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Diffstat (limited to 'man/idea.Rd')
| -rw-r--r-- | man/idea.Rd | 44 |
1 files changed, 25 insertions, 19 deletions
diff --git a/man/idea.Rd b/man/idea.Rd index f4c7d14..91c360b 100644 --- a/man/idea.Rd +++ b/man/idea.Rd @@ -1,31 +1,32 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/IDEA.R -\name{IDEA} -\alias{IDEA} -\title{IDEA method} +% Please edit documentation in R/idea.R +\name{idea} +\alias{idea} +\title{Incidence Decay and Exponential Adjustment (IDEA)} \usage{ -IDEA(NT, mu) +idea(cases, mu) } \arguments{ -\item{NT}{Vector of case counts.} +\item{cases}{Vector of case counts. The vector must be of length at least two +and only contain positive integers.} -\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.} +\item{mu}{Mean of the serial distribution. This must be a positive number. +The value should match the 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 \code{1}. If case counts are daily and the serial +distribution has a mean of seven days, then \code{mu} should be set to \code{7}.} } \value{ -\code{IDEA} returns a single value, the estimate of R0. +An estimate of the basic reproduction number (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 +This method is closely related to that implemented in \code{\link[=id]{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 case counts expected under the model. This method is based on an approximation of the SIR model, which is most @@ -37,12 +38,17 @@ are counts observed daily or weekly?) when implementing. } \examples{ # Weekly data. -NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) +cases <- 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) +idea(cases, mu = 5 / 7) # Obtain R0 when the serial distribution has a mean of three days. -IDEA(NT, mu = 3 / 7) - +idea(cases, mu = 3 / 7) +} +\references{ +\href{https://doi.org/10.1371/journal.pone.0083622}{Fisman et al. (PloS One, 2013)} +} +\seealso{ +\code{\link[=id]{id()}} for a similar method. } |