adding doc

R/get_R.R

@@ -29,11 +29,21 @@
 #' @return A list with the \code{earlyR} class, containing the following
 #'     components:
 #' \itemize{
-#' \item
+#' \item \code{$incidence}: the input incidence, in its original format
 #' 
-#' \item
+#' \item \code{$R_grid}: the grid of R values for which the likelihood has been
+#' computed.
 #' 
-#' \item
+#' \item \code{$R_like}: the values of likelihood corresponding to the
+#' \code{$R_grid}
+#' 
+#' \item \code{$R_ml}: the maximum likelihood estimate of R
+#' 
+#' \item \code{$dates}: the dates for which infectiousness has been computed
+#' 
+#' \item \code{$lambdas}: the corresponding values of force of infection
+#' 
+#' \item \code{$si}: the serial interval, stored as a \code{distcrete} object
 #' 
 #' }
 #' 

tests/testthat/test_get_R.R

@@ -15,6 +15,7 @@ test_that("Test against reference results", {
     R_1 <- get_R(i, si = si)
     expect_equal_to_reference(R_1, file = "rds/R_1.rds")
 
+    expect_identical(i, R_1$incidence)
 })