From e1c61de5a0e693e2f24a1c4a10336e2a1c4563cb Mon Sep 17 00:00:00 2001
From: Naeem Model <me@nmode.ca>
Date: Wed, 10 Jan 2024 14:50:22 +0000
Subject: Rename ID and IDEA

---
 man/id.Rd | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 man/id.Rd

(limited to 'man/id.Rd')

diff --git a/man/id.Rd b/man/id.Rd
new file mode 100644
index 0000000..1d32c50
--- /dev/null
+++ b/man/id.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ID.R
+\name{ID}
+\alias{ID}
+\title{ID method}
+\usage{
+ID(NT, mu)
+}
+\arguments{
+\item{NT}{Vector of case counts.}
+
+\item{mu}{Mean of the serial distribution. This needs to match case counts
+in time units. For example, if case counts are weekly and the
+serial distribution has a mean of seven days, then \code{mu} should
+be set to one. If case counts are daily and the serial distribution
+has a mean of seven days, then \code{mu} should be set to seven.}
+}
+\value{
+\code{ID} returns a single value, the estimate of R0.
+}
+\description{
+This function implements a least squares estimation method of R0 due to
+Fisman et al. (PloS One, 2013). See details for implementation notes.
+}
+\details{
+The method is based on a straightforward incidence decay model. The estimate
+of R0 is the value which minimizes the sum of squares between observed case
+counts and cases counts 'expected' under the model.
+
+This method is based on an approximation of the SIR model, which is most
+valid at the beginning of an epidemic. The method assumes that the mean of
+the serial distribution (sometimes called the serial interval) is known. The
+final estimate can be quite sensitive to this value, so sensitivity testing
+is strongly recommended. Users should be careful about units of time (e.g.,
+are counts observed daily or weekly?) when implementing.
+}
+\examples{
+# Weekly data:
+NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)
+
+# Obtain R0 when the serial distribution has a mean of five days.
+ID(NT, mu = 5 / 7)
+
+# Obtain R0 when the serial distribution has a mean of three days.
+ID(NT, mu = 3 / 7)
+
+}
-- 
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