sts-class: Class '"sts"' - surveillance time series

In jimhester/surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Description

This is a lightweight S4 class to implement multivariate time series of counts used for public health surveillance data. The class captures the time series data as well as the spatial layout of the regions, where the data originate from.

Slots

epoch:

Object of class numeric or specifying the time of observation. In old versions of the package this used to be the week numbers. However, depending on the freq argument, it can now be day or month as well. Furthermore, if epochAsDate=TRUE then it is the as.numeric representation of Date objects giving the exact date of the observation. Note: This slot used to be called week in earlier versions of the package, but has now been renamed to reflect the greater flexibility in the choice of observation time.

freq:

If weekly data freq corresponds to 52, in case of monthly data freq is 12.

start:

vector of length two denoting the year and the sample number (week, month, etc.) of the first observation

observed:

A matrix of size length(epoch) times the number of regions containing the weekly/monthly number of counts in each region. The colnames of the matrix should match the ID values of the shapes in the map slot.

state:

Matrix with the same dimension as observed containing booleans whether at the specific time point there was an outbreak in the region

alarm:

Matrix with the same dimension as observed specifying whether an outbreak detection algorithm declared a specific time point in the region as having an alarm. If the object containins just observations then this slot is null.

upperbound:

Matrix with upper bound values

neighbourhood:

Symmetric matrix of size (number of regions)^2 describing the neighbourhood structure. It may either be a binary adjacency matrix or contain neighbourhood orders.

populationFrac:

A matrix of population fractions (with dimensions dim(observed)).

map:

Object of class SpatialPolygonsDataFrame providing a shape of the areas which are monitored.

control:

Object of class list, this is a rather free data type to be returned by the surveillance algorithms.

epochAsDate:

Object of class "logical" stating whether to use a ISO 8601 representation of the epoch slot using the Date class (epochAsDate=TRUE) or just to interpret the epochs as numerics (epochAsDate=FALSE).

multinomialTS:

Object of class "logical" stating whether to interpret the object as observed out of population, i.e. a multinomial interpretation instead of a count interpretation.

Methods

dim

signature(x = "sts"): extract matrix dimensions of observed using dim.

observed

signature(x = "sts"): extract the observed slot of an sts object.

population

signature(x = "sts"): extract the population slot of an sts object.

multinomialTS

signature(x = "sts"): extract the multinomialTS slot of an sts object.

neighbourhood

signature(x = "sts"): extract the neighbourhood slot of an sts object.

alarms

signature(x = "sts"): extract the alarm slot of an sts object.

upperbound

signature(x = "sts"): extract the upperbound slot of an sts object.

control

signature(x = "sts"): extract the control slot of an sts object.

epoch

signature(x = "sts"): extract the epoch slot of an sts object. If ISO dates are used then the returned object is of class Date.

epochInYear

signature(x = "sts"): Returns the epoch number within the year of the epoch slot.

dimnames

signature(x="sts"): extract the dimnames of the observed matrix.

initialize

signature(x="sts"): the internal function init.sts is called, which assigns all slots.

aggregate

signature(x="sts"): see aggregate,sts-method

year

signature(x = "sts"): extracts the corresponding year of each observation of x

as.data.frame

signature(x = "sts"): converts the observed, epoch, state and alarm slots of x into a data frame with column names matching the colnames of the respective slots. Useful when one wants to fit a model based on the object

plot

signature(x="sts",y="missing"): this method is the entry point to a collection of plot variants. It is also the successor of the plot.disProg and plot.survRes functions. The type of plot is specified using a formula type. See stsplot for details.

Author(s)

M. Höhle

Examples

if (requireNamespace("maptools")) {
   # load disProg-object "ha" and convert to S4-class "sts"
   data("ha")
   shpfile <- system.file("shapes/berlin.shp",package="surveillance")
   ha.sts <- disProg2sts(ha, map=maptools::readShapePoly(shpfile,IDvar="SNAME"))
} else {
   data("ha.sts")
   # is almost identical to the above except that German umlauts
   # have been replaced in 'ha.sts@map@data$BEZIRK' for compatibility reasons
}

ha.sts
plot(ha.sts, type = observed ~ 1 | unit)

## convert ts/mts object to sts
z <- ts(matrix(rpois(300,10), 100, 3), start = c(1961, 1), frequency = 12)
z.sts <- as(z, "sts")
plot(z.sts)

## conversion to the quasi-standard "xts" class is also possible
## -> enables interactive time series plots using package "dygraphs"
if (require("xts")) {
    z.xts <- as.xts(z.sts)
    plot(z.xts)
}

jimhester/surveillance documentation built on May 19, 2019, 10:33 a.m.