qqplot.ppm: Q-Q Plot of Residuals from Fitted Point Process Model
In spatstat.model: Parametric Statistical Modelling and Inference for the 'spatstat' Family
qqplot.ppm R Documentation
Q-Q Plot of Residuals from Fitted Point Process Model
Description
Given a point process model fitted to a point pattern,
produce a Q-Q plot based on residuals from the model.
Usage
qqplot.ppm(fit, nsim=100, expr=NULL, ..., type="raw",
style="mean", fast=TRUE, verbose=TRUE, plot.it=TRUE,
dimyx=NULL, nrep=if(fast) 5e4 else 1e5,
control=update(default.rmhcontrol(fit), nrep=nrep),
saveall=FALSE,
monochrome=FALSE,
limcol=if(monochrome) "black" else "red",
maxerr=max(100, ceiling(nsim/10)),
check=TRUE, repair=TRUE, envir.expr)
Arguments
fit
The fitted point process model, which is to be assessed
using the Q-Q plot. An object of class "ppm".
Smoothed residuals obtained from this fitted model will provide the
“data” quantiles for the Q-Q plot.
nsim
The number of simulations from the “reference” point process model.
expr
Determines the simulation mechanism
which provides the “theoretical” quantiles for the
Q-Q plot. See Details.
...
Arguments passed to diagnose.ppm influencing the
computation of residuals.
type
String indicating the type of residuals or weights to be used.
Current options are "eem"
for the Stoyan-Grabarnik exponential energy weights,
"raw" for the raw residuals,
"inverse" for the inverse-lambda residuals,
and "pearson" for the Pearson residuals.
A partial match is adequate.
style
Character string controlling the type of Q-Q plot.
Options are "classical" and "mean".
See Details.
fast
Logical flag controlling the speed and accuracy of computation.
Use fast=TRUE for interactive use and fast=FALSE
for publication standard plots. See Details.
verbose
Logical flag controlling whether the algorithm prints progress
reports during long computations.
plot.it
Logical flag controlling whether the function produces a plot
or simply returns a value (silently).
dimyx
Dimensions of the pixel grid on which the smoothed residual field
will be calculated. A vector of two integers.
nrep
If control is absent, then nrep gives the
number of iterations of the Metropolis-Hastings algorithm
that should be used to generate one simulation of the fitted point process.
control
List of parameters controlling the Metropolis-Hastings algorithm
rmh which generates each simulated realisation from
the model (unless the model is Poisson).
This list becomes the argument control
of rmh.default. It overrides nrep.
saveall
Logical flag indicating whether to save all the intermediate
calculations.
monochrome
Logical flag indicating whether the plot should be
in black and white (monochrome=TRUE), or in colour
(monochrome=FALSE).
limcol
String. The colour to be used when plotting the 95% limit
curves.
maxerr
Maximum number of failures tolerated while generating
simulated realisations. See Details.
check
Logical value indicating whether to check the internal format
of fit. If there is any possibility that this object
has been restored from a dump file, or has otherwise lost track of
the environment where it was originally computed, set
check=TRUE.
repair
Logical value indicating whether to repair the internal format
of fit, if it is found to be damaged.
envir.expr
Optional. An environment in which the expression
expr should be evaluated.
Details
This function generates a Q-Q plot of the residuals from a
fitted point process model. It is an addendum to the suite of
diagnostic plots produced by the function diagnose.ppm,
kept separate because it is computationally intensive. The
quantiles of the theoretical distribution are estimated by simulation.
In classical statistics, a Q-Q plot of residuals is a useful
diagnostic for checking the distributional assumptions. Analogously,
in spatial statistics, a Q-Q plot of the (smoothed) residuals from a
fitted point process model is a useful way
to check the interpoint interaction part of the model
(Baddeley et al, 2005). The systematic part of the model
(spatial trend, covariate effects, etc) is assessed using
other plots made by diagnose.ppm.
The argument fit represents the fitted point process
model. It must be an object of class "ppm" (typically produced
by the maximum pseudolikelihood fitting algorithm ppm).
Residuals will be computed for this fitted model using
residuals.ppm,
and the residuals will be kernel-smoothed to produce a “residual
field”. The values of this residual field will provide the
“data” quantiles for the Q-Q plot.
The argument expr is not usually specified.
It provides a way to modify the “theoretical” or “reference”
quantiles for the Q-Q plot.
In normal usage we set expr=NULL. The default
is to generate nsim simulated realisations
of the fitted model fit, re-fit this model to
each of the simulated patterns,
evaluate the residuals from
these fitted models, and use the kernel-smoothed residual field
from these fitted models as a sample from the reference distribution
for the Q-Q plot.
In advanced use, expr may be an expression.
It will be re-evaluated nsim times, and should include
random computations so that the results are not identical
each time. The result of evaluating expr
should be either a point pattern (object of class
"ppp") or a fitted point process model (object of class
"ppm"). If the value is a point pattern, then the
original fitted model fit will be fitted to this new point
pattern using update.ppm, to yield another fitted
model. Smoothed residuals obtained from these
nsim fitted models will yield the “theoretical” quantiles for the
Q-Q plot.
Alternatively expr can be a list of point patterns,
or an envelope object that contains a list of point patterns
(typically generated by calling envelope with
savepatterns=TRUE). These point patterns will be used
as the simulated patterns.
Simulation is performed (if expr=NULL)
using the Metropolis-Hastings algorithm rmh.
Each simulated realisation is the result of
running the Metropolis-Hastings algorithm
from an independent random starting state each time.
The iterative and termination behaviour of the Metropolis-Hastings
algorithm are governed by the argument control.
See rmhcontrol for information about this argument.
As a shortcut, the argument nrep determines
the number of Metropolis-Hastings iterations used to generate
each simulated realisation, if control is absent.
By default, simulations are generated in an expanded
window. Use the argument control to change this,
as explained in the section on Warning messages.
The argument type selects the type of residual or weight
that will be computed. For options, see diagnose.ppm.
The argument style determines the type of Q-Q plot. It is
highly recommended to use the default, style="mean".
style="classical"-
The quantiles of the residual field for the data (on the y
axis) are plotted against the
quantiles of the pooled simulations (on the x axis).
This plot is biased, and therefore difficult to interpret,
because of strong autocorrelations in the residual field
and the large differences in sample size.
style="mean"-
The order statistics of the residual field for the data are plotted
against the sample means, over the nsim simulations,
of the corresponding order statistics of the residual field
for the simulated datasets.
Dotted lines show the 2.5 and 97.5 percentiles, over the
nsim simulations, of each order statistic.
The argument fast is a simple way to control
the accuracy and speed of computation.
If fast=FALSE, the residual field is computed on
a fine grid of pixels (by default 100 by 100 pixels, see below)
and the Q-Q plot is based on the complete set of order statistics
(usually 10,000 quantiles).
If fast=TRUE, the residual field is computed on a coarse
grid (at most 40 by 40 pixels) and the Q-Q plot is based on the
percentiles only. This is about 7 times faster.
It is recommended to use fast=TRUE for interactive data
analysis and fast=FALSE for definitive plots for
publication.
The argument dimyx gives full control over the resolution of the
pixel grid used to calculate the smoothed residuals.
Its interpretation is the same as the argument dimyx
to the function as.mask.
Note that dimyx[1] is the number of
pixels in the y direction, and dimyx[2] is the number
in the x direction.
If dimyx is not present, then the default pixel grid dimensions
are controlled by spatstat.options("npixel").
Since the computation is so time-consuming, qqplot.ppm returns
a list containing all the data necessary to re-display the Q-Q plot.
It is advisable to assign the result of qqplot.ppm to something
(or use .Last.value if you forgot to.)
The return value is an object of class "qqppm". There are methods for
plot.qqppm and print.qqppm. See the
Examples.
The argument saveall is usually set to FALSE.
If saveall=TRUE, then the intermediate results of calculation for each
simulated realisation are saved and returned. The return value
includes a 3-dimensional array sim containing the
smoothed residual field images for each of the nsim
realisations. When saveall=TRUE, the return value is an object of very
large size, and should not be saved on disk.
Errors may occur during the simulation process, because
random data are generated. For example:
one of the simulated patterns may be empty.
one of the simulated patterns may
cause an error in the code that fits the point process model.
the user-supplied argument expr may have a bug.
Empty point patterns do not cause a problem for the code,
but they are reported.
Other problems that would lead to a crash are trapped;
the offending simulated data are discarded, and the simulation is
retried. The argument maxerr determines the maximum number of
times that such errors will be tolerated (mainly as a
safeguard against an infinite loop).
Value
An object of class "qqppm" containing the information
needed to reproduce the Q-Q plot.
Entries x and y are numeric vectors containing
quantiles of the simulations and of the data, respectively.
Side Effects
Produces a Q-Q plot if plot.it is TRUE.
Warning messages
A warning message will be issued if any of the simulations
trapped an error (a potential crash).
A warning message will be issued if all, or many, of the
simulated point patterns are empty.
This usually indicates a problem with the simulation procedure.
The default behaviour of qqplot.ppm is to simulate patterns
on an expanded window (specified through the argument
control) in order to avoid edge effects.
The model's trend is extrapolated over this expanded
window. If the trend is strongly inhomogeneous, the
extrapolated trend may have very large (or even infinite)
values. This can cause the simulation algorithm to
produce empty patterns.
The only way to suppress this problem entirely is to
prohibit the expansion of the window, by setting
the control argument to something like
control=list(nrep=1e6, expand=1). Here expand=1
means there will be no expansion. See rmhcontrol
for more information about the argument control.
Author(s)
\adrian
and \rolf
References
Baddeley, A., Turner, R., \Moller, J. and Hazelton, M. (2005)
Residual analysis for spatial point processes.
Journal of the Royal Statistical Society, Series B
67, 617–666.
Stoyan, D. and Grabarnik, P. (1991)
Second-order characteristics for stochastic structures connected with
Gibbs point processes.
Mathematische Nachrichten, 151:95–100.
See Also
diagnose.ppm,
lurking,
residuals.ppm,
eem,
ppm.object,
ppm,
rmh,
rmhcontrol
Examples
fit <- ppm(cells ~1, Poisson())
diagnose.ppm(fit) # no suggestion of departure from stationarity
if(interactive()) {
qqplot.ppm(fit, 80) # strong evidence of non-Poisson interaction
diagnose.ppm(fit, type="pearson")
qqplot.ppm(fit, type="pearson")
}
# capture the plot coordinates
mypreciousdata <- qqplot.ppm(fit, 4, type="pearson")
## or use the idiom .Last.value if you forgot to assign them
qqplot.ppm(fit, 4, type="pearson")
mypreciousdata <- .Last.value
plot(mypreciousdata)
######################################################
# Q-Q plots based on fixed n
# The above QQ plots used simulations from the (fitted) Poisson process.
# But I want to simulate conditional on n, instead of Poisson
# Do this by setting rmhcontrol(p=1)
fixit <- list(p=1)
if(interactive()) {qqplot.ppm(fit, 100, control=fixit)}
######################################################
# Inhomogeneous Poisson data
X <- rpoispp(function(x,y){1000 * exp(-3*x)}, 1000)
plot(X)
# Inhomogeneous Poisson model
fit <- ppm(X ~x, Poisson())
if(interactive()) {qqplot.ppm(fit, 100)}
# conclusion: fitted inhomogeneous Poisson model looks OK
######################################################
# Advanced use of 'expr' argument
#
# set the initial conditions in Metropolis-Hastings algorithm
#
expr <- expression(rmh(fit, start=list(n.start=42), verbose=FALSE))
if(interactive()) qqplot.ppm(fit, 100, expr)
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| qqplot.ppm | R Documentation |
Q-Q Plot of Residuals from Fitted Point Process Model
Description
Given a point process model fitted to a point pattern, produce a Q-Q plot based on residuals from the model.
Usage
qqplot.ppm(fit, nsim=100, expr=NULL, ..., type="raw",
style="mean", fast=TRUE, verbose=TRUE, plot.it=TRUE,
dimyx=NULL, nrep=if(fast) 5e4 else 1e5,
control=update(default.rmhcontrol(fit), nrep=nrep),
saveall=FALSE,
monochrome=FALSE,
limcol=if(monochrome) "black" else "red",
maxerr=max(100, ceiling(nsim/10)),
check=TRUE, repair=TRUE, envir.expr)
Arguments
fit |
The fitted point process model, which is to be assessed
using the Q-Q plot. An object of class |
nsim |
The number of simulations from the “reference” point process model. |
expr |
Determines the simulation mechanism which provides the “theoretical” quantiles for the Q-Q plot. See Details. |
... |
Arguments passed to |
type |
String indicating the type of residuals or weights to be used.
Current options are |
style |
Character string controlling the type of Q-Q plot.
Options are |
fast |
Logical flag controlling the speed and accuracy of computation.
Use |
verbose |
Logical flag controlling whether the algorithm prints progress reports during long computations. |
plot.it |
Logical flag controlling whether the function produces a plot or simply returns a value (silently). |
dimyx |
Dimensions of the pixel grid on which the smoothed residual field will be calculated. A vector of two integers. |
nrep |
If |
control |
List of parameters controlling the Metropolis-Hastings algorithm
|
saveall |
Logical flag indicating whether to save all the intermediate calculations. |
monochrome |
Logical flag indicating whether the plot should be
in black and white ( |
limcol |
String. The colour to be used when plotting the 95% limit curves. |
maxerr |
Maximum number of failures tolerated while generating simulated realisations. See Details. |
check |
Logical value indicating whether to check the internal format
of |
repair |
Logical value indicating whether to repair the internal format
of |
envir.expr |
Optional. An environment in which the expression
|
Details
This function generates a Q-Q plot of the residuals from a
fitted point process model. It is an addendum to the suite of
diagnostic plots produced by the function diagnose.ppm,
kept separate because it is computationally intensive. The
quantiles of the theoretical distribution are estimated by simulation.
In classical statistics, a Q-Q plot of residuals is a useful
diagnostic for checking the distributional assumptions. Analogously,
in spatial statistics, a Q-Q plot of the (smoothed) residuals from a
fitted point process model is a useful way
to check the interpoint interaction part of the model
(Baddeley et al, 2005). The systematic part of the model
(spatial trend, covariate effects, etc) is assessed using
other plots made by diagnose.ppm.
The argument fit represents the fitted point process
model. It must be an object of class "ppm" (typically produced
by the maximum pseudolikelihood fitting algorithm ppm).
Residuals will be computed for this fitted model using
residuals.ppm,
and the residuals will be kernel-smoothed to produce a “residual
field”. The values of this residual field will provide the
“data” quantiles for the Q-Q plot.
The argument expr is not usually specified.
It provides a way to modify the “theoretical” or “reference”
quantiles for the Q-Q plot.
In normal usage we set expr=NULL. The default
is to generate nsim simulated realisations
of the fitted model fit, re-fit this model to
each of the simulated patterns,
evaluate the residuals from
these fitted models, and use the kernel-smoothed residual field
from these fitted models as a sample from the reference distribution
for the Q-Q plot.
In advanced use, expr may be an expression.
It will be re-evaluated nsim times, and should include
random computations so that the results are not identical
each time. The result of evaluating expr
should be either a point pattern (object of class
"ppp") or a fitted point process model (object of class
"ppm"). If the value is a point pattern, then the
original fitted model fit will be fitted to this new point
pattern using update.ppm, to yield another fitted
model. Smoothed residuals obtained from these
nsim fitted models will yield the “theoretical” quantiles for the
Q-Q plot.
Alternatively expr can be a list of point patterns,
or an envelope object that contains a list of point patterns
(typically generated by calling envelope with
savepatterns=TRUE). These point patterns will be used
as the simulated patterns.
Simulation is performed (if expr=NULL)
using the Metropolis-Hastings algorithm rmh.
Each simulated realisation is the result of
running the Metropolis-Hastings algorithm
from an independent random starting state each time.
The iterative and termination behaviour of the Metropolis-Hastings
algorithm are governed by the argument control.
See rmhcontrol for information about this argument.
As a shortcut, the argument nrep determines
the number of Metropolis-Hastings iterations used to generate
each simulated realisation, if control is absent.
By default, simulations are generated in an expanded
window. Use the argument control to change this,
as explained in the section on Warning messages.
The argument type selects the type of residual or weight
that will be computed. For options, see diagnose.ppm.
The argument style determines the type of Q-Q plot. It is
highly recommended to use the default, style="mean".
style="classical"-
The quantiles of the residual field for the data (on the
yaxis) are plotted against the quantiles of the pooled simulations (on thexaxis). This plot is biased, and therefore difficult to interpret, because of strong autocorrelations in the residual field and the large differences in sample size. style="mean"-
The order statistics of the residual field for the data are plotted against the sample means, over the
nsimsimulations, of the corresponding order statistics of the residual field for the simulated datasets. Dotted lines show the 2.5 and 97.5 percentiles, over thensimsimulations, of each order statistic.
The argument fast is a simple way to control
the accuracy and speed of computation.
If fast=FALSE, the residual field is computed on
a fine grid of pixels (by default 100 by 100 pixels, see below)
and the Q-Q plot is based on the complete set of order statistics
(usually 10,000 quantiles).
If fast=TRUE, the residual field is computed on a coarse
grid (at most 40 by 40 pixels) and the Q-Q plot is based on the
percentiles only. This is about 7 times faster.
It is recommended to use fast=TRUE for interactive data
analysis and fast=FALSE for definitive plots for
publication.
The argument dimyx gives full control over the resolution of the
pixel grid used to calculate the smoothed residuals.
Its interpretation is the same as the argument dimyx
to the function as.mask.
Note that dimyx[1] is the number of
pixels in the y direction, and dimyx[2] is the number
in the x direction.
If dimyx is not present, then the default pixel grid dimensions
are controlled by spatstat.options("npixel").
Since the computation is so time-consuming, qqplot.ppm returns
a list containing all the data necessary to re-display the Q-Q plot.
It is advisable to assign the result of qqplot.ppm to something
(or use .Last.value if you forgot to.)
The return value is an object of class "qqppm". There are methods for
plot.qqppm and print.qqppm. See the
Examples.
The argument saveall is usually set to FALSE.
If saveall=TRUE, then the intermediate results of calculation for each
simulated realisation are saved and returned. The return value
includes a 3-dimensional array sim containing the
smoothed residual field images for each of the nsim
realisations. When saveall=TRUE, the return value is an object of very
large size, and should not be saved on disk.
Errors may occur during the simulation process, because random data are generated. For example:
one of the simulated patterns may be empty.
one of the simulated patterns may cause an error in the code that fits the point process model.
the user-supplied argument
exprmay have a bug.
Empty point patterns do not cause a problem for the code,
but they are reported.
Other problems that would lead to a crash are trapped;
the offending simulated data are discarded, and the simulation is
retried. The argument maxerr determines the maximum number of
times that such errors will be tolerated (mainly as a
safeguard against an infinite loop).
Value
An object of class "qqppm" containing the information
needed to reproduce the Q-Q plot.
Entries x and y are numeric vectors containing
quantiles of the simulations and of the data, respectively.
Side Effects
Produces a Q-Q plot if plot.it is TRUE.
Warning messages
A warning message will be issued if any of the simulations trapped an error (a potential crash).
A warning message will be issued if all, or many, of the simulated point patterns are empty. This usually indicates a problem with the simulation procedure.
The default behaviour of qqplot.ppm is to simulate patterns
on an expanded window (specified through the argument
control) in order to avoid edge effects.
The model's trend is extrapolated over this expanded
window. If the trend is strongly inhomogeneous, the
extrapolated trend may have very large (or even infinite)
values. This can cause the simulation algorithm to
produce empty patterns.
The only way to suppress this problem entirely is to
prohibit the expansion of the window, by setting
the control argument to something like
control=list(nrep=1e6, expand=1). Here expand=1
means there will be no expansion. See rmhcontrol
for more information about the argument control.
Author(s)
\adrianand \rolf
References
Baddeley, A., Turner, R., \Moller, J. and Hazelton, M. (2005) Residual analysis for spatial point processes. Journal of the Royal Statistical Society, Series B 67, 617–666.
Stoyan, D. and Grabarnik, P. (1991) Second-order characteristics for stochastic structures connected with Gibbs point processes. Mathematische Nachrichten, 151:95–100.
See Also
diagnose.ppm,
lurking,
residuals.ppm,
eem,
ppm.object,
ppm,
rmh,
rmhcontrol
Examples
fit <- ppm(cells ~1, Poisson())
diagnose.ppm(fit) # no suggestion of departure from stationarity
if(interactive()) {
qqplot.ppm(fit, 80) # strong evidence of non-Poisson interaction
diagnose.ppm(fit, type="pearson")
qqplot.ppm(fit, type="pearson")
}
# capture the plot coordinates
mypreciousdata <- qqplot.ppm(fit, 4, type="pearson")
## or use the idiom .Last.value if you forgot to assign them
qqplot.ppm(fit, 4, type="pearson")
mypreciousdata <- .Last.value
plot(mypreciousdata)
######################################################
# Q-Q plots based on fixed n
# The above QQ plots used simulations from the (fitted) Poisson process.
# But I want to simulate conditional on n, instead of Poisson
# Do this by setting rmhcontrol(p=1)
fixit <- list(p=1)
if(interactive()) {qqplot.ppm(fit, 100, control=fixit)}
######################################################
# Inhomogeneous Poisson data
X <- rpoispp(function(x,y){1000 * exp(-3*x)}, 1000)
plot(X)
# Inhomogeneous Poisson model
fit <- ppm(X ~x, Poisson())
if(interactive()) {qqplot.ppm(fit, 100)}
# conclusion: fitted inhomogeneous Poisson model looks OK
######################################################
# Advanced use of 'expr' argument
#
# set the initial conditions in Metropolis-Hastings algorithm
#
expr <- expression(rmh(fit, start=list(n.start=42), verbose=FALSE))
if(interactive()) qqplot.ppm(fit, 100, expr)
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