add Eyam data to package, cache vignette intermediates

DESCRIPTION

@@ -12,13 +12,18 @@ Maintainer: Lam S.T. Ho <[email protected]>
 Description: A package for exact inference of multivariate birth-death
     processes.
 License: Apache License 2.0
-Depends:
+Depends: 
     R (>= 3.1.0)
-Imports:
+Imports: 
     Rcpp (>= 0.11.2),
     BH,
     RcppParallel
 LinkingTo: Rcpp, BH, RcppParallel
-Suggests:
-    testthat
-RoxygenNote: 5.0.0
+Suggests: 
+    testthat,
+    knitr,
+    rmarkdown,
+    matrixStats,
+    plotrix
+RoxygenNote: 5.0.1
+VignetteBuilder: knitr

R/Eyam.R

@@ -0,0 +1,21 @@
+#' Eyam plague.
+#' 
+#' A dataset containing the number of susceptible, infectious and removed
+#' individuals during the Eyam plague from June 18 to October 20, 1666.
+#' 
+#' @name Eyam
+#' 
+#' @docType data
+#' 
+#' @usage data(Eyam)
+#'
+#' @format A data frame with 8 rows and 4 variables:
+#' \describe{
+#'  \item{time}{Months past June 18 1666}
+#'  \item{S}{Susceptible}
+#'  \item{I}{Infectious}
+#'  \item{R}{Removed} 
+#' }
+#'
+#' @references Ragget G (1982). A stochastic model of the Eyam plague. Journal of Applied Statistics 9, 212-226.
+NULL

vignettes/SIRtrans.Rnw

@@ -38,12 +38,13 @@
 
 
 \begin{document}
+\SweaveOpts{concordance=TRUE}
 %\VignetteIndexEntry{bdsem_tutorial}
 %\VignetteEngine{knitr::knitr}
 <<setup, include=FALSE, cache=FALSE>>=
 library(knitr)
 # set global chunk options
-opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold')
+opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold', cache=TRUE)
 options(formatR.arrow=TRUE,width=90,tidy=FALSE)
 @