attrMort {FluMoDL}R Documentation

Influenza- and temperature-attributable mortality for a FluMoDL object

Description

This function uses an object of class FluMoDL to calculate mortality attributed to influenza and/or temperature.

Usage

attrMort(m, par = c("H1", "H3", "B", "temp", "RSV"), sel = "week",
  from = NULL, to = NULL, temprange = "cold", ci = TRUE,
  nsim = 5000, mcsamples = FALSE, progress = TRUE, blup = FALSE)

Arguments

m

An object of class FluMoDL.

par

A character vector indicating which exposures to calculate the attributable mortality for. Defaults to c("H1","H3","B","temp","RSV"), which indicates all three influenza proxies, temperature and RSV (if it exists in the model).

sel

For which time period(s) to calculate attributable mortality. This can be one of several choices. For sel="week" (the default) and sel="season" attributable mortality is calculated for each week or each season respectively. One can also provide to sel a list of index vectors (integer or logical) corresponding to particular rows of m$data, or a matrix of logical index vectors, or a single index vector. Note that the index vectors should point to consecutive rows of m$data.

from

Week (integer, in YYYYWW format) or season to start from, in case sel="week" or sel="season" respectively.

to

Week (integer, in YYYYWW format) or season to end with, in case sel="week" or sel="season" respectively.

temprange

In case temperature-attributable mortality is calculated (argument par includes "temp"), this argument specifies the temperature range or interest. This can be one of several choices.

If temprange="cold" (the default) mortality attributable to cold temperatures is calculated, i.e. temperatures below the MMP (minimum mortality point). If temprange="heat" mortality attributable to hot temperatures is calculated, i.e. those above the MMP. If temperature="all" the entire range of temperatures is used, i.e. any temperature other than the MMP.

Alternatively one can provide a numeric vector of length two, indicating a specific temperature range; this can also be provided as a character vector of length two, where one of the elements can be the word "MMP", which will be replaced with the MMP temperature.

ci

If TRUE, empirical (Monte Carlo) 95 for all attributable mortality estimates.

nsim

Number of Monte Carlo simulations to run per attributable mortality estimate. Defaults to 5000. Increase if higher precision is required (and you don't mind the wait).

mcsamples

If TRUE, return all Monte Carlo simulation samples in the output. See below.

progress

If TRUE, a progress bar appears if Monte Carlo simulations are run and if there are more than three time periods selected in argument sel. Set to FALSE to suppress the progress bar.

blup

If FALSE (the default), the model coefficients stored in m$model are used for the calculation of attributable mortality. If TRUE, the coefficients stored in the FluMoDL object are used; if blup=TRUE but blup(m) is NULL, a warning is generated. Alternatively, blup can be another object of class summary.FluMoDL, whose coefficients are used for the calculation.

Details

All attributable mortalities are calculated using the "backward" perspective, meaning the mortality at any given day that is attributable to exposures up to 30 days previously (=the maximum lag).

Confidence intervals (when ci=TRUE) are obtained empirically through Monte Carlo simulations; this can take quite some time if lots of CIs need to be calculated (for example if sel=TRUE). For this reason, a progress bar is shown by default in this case (which can be suppressed by progress=FALSE).

Temperature-attributable mortalities are by default calculated for cold temperatures, i.e. temperatures lower than the minimum mortality point (MMP). Note, however, that the adjustment in the FluMoDL is made for the entire range of daily mean temperatures, not just for cold. Therefore mortality attributable to any range of temperatures can be calculated, e.g. for heat, extreme cold, extreme heat, etc. See argument temprange above for details.

Value

If mcsamples=FALSE (the default), a data.frame is returned with columns named 'FluH1', 'FluH3', 'FluB' and 'Temp' (and/or 'RSV'), depending on the argument par, and also 'FluH1.lo', 'FluH1.hi', 'FluH3.lo', ..., if ci=TRUE. Each row in the output corresponds to a selection made in argument sel, for example if sel="week" (the default) rows correspond to each week available in the data. If all influenza types/subtypes are selected in par, a column named 'AllFlu' is also calculated automatically, with the mortality (and 95 attributable to all influenza types/subtypes.

If mcsamples=TRUE, a list is returned with elements 'result' and 'mcsamples'. The first contains the data.frame with point estimates of influenza- and/or temperature-attributable mortality, as before (no 95 element contains a list of the Monte Carlo simulation samples for each parameter in par.

References

Examples

data(greece) # Use example surveillance data from Greece
m <- with(greece, fitFluMoDL(deaths = daily$deaths,
    temp = daily$temp, dates = daily$date,
    proxyH1 = weekly$ILI * weekly$ppH1,
    proxyH3 = weekly$ILI * weekly$ppH3,
    proxyB = weekly$ILI * weekly$ppB,
    yearweek = weekly$yearweek))


# Calculate influenza-attributable estimates by season, until 2016-17:
attr1 <- attrMort(m, par=c("H1","H3","B"), sel="season", to=2016)
attr1

# Calculate influenza-attributable estimates by week, only point
#    estimates, for the 2014-15 season:
attr2 <- attrMort(m, par=c("H1","H3","B"), sel="week",
    from=201440, to=201520, ci=FALSE)
attr2


# Calculate mortality attributable to temperatures below 5 celsius, for
#    the period of January 2017:
attr3 <- attrMort(m, par="temp",
    sel=with(m$data, which(dates>="2017-1-1" & dates<="2017-1-31")),
    temprange=c(5,-20))


# Calculate attributable mortalities for the entire 2017-18 season, and
#    return the Monte Carlo simulation samples in the output
attr4 <- attrMort(m, sel="season", from=2017, to=2017, mcsamples=TRUE)
[Package FluMoDL version 0.0.3 Index]