Add input validation to estimators

5 files changed, 125 insertions, 2 deletions

diff --git a/R/id.R b/R/id.R
index 5277591..c7c28d3 100644
--- a/R/id.R
+++ b/R/id.R
@@ -41,5 +41,12 @@
 #' # Obtain R0 when the serial distribution has a mean of three days.
 #' id(cases, mu = 3 / 7)
 id <- function(cases, mu) {
+  validate_cases(cases, min_length = 1, min_count = 1)
+  if (!is_real(mu) || mu <= 0) {
+    stop("The serial interval (`mu`) must be a number greater than 0.",
+      call. = FALSE
+    )
+  }
+
   exp(sum((log(cases) * mu) / seq_along(cases)) / length(cases))
 }
diff --git a/R/idea.R b/R/idea.R
index 14ba838..dad4220 100644
--- a/R/idea.R
+++ b/R/idea.R
@@ -42,6 +42,13 @@
 #' # Obtain R0 when the serial distribution has a mean of three days.
 #' idea(cases, mu = 3 / 7)
 idea <- function(cases, mu) {
+  validate_cases(cases, min_length = 2, min_count = 1)
+  if (!is_real(mu) || mu <= 0) {
+    stop("The serial interval (`mu`) must be a number greater than 0.",
+      call. = FALSE
+    )
+  }
+
   s <- seq_along(cases) / mu
 
   x1 <- sum(s)
diff --git a/R/seq_bayes.R b/R/seq_bayes.R
index d486d2b..ccc9a41 100644
--- a/R/seq_bayes.R
+++ b/R/seq_bayes.R
@@ -84,10 +84,31 @@
 #' # Note that the following always holds:
 #' estimate == sum(posterior$supp * posterior$pmf)
 seq_bayes <- function(cases, mu, kappa = 20, post = FALSE) {
+  validate_cases(cases, min_length = 2, min_count = 0)
+  if (!is_real(mu) || mu <= 0) {
+    stop("The serial interval (`mu`) must be a number greater than 0.",
+      call. = FALSE
+    )
+  }
+  if (!is_real(kappa) || kappa < 1) {
+    stop(
+      paste("The largest value of the uniform prior (`kappa`)",
+        "must be a number greater than or equal to 1."
+      ), call. = FALSE
+    )
+  }
+  if (!identical(post, TRUE) && !identical(post, FALSE)) {
+    stop("The posterior flag (`post`) must be set to `TRUE` or `FALSE`.",
+      call. = FALSE
+    )
+  }
+
   if (any(cases == 0)) {
     times <- which(cases > 0)
     if (length(times) < 2) {
-      stop("Vector of case counts must contain at least two positive integers.")
+      stop("Case counts must contain at least two positive integers.",
+        call. = FALSE
+      )
     }
     cases <- cases[times]
   } else {
diff --git a/R/util.R b/R/util.R
new file mode 100644
index 0000000..d8b0b59
--- /dev/null
+++ b/R/util.R
@@ -0,0 +1,55 @@
+#' Case Counts Validation
+#'
+#' This is an internal function called by the estimators. It validates the
+#' supplied case counts by ensuring it is a vector of integers of length at
+#' least `min_length` with entries greater than or equal to `min_count`.
+#' Execution is halted if these requirements are not satisfied.
+#'
+#' @param cases The case counts to be validated.
+#' @param min_length The minimum length of the vector of case counts.
+#' @param min_count The minimum value of the case count vector's entries.
+#'
+#' @noRd
+validate_cases <- function(cases, min_length, min_count) {
+  if (!is.vector(cases) || !is.numeric(cases) || any(floor(cases) != cases)) {
+    stop("Case counts must be a vector of integers.", call. = FALSE)
+  }
+  if (length(cases) < min_length) {
+    stop(paste("Case counts must have at least", min_length, "entries."),
+      call. = FALSE
+    )
+  }
+  if (any(cases < min_count)) {
+    stop(paste0("Case counts cannot be less than ", min_count, "."),
+      call. = FALSE
+    )
+  }
+}
+
+#' Real Number Testing
+#'
+#' This is an internal function which checks whether the given argument is a
+#' real number.
+#'
+#' @param x The argument to test for being a real number.
+#'
+#' @return `TRUE` if the argument is a real number, `FALSE` otherwise.
+#'
+#' @noRd
+is_real <- function(x) {
+  is.vector(x) && is.numeric(x) && length(x) == 1
+}
+
+#' Integer Testing
+#'
+#' This is an internal function which checks whether the given argument is an
+#' integer.
+#'
+#' @param n The argument to test for being an integer.
+#'
+#' @return `TRUE` if the argument is an integer, `FALSE` otherwise.
+#'
+#' @noRd
+is_integer <- function(n) {
+  is_real(n) && floor(n) == n
+}
diff --git a/R/wp.R b/R/wp.R
index 16b4bbb..fbb6ad7 100644
--- a/R/wp.R
+++ b/R/wp.R
@@ -111,12 +111,45 @@
 #' estimate$pmf
 wp <- function(cases, mu = NA, serial = FALSE,
                grid_length = 100, max_shape = 10, max_scale = 10) {
-  if (is.na(mu)) {
+  validate_cases(cases, min_length = 2, min_count = 1)
+  if (!identical(serial, TRUE) && !identical(serial, FALSE)) {
+    stop(
+      paste("The serial distribution flag (`serial`) must be set to",
+        "`TRUE` or `FALSE`."
+      ), call. = FALSE
+    )
+  }
+
+  if (identical(mu, NA)) {
+    if (!is_integer(grid_length) || grid_length < 1) {
+      stop("The grid length must be a positive integer.", call. = FALSE)
+    }
+    if (!is_real(max_shape) || max_shape <= 0) {
+      stop(
+        paste("The largest value of the shape parameter (`max_shape`)",
+          "must be a positive number."
+        ), call. = FALSE
+      )
+    }
+    if (!is_real(max_scale) || max_scale <= 0) {
+      stop(
+        paste("The largest value of the scale parameter (`max_scale`)",
+          "must be a positive number."
+        ), call. = FALSE
+      )
+    }
+
     search <- wp_search(cases, grid_length, max_shape, max_scale)
     r0 <- search$r0
     serial_supp <- search$supp
     serial_pmf <- search$pmf
   } else {
+    if (!is_real(mu) || mu <= 0) {
+      stop("The serial interval (`mu`) must be a positive number or `NA`.",
+        call. = FALSE
+      )
+    }
+
     max_range <- ceiling(qgamma(0.999, shape = 1, scale = mu))
     serial_supp <- seq_len(max_range)
     serial_pmf <- diff(pgamma(0:max_range, shape = 1, scale = mu))