Description Usage Arguments Value Author(s) References See Also Examples
The function plots the fitted temporal or (isotropic) spatial
interaction function of a twinstim
object.
The implementation is illustrated in Meyer et al. (2017, Section 3),
see vignette("twinstim")
.
1 2 3 4 5 6 7 8 9  iafplot(object, which = c("siaf", "tiaf"), types = NULL,
scaled = c("intercept", "standardized", "no"), truncated = FALSE,
log = "", conf.type = if (length(pars) > 1) "MC" else "parbounds",
conf.level = 0.95, conf.B = 999, xgrid = 101,
col.estimate = rainbow(length(types)), col.conf = col.estimate,
alpha.B = 0.15, lwd = c(3,1), lty = c(1,2),
verticals = FALSE, do.points = FALSE,
add = FALSE, xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL,
legend = !add && (length(types) > 1), ...)

object 
object of class 
which 
argument indicating which of the two interaction functions to plot.
Possible values are 
types 
integer vector indicating for which event 
scaled 
character string determining if/how the the interaction function should be scaled. Possible choices are:
The first one is the default and required for the comparison of
estimated interaction functions from different models.
For backward compatibility, 
truncated 
logical indicating if the plotted interaction function should
take the maximum range of interaction ( 
log 
a character string passed to 
conf.type 
type of confidence interval to produce. 
conf.level 
the confidence level required. For 
conf.B 
number of samples for the 
xgrid 
either a numeric vector of xvalues (distances from the host) where
to evaluate 
col.estimate 
vector of colours to use for the function point estimates of the different 
col.conf 
vector of colours to use for the confidence intervals of the different 
alpha.B 
alpha transparency value (as relative opacity) used for the 
lwd, lty 
numeric vectors of length two specifying the line width and type of point estimates (first element) and confidence limits (second element), respectively. 
verticals,do.points 
graphical settings for step function
kernels. These can be logical (as in 
add 
add to an existing plot? 
xlim, ylim 
vectors of length two containing the x and yaxis limit of the
plot. The default yaxis range (

xlab, ylab 
labels for the axes with 
legend 
logical indicating if a legend for the 
... 
additional arguments passed to the default 
A plot is created – see e.g. Figure 3(b) in Meyer et al. (2012).
The function invisibly returns a matrix of the plotted values of the
interaction function (evaluated on xgrid
, by type). The first
column of the matrix contains the distance x, and the remaining
length(types)
columns contain the (scaled) function values for
each type.
The pointwise confidence intervals of the interaction functions are
returned in similar matrices as attributes: if
length(types)==1
, there is a single attribute "CI"
,
whereas for multiple types, the attributes are named
paste0("CI.",typeNames)
(where the typeNames
are
retrieved from object$qmatrix
).
Sebastian Meyer
Meyer, S., Elias, J. and Höhle, M. (2012): A spacetime conditional intensity model for invasive meningococcal disease occurrence. Biometrics, 68, 607616. doi: 10.1111/j.15410420.2011.01684.x
Meyer, S., Held, L. and Höhle, M. (2017): Spatiotemporal analysis of epidemic phenomena using the R package surveillance. Journal of Statistical Software, 77 (11), 155. doi: 10.18637/jss.v077.i11
plot.twinstim
, which calls this function.
1 2 3 4 5 6 7 8 9  data("imdepifit")
iafplot(imdepifit, "tiaf", scaled=FALSE) # tiaf.constant(), not very exciting
iafplot(imdepifit, "siaf", scaled=FALSE)
# scaled version uses a MonteCarloCI
set.seed(1) # result depends on .Random.seed
iafplot(imdepifit, "siaf", scaled=TRUE, conf.type="MC", conf.B=199,
col.conf=gray(0.4), conf.level=NA) # show MC samples

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