View source: R/contagdiscstate.R
contagdiscstate  R Documentation 
Calculates the discstate contagion landscape metric as described in (Hingee, 2016; Hingee, 2019). The discstate contagion landscape metric describes the entropy (mixing) between four possible states of a disc:
the disc is completely
contained in \Xi
the disc does not intersect \Xi
the centre of the disc is in \Xi
but the disc is not contained in
\Xi
the disc intersects \Xi
but the centre is outside
\Xi
Discstate contagion is a function of the disc radius.
The main difference to classical contagion (O'Neill, 1988) is that discstate contagion
is based on the spherical contact distribution instead of pixel neighbours.
One impact of this design is that the distance with which to quantify the
mixing between \Xi
and the background may be chosen by the user by
choosing the disc radius (for classical contagion this distance is fixed by
the map resolution).
Note: to create fv
objects the function copies about 20 lines of code from the spatstat collection of packages.
contagdiscstate(XiH, XicH, p, normalise = FALSE)
XiH 
Conditional spherical contact distribution function for 
XicH 
Conditional spherical contact distribution for the complement of

p 
The coverage probability of 
normalise 
Optional. If TRUE 
XiH
should be a function of radius that contains (estimates of) the
probability of a disc of radius r
not intersecting \Xi
if the
disc's centre is not in \Xi
\code{XiH}(r) = P(B_r(x) \subseteq
\Xi^c  x \in \Xi^c).
Similarly XicH
should be (an estimate of) the
probability of a disc being fully contained in \Xi
given its centre
is in \Xi
\code{XicH}(r)\approx P(B_r(x) \subseteq \Xi  x \in
\Xi).
These can both be obtained using Hest
in
spatstat. For XicH
take care to apply Hest
to the complement
of \Xi
with the observation window W
.
If normalise
is TRUE
then the result is divided by
2ln(2)
and increased by 1 so that contagion will always be between 0
and 1.
If XiH
is an fv
object then an fv
object is returned.
If XiH
is a vector then the returned object is a vector the same length as XiH
with each element
corresponding to the contagion at each r
value of XiH
.
Hingee, K.L. (2016) Statistics for patch observations. International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences pp. 235242. Prague: ISPRS.
Hingee, K.L. (2019) Spatial Statistics of Random Closed Sets for Earth Observations. PhD: Perth, Western Australia: University of Western Australia. Submitted.
O'Neill, R.V., Krummel, J.R., Gardner, R.H., Sugihara, G., Jackson, B., DeAngelis, D.L., et al. (1988) Indices of landscape pattern. Landscape Ecology, 1, 153162.
xi < heather$coarse
obswindow < Frame(heather$coarse)
p < coverageprob(xi, Frame(xi))
xiH < Hest(xi, W = obswindow) #Sph. Contact Distrution Estimate
xicH < Hest(complement.owin(xi), W = obswindow) #Conditional Core Prob. Estimate
contagion < contagdiscstate(xiH, xicH, p)
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