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author | Naeem Model <me@nmode.ca> | 2024-01-10 14:50:22 +0000 |
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committer | Naeem Model <me@nmode.ca> | 2024-01-10 14:50:22 +0000 |
commit | e1c61de5a0e693e2f24a1c4a10336e2a1c4563cb (patch) | |
tree | 92b4c42ef15fbda45dde6f5ec306d4bfe344a798 /man/idea.Rd | |
parent | 95b5ad6ce6ec5f76094b1e7176acfd44ffeef4e9 (diff) |
Rename ID and IDEA
Diffstat (limited to 'man/idea.Rd')
-rw-r--r-- | man/idea.Rd | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/man/idea.Rd b/man/idea.Rd new file mode 100644 index 0000000..f4c7d14 --- /dev/null +++ b/man/idea.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IDEA.R +\name{IDEA} +\alias{IDEA} +\title{IDEA method} +\usage{ +IDEA(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{IDEA} 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{ +This method is closely related to that implemented in \code{ID}. The method +is based on an 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. +IDEA(NT, mu = 5 / 7) + +# Obtain R0 when the serial distribution has a mean of three days. +IDEA(NT, mu = 3 / 7) + +} |