Description Usage Arguments Details Value Note Author(s) See Also Examples
The function as.epidata
is used to generate objects
of class
"epidata"
. Objects of this class are
specific data frames containing the event history of an epidemic together
with some additional attributes. These objects are the basis for fitting
spatio-temporal epidemic intensity models with the function
twinSIR
. Note that the spatial information itself, i.e.
the positions of the individuals, is assumed to be constant over time.
Besides epidemics following the SIR compartmental model, also data from SI,
SIRS and SIS epidemics may be supplied. Inference for the infectious process
works as usual and simulation of such epidemics is also possible.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | as.epidata(data, ...)
## S3 method for class 'data.frame'
as.epidata(data, t0,
tE.col, tI.col, tR.col, id.col, coords.cols,
f = list(), w = list(), D = dist, keep.cols = TRUE, ...)
## Default S3 method:
as.epidata(data, id.col, start.col, stop.col,
atRiskY.col, event.col, Revent.col, coords.cols,
f = list(), w = list(), D = dist, ...)
## S3 method for class 'epidata'
print(x, ...)
## S3 method for class 'epidata'
x[i, j, drop]
## S3 method for class 'epidata'
update(object, f = list(), w = list(), D = dist, ...)
|
data |
For the |
t0 |
start time of the observation period. Will be subtracted
from the time columns |
tE.col, tI.col, tR.col |
single numeric or character indexes of the time columns in
|
id.col |
single numeric or character index of the |
start.col |
single index of the |
stop.col |
single index of the |
atRiskY.col |
single index of the |
event.col |
single index of the |
Revent.col |
single index of the |
coords.cols |
indexes of the |
f |
a named list of vectorized functions for a
distance-based force of infection.
The functions must interact elementwise on a (distance) matrix |
w |
a named list of vectorized functions for extra
covariate-based weights w_ij in the epidemic component.
Each function operates on a single time-constant covariate in
|
D |
either a function to calculate the distances between the individuals
with locations taken from |
keep.cols |
logical indicating if all columns in |
x,object |
an object of class |
... |
arguments passed to |
i,j,drop |
arguments passed to |
The print
method for objects of class "epidata"
simply prints
the data frame with a small header containing the time range of the observed
epidemic and the number of infected individuals. Usually, the data frames
are quite long, so the summary method summary.epidata
might be
useful. Also, indexing/subsetting "epidata"
works exactly as for
data.frame
s, but there is an own method, which
assures consistency of the resulting "epidata"
or drops this class, if
necessary.
The update
-method can be used to add or replace distance-based
(f
) or covariate-based (w
) epidemic variables in an
existing "epidata"
object.
SIS epidemics are implemented as SIRS epidemics where the length of the removal period equals 0. This means that an individual, which has an R-event will be at risk immediately afterwards, i.e. in the following time block. Therefore, data of SIS epidemics have to be provided in that form containing “pseudo-R-events”.
a data.frame
with the columns "BLOCK"
, "id"
,
"start"
, "stop"
, "atRiskY"
, "event"
,
"Revent"
and the coordinate columns (with the original names from
data
), which are all obligatory. These columns are followed by any
remaining columns of the input data
. Last but not least, the newly
generated columns with epidemic variables corresponding to the functions
in the list f
are appended, if length(f)
> 0.
The data.frame
is given the additional attributes
"eventTimes" |
numeric vector of infection time points (sorted chronologically). |
"timeRange" |
numeric vector of length 2: |
"coords.cols" |
numeric vector containing the column indices of the coordinate columns in the resulting data frame. |
"f" |
this equals the argument |
"w" |
this equals the argument |
The column name "BLOCK"
is a reserved name. This column will be
added automatically at conversion and the resulting data frame will be
sorted by this column and by id. Also the names "id"
, "start"
,
"stop"
, "atRiskY"
, "event"
and "Revent"
are
reserved for the respective columns only.
Sebastian Meyer
The hagelloch
data for a “real” "epidata"
object.
The code for the conversion from the simple data frame to the SIR event
history using as.epidata.data.frame
is given in
example(hagelloch)
.
The plot
and the
summary
method for class "epidata"
.
Furthermore, the function animate.epidata
for the animation of
epidemics.
Function twinSIR
for fitting spatio-temporal epidemic intensity
models to epidemic data.
Function simEpidata
for the simulation of epidemic data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | # see example(hagelloch)
# here is an artificial event history
data("foodata")
str(foodata)
# convert the data to an object of class "epidata",
# also generating some epidemic covariates
myEpidata <- as.epidata(foodata,
id.col = 1, start.col = "start", stop.col = "stop",
atRiskY.col = "atrisk", event.col = "infected", Revent.col = "removed",
coords.cols = c("x","y"),
f = list(B1 = function(u) u <= 1, B2 = function(u) u > 1))
# this is how data("fooepidata") has been generated
data("fooepidata")
stopifnot(all.equal(myEpidata, fooepidata))
# add covariate-based weight for the force of infection, e.g.,
# to model an increased force if i and j have the same value in z1
myEpidata2 <- update(fooepidata,
w = list(samez1 = function(z1.i, z1.j) z1.i == z1.j))
str(fooepidata)
subset(fooepidata, BLOCK == 1)
summary(fooepidata) # see 'summary.epidata'
plot(fooepidata) # see 'plot.epidata' and also 'animate.epidata'
stateplot(fooepidata, "15") # see 'stateplot'
|
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