making sure the right incidence is attached to the object

R/get_R.R

@@ -26,6 +26,17 @@
 #'     \code{as.data.frame} to double-check that the epicurve includes the last
 #'     'zeros'.
 #'
+#' @return A list with the \code{earlyR} class, containing the following
+#'     components:
+#' \itemize{
+#' \item
+#' 
+#' \item
+#' 
+#' \item
+#' 
+#' }
+#' 
 #' @examples
 #'
 #' if (require(incidence)) {
@@ -35,7 +46,7 @@
 #'  x
 #'  as.data.frame(x)
 #'  plot(x)
-#'  res <- get_R(x)
+#'  res <- get_R(x, disease = "ebola")
 #'  res
 #'  plot(res)
 #'  plot(res, "lambdas")
@@ -186,7 +197,8 @@ get_R.integer <- function(x, disease = NULL, si = NULL,
 #' @aliases get_R.numeric
 
 get_R.numeric <- function(x, ...) {
-  get_R(as.integer(x), ...)
+    out <- get_R(as.integer(x), ...)
+    out$incidence <- x
 }
 
 
@@ -219,5 +231,6 @@ get_R.incidence <- function(x, ...) {
     out$dates <- min(x$dates) - 1 + out$dates
   }
 
+  out$incidence <- x
   return(out)
 }

R/plot.earlyR.R

@@ -22,7 +22,22 @@
 #'
 #' @param ... Further arguments to be passed to other methods (not used).
 #'
-
+#' if (require(incidence)) {
+#'
+#' ## example: onsets on days 1, 5, 6 and 12; estimation on day 24
+#' onset <- c(1, 5, 6, 12)
+#' x <- incidence(onset, last_date = 24)
+#' x
+#'
+#' res <- get_R(x, disease = "ebola")
+#' res
+#' plot(res)
+#' plot(res, "lambdas")
+#' plot(res, "lambdas", scaling = 5)
+#' points(onset, 1:4, cex = 3, pch = 20)
+#'
+#' }
+#
 plot.earlyR <- function(x, type = c("R", "lambdas"), scale = 1, ...) {
 
   type <- match.arg(type)

R/sample_R.R

@@ -14,7 +14,7 @@
 #' if (require(incidence)) {
 #'  x <- incidence(c(1, 5, 5, 12, 45, 65))
 #'  plot(x)
-#'  res <- get_R(x)
+#'  res <- get_R(x, disease = "ebola")
 #'  res
 #'  plot(res)
 #'