alltypes: Calculate Summary Statistic for All Types in a Multitype...
In spatstat.core: Core Functionality of the 'spatstat' Family
alltypes R Documentation
Calculate Summary Statistic for All Types in a Multitype Point Pattern
Description
Given a marked point pattern, this computes the estimates of
a selected summary function (F,G, J, K etc)
of the pattern, for all possible combinations of marks,
and returns these functions in an array.
Usage
alltypes(X, fun="K", ...,
dataname=NULL,verb=FALSE,envelope=FALSE,reuse=TRUE)
Arguments
X
The observed point pattern, for which summary function
estimates are required. An object of class "ppp" or "lpp".
fun
The summary function. Either an R function,
or a character string indicating the summary function
required. Options for strings are
"F", "G", "J", "K", "L", "pcf",
"Gcross", "Jcross", "Kcross", "Lcross",
"Gdot", "Jdot", "Kdot", "Ldot".
...
Arguments passed to the summary function
(and to the function envelope if appropriate)
dataname
Character string giving an optional (alternative)
name to the point pattern, different from what is given
in the call. This name, if supplied, may be used by
plot.fasp() in forming the title of the plot.
If not supplied it defaults to the parsing of the argument
supplied as X in the call.
verb
Logical value. If verb is
true then terse “progress reports” (just the values of the
mark indices) are printed out when the calculations for that
combination of marks are completed.
envelope
Logical value. If envelope is true, then simulation envelopes
of the summary function will also be computed. See Details.
reuse
Logical value indicating whether the envelopes in each panel
should be based on the same set of simulated patterns
(reuse=TRUE) or on different, independent sets of simulated
patterns (reuse=FALSE).
Details
This routine is a convenient way to analyse the dependence between
types in a multitype point pattern.
It computes the estimates of a selected summary function of the
pattern, for all possible combinations of marks.
It returns these functions in an array
(an object of class "fasp") amenable to plotting
by plot.fasp().
The argument fun specifies the summary function that will
be evaluated for each type of point, or for each pair of types.
It may be either an R function or a character string.
Suppose that the points have possible types 1,2,…,m
and let X[i] denote the pattern of points of type i only.
If fun="F" then this routine
calculates, for each possible type i,
an estimate of the Empty Space Function F[i](r) of
X[i]. See Fest
for explanation of the empty space function.
The estimate is computed by applying Fest
to X[i] with the optional arguments ....
If fun is
"Gcross", "Jcross", "Kcross" or "Lcross",
the routine calculates, for each pair of types (i,j),
an estimate of the “i-toj” cross-type function
G[i,j](r),
J[i,j](r),
K[i,j](r) or
L[i,j](r) respectively describing the
dependence between
X[i] and X[j].
See Gcross, Jcross, Kcross
or Lcross respectively for explanation of these
functions.
The estimate is computed by applying the relevant function
(Gcross etc)
to X using each possible value of the arguments i,j,
together with the optional arguments ....
If fun is "pcf" the routine calculates
the cross-type pair correlation function pcfcross
between each pair of types.
If fun is
"Gdot", "Jdot", "Kdot" or "Ldot",
the routine calculates, for each type i,
an estimate of the “i-to-any” dot-type function
G[i.](r),
J[i.](r) or
K[i.](r) or
L[i.](r) respectively describing the
dependence between X[i] and X.
See Gdot, Jdot, Kdot
or Ldot respectively for explanation of these functions.
The estimate is computed by applying the relevant function
(Gdot etc)
to X using each possible value of the argument i,
together with the optional arguments ....
The letters "G", "J", "K" and "L"
are interpreted as abbreviations for Gcross,
Jcross, Kcross and Lcross
respectively, assuming the point pattern is
marked. If the point pattern is unmarked, the appropriate
function Fest, Jest,
Kest or Lest is invoked instead.
If envelope=TRUE, then as well as computing the value of the
summary function for each combination of types, the algorithm also
computes simulation envelopes of the summary function for each
combination of types. The arguments ... are passed to the function
envelope to control the number of
simulations, the random process generating the simulations,
the construction of envelopes, and so on.
When envelope=TRUE it is possible that errors could occur
because the simulated point patterns do not satisfy the requirements
of the summary function (for example, because the simulated pattern
is empty and fun requires at least one point). If the number
of such errors exceeds the maximum permitted number maxnerr,
then the envelope algorithm will give up, and will return
the empirical summary function for the data point pattern,
fun(X), in place of the envelope.
Value
A function array (an object of class "fasp",
see fasp.object). This can be plotted
using plot.fasp.
If the pattern is not marked, the resulting “array” has dimensions
1 x 1. Otherwise the following is true:
If fun="F",
the function array has dimensions m * 1
where m is the number of different marks in the point pattern.
The entry at position [i,1] in this array
is the result of applying Fest to the
points of type i only.
If fun is "Gdot", "Jdot", "Kdot"
or "Ldot", the function array
again has dimensions m * 1.
The entry at position [i,1] in this array
is the result of Gdot(X, i), Jdot(X, i)
Kdot(X, i) or Ldot(X, i) respectively.
If fun is "Gcross", "Jcross", "Kcross"
or "Lcross"
(or their abbreviations "G", "J", "K" or "L"),
the function array has dimensions m * m.
The [i,j] entry of the function array
(for i != j) is the
result of applying the function Gcross,
Jcross, Kcross orLcross to
the pair of types (i,j). The diagonal
[i,i] entry of the function array is the result of
applying the univariate function Gest,
Jest, Kest or Lest to the
points of type i only.
If envelope=FALSE, then
each function entry fns[[i]] retains the format
of the output of the relevant estimating routine
Fest, Gest, Jest,
Kest, Lest, Gcross,
Jcross ,Kcross, Lcross,
Gdot, Jdot, Kdot or
Ldot
The default formulae for plotting these functions are
cbind(km,theo) ~ r for F, G, and J functions, and
cbind(trans,theo) ~ r for K and L functions.
If envelope=TRUE, then each function entry fns[[i]]
has the same format as the output of the envelope command.
Note
Sizeable amounts of memory may be needed during the calculation.
Author(s)
\adrian
and \rolf.
See Also
plot.fasp,
fasp.object,
Fest,
Gest,
Jest,
Kest,
Lest,
Gcross,
Jcross,
Kcross,
Lcross,
Gdot,
Jdot,
Kdot,
envelope.
Examples
# bramblecanes (3 marks).
bram <- bramblecanes
bF <- alltypes(bram,"F",verb=TRUE)
plot(bF)
if(interactive()) {
plot(alltypes(bram,"G"))
plot(alltypes(bram,"Gdot"))
}
# Swedishpines (unmarked).
swed <- swedishpines
plot(alltypes(swed,"K"))
plot(alltypes(amacrine, "pcf"), ylim=c(0,1.3))
# A setting where you might REALLY want to use dataname:
# xxx <- alltypes(ppp(Melvin$x,Melvin$y,
# window=as.owin(c(5,20,15,50)),marks=clyde),
# fun="F",verb=TRUE,dataname="Melvin")
# envelopes
bKE <- alltypes(bram,"K",envelope=TRUE,nsim=19)
# global version:
# bFE <- alltypes(bram,"F",envelope=TRUE,nsim=19,global=TRUE)
# extract one entry
as.fv(bKE[1,1])
spatstat.core documentation built on May 18, 2022, 9:05 a.m.
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| alltypes | R Documentation |
Calculate Summary Statistic for All Types in a Multitype Point Pattern
Description
Given a marked point pattern, this computes the estimates of a selected summary function (F,G, J, K etc) of the pattern, for all possible combinations of marks, and returns these functions in an array.
Usage
alltypes(X, fun="K", ...,
dataname=NULL,verb=FALSE,envelope=FALSE,reuse=TRUE)
Arguments
X |
The observed point pattern, for which summary function
estimates are required. An object of class |
fun |
The summary function. Either an R function,
or a character string indicating the summary function
required. Options for strings are
|
... |
Arguments passed to the summary function
(and to the function |
dataname |
Character string giving an optional (alternative)
name to the point pattern, different from what is given
in the call. This name, if supplied, may be used by
|
verb |
Logical value. If |
envelope |
Logical value. If |
reuse |
Logical value indicating whether the envelopes in each panel
should be based on the same set of simulated patterns
( |
Details
This routine is a convenient way to analyse the dependence between
types in a multitype point pattern.
It computes the estimates of a selected summary function of the
pattern, for all possible combinations of marks.
It returns these functions in an array
(an object of class "fasp") amenable to plotting
by plot.fasp().
The argument fun specifies the summary function that will
be evaluated for each type of point, or for each pair of types.
It may be either an R function or a character string.
Suppose that the points have possible types 1,2,…,m and let X[i] denote the pattern of points of type i only.
If fun="F" then this routine
calculates, for each possible type i,
an estimate of the Empty Space Function F[i](r) of
X[i]. See Fest
for explanation of the empty space function.
The estimate is computed by applying Fest
to X[i] with the optional arguments ....
If fun is
"Gcross", "Jcross", "Kcross" or "Lcross",
the routine calculates, for each pair of types (i,j),
an estimate of the “i-toj” cross-type function
G[i,j](r),
J[i,j](r),
K[i,j](r) or
L[i,j](r) respectively describing the
dependence between
X[i] and X[j].
See Gcross, Jcross, Kcross
or Lcross respectively for explanation of these
functions.
The estimate is computed by applying the relevant function
(Gcross etc)
to X using each possible value of the arguments i,j,
together with the optional arguments ....
If fun is "pcf" the routine calculates
the cross-type pair correlation function pcfcross
between each pair of types.
If fun is
"Gdot", "Jdot", "Kdot" or "Ldot",
the routine calculates, for each type i,
an estimate of the “i-to-any” dot-type function
G[i.](r),
J[i.](r) or
K[i.](r) or
L[i.](r) respectively describing the
dependence between X[i] and X.
See Gdot, Jdot, Kdot
or Ldot respectively for explanation of these functions.
The estimate is computed by applying the relevant function
(Gdot etc)
to X using each possible value of the argument i,
together with the optional arguments ....
The letters "G", "J", "K" and "L"
are interpreted as abbreviations for Gcross,
Jcross, Kcross and Lcross
respectively, assuming the point pattern is
marked. If the point pattern is unmarked, the appropriate
function Fest, Jest,
Kest or Lest is invoked instead.
If envelope=TRUE, then as well as computing the value of the
summary function for each combination of types, the algorithm also
computes simulation envelopes of the summary function for each
combination of types. The arguments ... are passed to the function
envelope to control the number of
simulations, the random process generating the simulations,
the construction of envelopes, and so on.
When envelope=TRUE it is possible that errors could occur
because the simulated point patterns do not satisfy the requirements
of the summary function (for example, because the simulated pattern
is empty and fun requires at least one point). If the number
of such errors exceeds the maximum permitted number maxnerr,
then the envelope algorithm will give up, and will return
the empirical summary function for the data point pattern,
fun(X), in place of the envelope.
Value
A function array (an object of class "fasp",
see fasp.object). This can be plotted
using plot.fasp.
If the pattern is not marked, the resulting “array” has dimensions 1 x 1. Otherwise the following is true:
If fun="F",
the function array has dimensions m * 1
where m is the number of different marks in the point pattern.
The entry at position [i,1] in this array
is the result of applying Fest to the
points of type i only.
If fun is "Gdot", "Jdot", "Kdot"
or "Ldot", the function array
again has dimensions m * 1.
The entry at position [i,1] in this array
is the result of Gdot(X, i), Jdot(X, i)
Kdot(X, i) or Ldot(X, i) respectively.
If fun is "Gcross", "Jcross", "Kcross"
or "Lcross"
(or their abbreviations "G", "J", "K" or "L"),
the function array has dimensions m * m.
The [i,j] entry of the function array
(for i != j) is the
result of applying the function Gcross,
Jcross, Kcross orLcross to
the pair of types (i,j). The diagonal
[i,i] entry of the function array is the result of
applying the univariate function Gest,
Jest, Kest or Lest to the
points of type i only.
If envelope=FALSE, then
each function entry fns[[i]] retains the format
of the output of the relevant estimating routine
Fest, Gest, Jest,
Kest, Lest, Gcross,
Jcross ,Kcross, Lcross,
Gdot, Jdot, Kdot or
Ldot
The default formulae for plotting these functions are
cbind(km,theo) ~ r for F, G, and J functions, and
cbind(trans,theo) ~ r for K and L functions.
If envelope=TRUE, then each function entry fns[[i]]
has the same format as the output of the envelope command.
Note
Sizeable amounts of memory may be needed during the calculation.
Author(s)
\adrianand \rolf.
See Also
plot.fasp,
fasp.object,
Fest,
Gest,
Jest,
Kest,
Lest,
Gcross,
Jcross,
Kcross,
Lcross,
Gdot,
Jdot,
Kdot,
envelope.
Examples
# bramblecanes (3 marks).
bram <- bramblecanes
bF <- alltypes(bram,"F",verb=TRUE)
plot(bF)
if(interactive()) {
plot(alltypes(bram,"G"))
plot(alltypes(bram,"Gdot"))
}
# Swedishpines (unmarked).
swed <- swedishpines
plot(alltypes(swed,"K"))
plot(alltypes(amacrine, "pcf"), ylim=c(0,1.3))
# A setting where you might REALLY want to use dataname:
# xxx <- alltypes(ppp(Melvin$x,Melvin$y,
# window=as.owin(c(5,20,15,50)),marks=clyde),
# fun="F",verb=TRUE,dataname="Melvin")
# envelopes
bKE <- alltypes(bram,"K",envelope=TRUE,nsim=19)
# global version:
# bFE <- alltypes(bram,"F",envelope=TRUE,nsim=19,global=TRUE)
# extract one entry
as.fv(bKE[1,1])
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