Merge pull request #5 from EpiForeSITE/EpiEstim

Adds EpiEstim method

DESCRIPTION

@@ -15,5 +15,5 @@ Imports:
     cli,
     tibble
 Suggests: 
-    rtestim, tinytest, EpiNow2
+    rtestim, tinytest, EpiNow2, EpiEstim
 Remotes: dajmcdon/rtestim

NAMESPACE

@@ -3,7 +3,9 @@
 S3method(summarize_rtestimate,cv_poisson_rt)
 S3method(summarize_rtestimate,default)
 S3method(summarize_rtestimate,epinow)
+S3method(summarize_rtestimate,estimate_R)
 S3method(summarize_rtestimate,poisson_rt)
+export(new_summarize)
 export(summarize_rtestimate)
 importFrom(cli,cli_abort)
 importFrom(stats,median)

R/summarize_rtestimate.R

@@ -1,3 +1,52 @@
+
+#' Create a new summary object
+#' 
+#' Creates a new summary object for the `summrt` package while validating the input.
+#' 
+#' @param date Integer vector. vector of index dates.
+#' @param median Double vector. vector of median values.
+#' @param lb Double vector. vector of lower bounds.
+#' @param ub Double vector. vector of upper bounds.
+#' @param package String. Name of the package.
+#' @export 
+#' @return A list of class `summrt_summary`. with the following components:
+#' - `date`: Integer vector. vector of index dates.
+#' - `median`: Double vector. vector of median values.
+#' - `lb`: Double vector. vector of lower bounds.
+#' - `ub`: Double vector. vector of upper bounds.
+#' - `package`: String. Name of the package.
+new_summarize <- function(
+  date, median, lb, ub, package
+) {
+
+  # Asserting the types
+  checkmate::assert_integer(date)
+  checkmate::assert_double(median)
+  checkmate::assert_double(lb)
+  checkmate::assert_double(up)
+  checkmate::assert_string(package)
+
+  # Checking the length
+  len_date <- length(date)
+  len_median <- length(median)
+  len_lb <- length(lb)
+  len_up <- length(up)
+  if (len_date != len_median || len_date != len_lb || len_date != len_up) {
+    stop("The length of the date, median, lb, and ub should be the same.")
+  }
+
+  structure(
+    list(
+      date = date,
+      median = median,
+      lb = lb,
+      ub = ub,
+      package = package
+    ),
+    class = "summrt_summary"
+  )
+}
+
 #' Extract Rt estimation from a model fit
 #' @param x Object to extract Rt from.
 #' @param ... Additional arguments passed to methods.
@@ -63,10 +112,28 @@ summarize_rtestimate.poisson_rt <- function(x, level = 0.95, lambda = NULL, ...)
 #' @export
 summarize_rtestimate.epinow <- function(x, level = 0.95, ...) {
 
-  if (!requireNamespace("epinow2", quietly = TRUE)) {
-    cli::cli_abort("You must install the {.pkg epinow2} package for this functionality.")
+  if (!requireNamespace("EpiNow2", quietly = TRUE)) {
+    cli::cli_abort("You must install the {.pkg EpiNow2} package for this functionality.")
   }
   checkmate::assert_number(level, lower = 0, upper = 1)
 
   # res <- x$estimates$summarized |> dplyr::select()
 }
+
+#' @export 
+#' @details The `estimate_R` method is for the `EpiEstim` package.
+#' @rdname summarize_rtestimate
+summarize_rtestimate.estimate_R <- function(x, ...) {
+  if (!requireNamespace("EpiEstim", quietly = TRUE)) {
+    cli::cli_abort("You must install the {.pkg EpiEstim} package for this functionality.")
+  }
+  checkmate::assert_number(level, lower = 0, upper = 1)
+
+  new_summarize(
+    date    = x$R$t_end,
+    median  = x$R$`Median(R)`,
+    lb      = x$R$`Quantile.0.025(R)`,
+    ub      = x$R$`Quantile.0.975(R)`,
+    package = "EpiEstim"
+  )
+}