sts-class {surveillance} | R Documentation |
This is a rather leightweight class to implement multivariate time series of count 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.
week
:numeric
specifying the week
numbers. Actually this is not really used at the moment. freq
:freq
corresponds to 52, in
case of monthly data freq
is 12.start
:observed
:length(week)
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
:observed
containing booleans whether at the specific time point there was an
outbreak in the regionalarm
: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
:neighbourhood
:populationFrac
:matrix
.map
:SpatialPolygonsDataFrame
providing a shape of the areas which are monitored. control
:list
, thais is a
rather free data type to be returned by the surveillance algorithms. epochAsDate
:"logical"
stating
whether to use a ISO 8601 representation of the epoch/week slot using
the Date
class (epochAsDate=TRUE
) or just to
interpret the epochs/weeks as numerics (epochAsDate=FALSE
).multinomialTS
:"logical"
stating whether to interpret the object as observed
out of
population
, i.e. a multinomial interpretation instead of a
count interpretation.signature(x = "sts")
:
extract number of rows of the observed
matrix slot. The
dimension of the other matrix slots is similar.signature(x = "sts")
:
extract number of columns of the observed
matrix slot.signature(x = "sts")
: extract matrix dimensions of
observed
using dim
.signature(x = "sts")
: extract the observed
slot of an sts
object.signature(x = "sts")
: extract the population
slot of an sts
object.signature(x = "sts")
: extract the alarm
slot of an sts
object.signature(x = "sts")
: extract the upperbound
slot of an sts
object.signature(x = "sts")
: extract the control
slot of an sts
object.signature(x = "sts")
: extract the epoch
slot of an sts
object. If ISO dates are used then the
returned object is of class Date
.signature(x = "sts")
: Returns the epoch
number within the year of the epoch
slot.signature(x="sts",do.NULL="missing",prefix="missing")
: extract colnames
of the observed
matrix.signature(x="sts")
: the internal function
init.sts
is called, which assigns all slots. signature(x="sts")
: see
aggregate,sts-method
signature(x = "sts")
:
extracts the corresponding year of each observation of x
signature(x = "sts")
:
extracts the corresponding week number within the year of each
observation of x
signature(x = "sts")
:
converts the observed
, week
, 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 objectsignature(x="sts",y="missing",function(x, y, type,...)...)
: this function is
the successor of the plot.disProg
and
plot.survRes
functions. It takes (more or less) the
same arguments as plot.survRes
. The most important
difference is the type of plot, which is specified using
type
. See show,sts-method
for details.
M. Höhle
data("ha") shp <- system.file("shapes/berlin.shp",package="surveillance") ha <- disProg2sts(ha, map=readShapePoly(shp,IDvar="SNAME")) plot(ha,type=observed ~ 1 | unit)