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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sir.R
\name{sir_exp}
\alias{sir_exp}
\alias{sir_lex}
\alias{sir_ag}
\title{Calculate SMR}
\usage{
sir_exp(
x,
obs,
exp,
pyrs = NULL,
print = NULL,
conf.type = "profile",
test.type = "homogeneity",
conf.level = 0.95,
subset = NULL
)
sir_lex(x, print = NULL, breaks = NULL, ...)
sir_ag(
x,
obs = "from0to1",
print = attr(x, "aggre.meta")$by,
exp = "d.exp",
pyrs = "pyrs",
...
)
}
\arguments{
\item{x}{Data set e.g. \code{aggre} or \code{Lexis} object
(see: \verb{[lexpand]})}
\item{obs}{Variable name of the observed cases in the data set}
\item{exp}{Variable name or expression for expected cases}
\item{pyrs}{Variable name for person-years (optional)}
\item{print}{Variables or expression to stratify the results}
\item{conf.type}{select confidence interval type: (default=) \code{profile}, \code{wald}, \code{univariate}}
\item{test.type}{Test for equal SIRs. Test available are 'homogeneity' and 'trend'}
\item{conf.level}{Level of type-I error in confidence intervals, default 0.05 is 95\% CI}
\item{subset}{a logical vector for subsetting data}
\item{breaks}{a named list to split age group (age), period (per) or follow-up (fot).}
\item{...}{pass arguments to \code{sir_exp}}
}
\value{
A sir object
}
\description{
Calculate Standardized Mortality Ratios (SMRs) using
a single data set that includes
observed and expected cases and additionally person-years.
\code{sir_lex} solves SMR from an \verb{[Epi::Lexis]} object
calculated with \verb{[lexpand]}.
\code{sir_ag} solves SMR from a \verb{[aggre]} object
calculated using \verb{[lexpand]}.
}
\details{
These functions are intended to calculate SMRs from a single data set
that includes both observed and expected number of cases. For example utilizing the
argument \code{pop.haz} of the \verb{[lexpand]}.
\code{sir_lex} automatically exports the transition \code{fromXtoY} using the first
state in \code{lex.Str} as \code{0} and all other as \code{1}. No missing values
is allowed in observed, pop.haz or person-years.
}
\section{Functions}{
\itemize{
\item \code{sir_lex()}:
\item \code{sir_ag()}:
}}
\examples{
\donttest{
BL <- list(fot = 0:5, per = c("2003-01-01","2008-01-01", "2013-01-01"))
## Aggregated data
x1 <- lexpand(sire, breaks = BL, status = status != 0,
birth = bi_date, entry = dg_date, exit = ex_date,
pophaz=popmort,
aggre=list(sex, period = per, surv.int = fot))
sir_ag(x1, print = 'period')
# no aggreate or breaks
x2 <- lexpand(sire, status = status != 0,
birth = bi_date, entry = dg_date, exit = ex_date,
pophaz=popmort)
sir_lex(x2, breaks = BL, print = 'per')
}
}
\seealso{
\verb{[lexpand]}
\href{../doc/sir.html}{A SIR calculation vignette}
Other sir functions:
\code{\link{lines.sirspline}()},
\code{\link{plot.sirspline}()},
\code{\link{sir}()},
\code{\link{sir_ratio}()},
\code{\link{sirspline}()}
}
\author{
Matti Rantanen
}
\concept{sir functions}
|
