TODO: pkgdown -->
+2. Age-stratified analysis of norovirus counts in Berlin using "hhh4"
+   --> `vignette("BNV")`
 
 
 ## Installation
 
-To compile the vignettes on your machine, you can install
-**HIDDA.forecasting** and the other required packages with
+To compile the [vignettes](https://HIDDA.github.io/forecasting/articles/)
+on your machine, you can install **HIDDA.forecasting** and the other
+required packages with
 
 ```r
 # install.packages("remotes")

_pkgdown.yml

@@ -0,0 +1,49 @@
+navbar:
+  components:
+    articles:
+      text: Vignettes
+      menu: ~
+      href: articles/index.html
+
+reference:
+- title: Datasets
+  desc: >
+    The R package **HIDDA.forecasting** provides the Swiss ILI data (`CHILI`).
+    The age-stratified norovirus time series data analyzed in `vignette("BNV")`
+    are available from the [**hhh4contacts**](https://CRAN.R-project.org/package=hhh4contacts) package.
+  contents:
+  - CHILI
+- title: Fanplot with scores
+  contents:
+  - osaplot
+- title: Simulation-based forecast distributions
+  contents:
+  - dhhh4sims
+  - logs_hhh4sims
+  - dnbmix
+  - logs_nbmix
+- title: Wrapper functions for scoringRules
+  contents:
+  - scores_lnorm
+  - scores_sample
+- title: Auxiliary functions for forecast::arima
+  contents:
+  - update.Arima
+
+articles:
+- title: Univariate Forecasting
+  contents:
+  - CHILI
+  - CHILI_arima
+  - CHILI_glarma
+  - CHILI_hhh4
+  - CHILI_naive
+  - CHILI_prophet
+- title: Multivariate Forecasting
+  contents:
+  - BNV
+- title: Experimental extras
+  contents:
+  - extra/CHILI_kcde
+  - extra/CHILI_tscount
+  - extra/BNV_addon