Comments in-ine below.
Tom Richardson wrote:
Hi R users,
This query is regarding the use of the 'envelope' function in Spatstat.
My data can be represented as a point process with CONTINUOUS marks:
points <- ppp(x=x,y=y, marks=m, window= wind)
However the marks are alignments (lines), and so have to be treated
differently to normal scalar marks. Hence to create a mcf object with the
appropriate test function for alignment marks, I input 'func' (below)
suggested by Stoyan & Penttinen (1989):
func <- function(m1,m2) { sin(abs(m1-m2))^2}
mcf <- markcorr(points, func, normalise = TRUE, method="density")
So far, so good.
Really? You must have modified the markcorr() function then. In the
current
release of spatstat (1.18-2) markcorr() throws an errror if the marks
are a
data frame. As they must effectively be if the marks are line
segments. Or
even ``lines''. You need two parameters to specify a line, four to
specify a line
segment.
I also don't get what your function ``func()'' is actually doing. If
m1 and m2 represent
line segments (or even lines) sin(abs(m1-m2))^2 is a vector, not a
scalar as is needed by
markcorr().
If the marks really are scalars, then it is mysterious to me how they
represent lines.
I am not familiar with the Stoyan and Penttinen paper to which you
refer, and cannot get
access to it at this moment; perhaps things are all explained therein.
However, usinf 'envelope' and 'rlabel' I would like to
check if the pattern in the data is lost when randomly relabeling the mark
for each point. If the test function, 'func' were the usual G(m1,m2)=m1*m2,
then the following would work:
E <- envelope(points, markcorr, nsim=20,
simulate=expression(rlabel(points)))
Howeve, in the above 'markcorr' calculates G(m1,m2)=m1*m2 by default. So
need to specify the test function to be G(m1,m2)= sin(abs(m1-m2))^2.
According to the spatstat manual (p177), I may need to 'cook up' a specific
function, like this:
Kdif = function(X, ..., i) {
Kidot = Kdot(X, ..., i = i)
K = Kest(X, ...)
dif = eval.fv(Kidot - K)
return(dif)
}
E = envelope(lansing, Kdif, i='blackoak',
simulate=expression(rlabel(lansing)))
So how do I tell 'envelope' that I want to specify the mark correlation
test function ??
Be that as it may; let us assume that you have some sort of numeric
marks,
so that func(m1,m2){sin(abs(m1-m2))^2} is a scalar and thereby makes
sense.
And you want to use func() as the value of ``f'' in markcorr(). And
you want
to do envelope() to the resulting markcorr().
Do the following:
# Generate toy data:
set.seed(42)
X <- rpoispp(100)
marks(X) <- rnorm(X$n)
# Cook up your ``specific function'':
mcspecial <- function(X,r=NULL){
markcorr(X,f=function(m1,m2){sin(abs(m1-m2))^2},r=r)
}
# Now do the envelope:
Env <- envelope(X,fun=mcspecial,simulate=expression(rlabel(X)))
cheers,
Rolf Turner
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