| Title: | Spatial and Space-Time Point Pattern Analysis |
|---|---|
| Description: | The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode". |
| Authors: | Roger Bivand [cre], Barry Rowlingson [aut], Peter Diggle [aut], Giovanni Petris [ctb], Stephen Eglen [ctb] |
| Maintainer: | Roger Bivand <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 2.01-41 |
| Built: | 2024-09-07 04:19:25 UTC |
| Source: | https://github.com/barryrowlingson/splancs |
Add points interactively to a point data set.
addpoints(pts,plot=FALSE,quiet=FALSE)addpoints(pts,plot=FALSE,quiet=FALSE)
pts |
A points data set. |
plot |
if true, plot the |
quiet |
if true, don't print a prompt to enter points. |
The points entered are displayed on the current graphics device.
A points data set consisting of pts and the points entered on the current
graphics device.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Two two-column matrices of points marked on and off
data(amacrines)data(amacrines)
Two two-column matrices of points marked on and off
http://www.maths.lancs.ac.uk/~diggle/pointpatterns/Datasets/, Peter J. Diggle, Department of Mathematics and Statistics, Lancaster University, Lancaster LA1 4YF, UK: public-domain spatial point pattern data-sets.
Calculate area of polygon. If the polygon is self-intersecting, the area will not be correct.
areapl(poly)areapl(poly)
poly |
a polygon data set |
The area of the polygon is returned
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
x <- c(1,0,0,1,1,1,1,3,3,1) y <- c(0,0,1,1,0,0,-1,-1,0,0) m <- cbind(x, y) plot(m, type="b") areapl(m) areapl(m[1:5,]) areapl(m[6:10,])x <- c(1,0,0,1,1,1,1,3,3,1) y <- c(0,0,1,1,0,0,-1,-1,0,0) m <- cbind(x, y) plot(m, type="b") areapl(m) areapl(m[1:5,]) areapl(m[6:10,])
Creates data in spatial point format.
as.points(...)as.points(...)
... |
any object(s), such as x and y vectors of the same length, or a list or data
frame containing x and y vectors. Valid options for |
as.points tries to return the argument(s) as a points object.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Generate a non-closed bounding polygon from the bounding box of an object
bboxx(obj)bboxx(obj)
obj |
A matrix with two rows and two columns reporting the bounding box of an object |
The object used by bboxx may easily be created by using the sp bbox method on an object of interest, such as a points data set.
A points data set of four points giving the non-closed coordinates of the bounding box
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Locations of 35 granite tors on Bodmin Moor, taken from Infomap data set (northings multiplied by -1 to correspond to Figure 3.2, p. 82, Bailey and Gatrell.
data(bodmin)data(bodmin)
A list corresponding to a Venables and Ripley point object with 35 observations
| x | numeric | grid eastings |
| y | numeric | grid northings |
| area | list | bounding box with xl, xu, yl, yu |
| poly | array | polygon boundary with columns x and y |
Pinder and Witherick, 1977 - Bailey and Gatrell 1995, ch. 3.
Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow.
Locations of cases of Burkitt's lymphoma in the Western Nile
district of Uganda 1960-1975. The time variable is recorded as the number of
days starting from an origin of 1 Jan 1960. The examples given below show
how the chron() function and derived time structures may be used to
analyse the data in the time dimension.
data(burkitt)data(burkitt)
The data is provided as a data table:
| x | numeric | grid eastings |
| y | numeric | grid northings |
| t | numeric | day number starting at 1/1/1960 of onset |
| age | numeric | age of child patient |
| dates | factor | day as string yy-mm-dd |
as a points object burpts of burkitt$x and burkitt$y; and a point object of the area boundary burbdy.
Williams, E. H. et al. 1978, - Bailey and Gatrell 1995, ch. 3.
Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow.
data(burkitt) burDates <- as.Date(as.character(burkitt$dates), "%y-%m-%d") res <- aggregate(rep(1, length(burDates)), list(quarters(burDates), format(burDates, "%y")), sum) plot(as.numeric(as.character(res$Group.2)) + 0.25*(as.numeric(substr(as.character(res$Group.1), 2, 2))-1), res$x, type="h", lwd=3, col=ifelse(as.character(res$Group.1)=="Q3", "grey","red"), xlab="year", ylab="count", xaxt="n") axis(1, at=seq(61,75,4), labels=format(seq.Date(as.Date("1961/1/1"), as.Date("1975/1/1"), "4 years"))) title("Plot of Burkitt's lymphoma in West Nile district,\nQ3 grey shaded") op <- par(mfrow=c(3,5)) for (i in unique(format(burDates, "%y"))) { polymap(burbdy) pointmap(burpts[which(format(burDates, "%y") == i),], add=TRUE, pch=19) title(main=paste("19", i, sep="")) } par(op) op <- par(mfrow=c(2,2)) for (i in c("Q1", "Q2", "Q3", "Q4")) { polymap(burbdy) pointmap(burpts[which(unclass(quarters(burDates)) == i),], add=TRUE, pch=19) title(main=i) } par(op) op <- par(mfrow=c(3,4)) for (i in months(seq(as.Date("70-01-01", "%y-%m-%d"), len=12, by="1 month"))) { polymap(burbdy) pointmap(burpts[which(unclass(months(burDates)) == i),], add=TRUE, pch=19) title(main=i) } par(op)data(burkitt) burDates <- as.Date(as.character(burkitt$dates), "%y-%m-%d") res <- aggregate(rep(1, length(burDates)), list(quarters(burDates), format(burDates, "%y")), sum) plot(as.numeric(as.character(res$Group.2)) + 0.25*(as.numeric(substr(as.character(res$Group.1), 2, 2))-1), res$x, type="h", lwd=3, col=ifelse(as.character(res$Group.1)=="Q3", "grey","red"), xlab="year", ylab="count", xaxt="n") axis(1, at=seq(61,75,4), labels=format(seq.Date(as.Date("1961/1/1"), as.Date("1975/1/1"), "4 years"))) title("Plot of Burkitt's lymphoma in West Nile district,\nQ3 grey shaded") op <- par(mfrow=c(3,5)) for (i in unique(format(burDates, "%y"))) { polymap(burbdy) pointmap(burpts[which(format(burDates, "%y") == i),], add=TRUE, pch=19) title(main=paste("19", i, sep="")) } par(op) op <- par(mfrow=c(2,2)) for (i in c("Q1", "Q2", "Q3", "Q4")) { polymap(burbdy) pointmap(burpts[which(unclass(quarters(burDates)) == i),], add=TRUE, pch=19) title(main=i) } par(op) op <- par(mfrow=c(3,4)) for (i in months(seq(as.Date("70-01-01", "%y-%m-%d"), len=12, by="1 month"))) { polymap(burbdy) pointmap(burpts[which(unclass(months(burDates)) == i),], add=TRUE, pch=19) title(main=i) } par(op)
Locations of homes of 168 juvenile offenders on a Cardiff housing estate
data(cardiff)data(cardiff)
A list corresponding to a Venables and Ripley point object with 168 observations
| x | numeric | grid eastings |
| y | numeric | grid northings |
| area | list | bounding box with xl, xu, yl, yu |
| poly | array | polygon boundary with columns x and y |
Herbert, 1980, - Bailey and Gatrell 1995, ch. 3.
Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow.
Generate completely spatially random points on a polygon.
csr(poly,npoints)csr(poly,npoints)
poly |
A polygon data set. |
npoints |
The number of points to generate. |
csr generates points randomly in the bounding box of poly, then uses
pip to extract those in the polygon. If the number of points remaining is
less than that required, csr generates some more points in the
bounding box until at least npoints remain inside the polygon. If too many
points are generated then the list of points is truncated.
Uses runif() to generate random numbers and so updates .Random.seed,
the standard S random number generator seed.
A point data set consisting of npoints points distributed randomly,
i.e. as an independent random sample from the uniform distribution
in the polygon defined by poly.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(cardiff) nsim <- 29 emp.Ghat <- Ghat(as.points(cardiff), seq(0,30,1)) av.Ghat <- numeric(length(emp.Ghat)) U.Ghat <- numeric(length(emp.Ghat)) L.Ghat <- numeric(length(emp.Ghat)) U.Ghat <- -99999 L.Ghat <- 99999 for(i in 1:nsim) { S.Ghat <- Ghat(csr(cardiff$poly, length(cardiff$x)), seq(0,30,1)) av.Ghat <- av.Ghat + S.Ghat L.Ghat <- pmin(S.Ghat, L.Ghat) U.Ghat <- pmax(S.Ghat, U.Ghat) } av.Ghat <- av.Ghat/nsim plot(av.Ghat, emp.Ghat, type="l", xlim=c(0,1), ylim=c(0,1), xlab="Simulated average G", ylab="Empirical G") lines(c(0,1),c(0,1),lty=2) lines(U.Ghat,emp.Ghat,lty=3) lines(L.Ghat,emp.Ghat,lty=3)data(cardiff) nsim <- 29 emp.Ghat <- Ghat(as.points(cardiff), seq(0,30,1)) av.Ghat <- numeric(length(emp.Ghat)) U.Ghat <- numeric(length(emp.Ghat)) L.Ghat <- numeric(length(emp.Ghat)) U.Ghat <- -99999 L.Ghat <- 99999 for(i in 1:nsim) { S.Ghat <- Ghat(csr(cardiff$poly, length(cardiff$x)), seq(0,30,1)) av.Ghat <- av.Ghat + S.Ghat L.Ghat <- pmin(S.Ghat, L.Ghat) U.Ghat <- pmax(S.Ghat, U.Ghat) } av.Ghat <- av.Ghat/nsim plot(av.Ghat, emp.Ghat, type="l", xlim=c(0,1), ylim=c(0,1), xlab="Simulated average G", ylab="Empirical G") lines(c(0,1),c(0,1),lty=2) lines(U.Ghat,emp.Ghat,lty=3) lines(L.Ghat,emp.Ghat,lty=3)
Select points to delete from a points data set.
delpoints(pts,add=FALSE)delpoints(pts,add=FALSE)
pts |
a points data set |
add |
if false, plot the points using |
Using the mouse, the user selects points on the current graphics device.
These points are marked on the plot as they are selected. The function
returns the remaining points as a points object.
If add is false the points are plotted on the current plot device.
A points object containing the undeleted points.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Computes the distance-squared from a number of points to a number of sources.
dsquare(pts, srcs, namepref="d")dsquare(pts, srcs, namepref="d")
pts |
A number of points representing the locations of cases and controls. |
srcs |
A number of points representing source locations |
namepref |
A prefix given to the name of the results. |
A data frame with the same number of columns as srcs. The column names will
be the value of namepref prefixing the numbers from 1 to the number
of sources.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculates an estimate of the F nearest neighbour distribution function
Fhat(pts1,pts2,s)Fhat(pts1,pts2,s)
pts1 |
A points data set |
pts2 |
A points data set |
s |
A vector of distances at which to evaluate Fhat |
The function Fhat(pts1,pts2,s) is defined as the proportion of members of a
point set pts2 for which the distance to the nearest member of
another points set pts1 is less than or equal to s.
A vector of the same length as s, containing the value of Fhat at the
distances in s.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(uganda) plot(seq(20, 500, 20), Fhat(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))), seq(20, 500, 20)), type="l", xlab="distance", ylab="Estimated F") plot(Ghat(as.points(uganda), seq(20, 500, 20)), Fhat(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))), seq(20, 500, 20)), type="l", xlab="Estimated G", ylab="Estimated F") lines(c(0,1),c(0,1),lty=2)data(uganda) plot(seq(20, 500, 20), Fhat(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))), seq(20, 500, 20)), type="l", xlab="distance", ylab="Estimated F") plot(Ghat(as.points(uganda), seq(20, 500, 20)), Fhat(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))), seq(20, 500, 20)), type="l", xlab="Estimated G", ylab="Estimated F") lines(c(0,1),c(0,1),lty=2)
Calculate the theoretical nearest neighbour distribution function.
Fzero(density,s)Fzero(density,s)
density |
The density of the point pattern, i.e. the number of points per unit area. |
s |
A vector of distances at which to evaluate Fzero |
Fzero returns the nearest neighbour distribution for a homogeneous planar
Poisson process. In fortran notation, Fzero(s) is
FZERO = 1-EXP(-PI*DENSITY*(S**2)).
A vector of the same length as s, containing the value of Fzero at the
distances in s.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(uganda) plot(Ghat(as.points(uganda), seq(20, 500, 20)), Fzero(pdense(as.points(uganda), uganda$poly), seq(20, 500, 20)), type="l", ylab="Theoretical G", xlab="Estimated G") lines(c(0,1),c(0,1),lty=2)data(uganda) plot(Ghat(as.points(uganda), seq(20, 500, 20)), Fzero(pdense(as.points(uganda), uganda$poly), seq(20, 500, 20)), type="l", ylab="Theoretical G", xlab="Estimated G") lines(c(0,1),c(0,1),lty=2)
generates random points within a defined polygon, trying to reach npoints
points - used in csr.
gen(poly, npoints)gen(poly, npoints)
poly |
A polygon data set |
npoints |
The number of points to generate |
returns a point object.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Draw a polygon on the current graphics device
getpoly(quiet=FALSE)getpoly(quiet=FALSE)
quiet |
if TRUE, don't prompt for input of a polygon. |
The system prompts the user to enter points on the current graphics device using the mouse or other pointing device. The points are joined on the screen with the current line symbol. A polygon of the points entered is drawn on the current graphics device.
A polygon data set consisting of the points entered. The current coordinate system is used.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculates an estimate of the G nearest neighbour distribution function.
Ghat(pts,s)Ghat(pts,s)
pts |
A points data set |
s |
A vector of distances at which to evaluate the G function |
The function Ghat(pts,s) is defined as the proportion of members of a
point set for which the distance to the nearest other member of the set
is less than or equal to s.
A vector of the same length as s, containing the estimate of G at the
distances in s.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(uganda) plot(seq(20, 500, 20), Ghat(as.points(uganda), seq(20, 500, 20)), type="l", xlab="distance", ylab="Estimated G")data(uganda) plot(seq(20, 500, 20), Ghat(as.points(uganda), seq(20, 500, 20)), type="l", xlab="distance", ylab="Estimated G")
Generate a grid of points
gridpts(poly,npts,xs,ys)gridpts(poly,npts,xs,ys)
poly |
polygon in which to generate the points |
npts |
approximate number of points to generate |
xs, ys
|
grid spacing in x and y Either |
A points object containing a grid of points inside the polygon. If npts
is specified, then a grid spacing xs and ys will be calculated to give
approximately npts in the polygon. If xs and ys are given then these
will be used to generate a number of points in the polygon.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Test points for inclusion in a polygon.
inout(pts,poly,bound=NULL,quiet=TRUE)inout(pts,poly,bound=NULL,quiet=TRUE)
pts |
A points data set |
poly |
A polygon data set |
bound |
If points fall exactly on polygon boundaries, the default NULL gives arbitrary assignments. If TRUE, then all points "on" boundaries are set as within the polygon, if FALSE, outside. |
quiet |
Do not report which points are on boundary for non-NULL bound |
A vector of logical values. TRUE means the point was inside the
polygon, FALSE means the point was outside. Note that "inside" is an arbitrary concept for points "on" the polygon boundary.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(uganda) suganda <- sbox(uganda$poly) ruganda <- csr(suganda, 1000) polymap(suganda) polymap(uganda$poly, add=TRUE) def <- inout(ruganda, uganda$poly, bound=NULL) pointmap(as.points(ruganda[def,1], ruganda[def,2]), add=TRUE, col="black") pointmap(as.points(ruganda[!def,1], ruganda[!def,2]), add=TRUE, col="red") tru <- inout(ruganda, uganda$poly, bound=TRUE, quiet=FALSE) which(tru & !def) ds1 <- as.points(expand.grid(x=seq(-1.5,1.5,0.5), y=seq(-1.5,1.5,0.5))) ds1.poly <- ds1[chull(ds1),] ds2 <- as.points(rnorm(300),rnorm(300)) plot(ds2, type="n", asp=1) polymap(ds1.poly, add=TRUE, border="lightblue", col="lightblue", lwd=1) points(ds2[inout(ds2,ds1.poly),], col="green", pch=20) points(ds2[!inout(ds2,ds1.poly),], col="orange", pch=20) points(ds1[inout(ds1,ds1.poly),], col="black", pch=20) points(ds1[!inout(ds1,ds1.poly),], col="red", pch=20) plot(ds2, type="n", asp=1) polymap(ds1.poly, add=TRUE, border="lightblue", col="lightblue", lwd=1) points(ds2[inout(ds2,ds1.poly,bound=TRUE),], col="green", pch=20) points(ds2[!inout(ds2,ds1.poly,bound=TRUE),], col="orange", pch=20) points(ds1[inout(ds1,ds1.poly,bound=TRUE),], col="black", pch=20) points(ds1[!inout(ds1,ds1.poly,bound=TRUE),], col="red", pch=20) plot(ds2, type="n", asp=1) polymap(ds1.poly, add=TRUE, border="lightblue", col="lightblue", lwd=1) points(ds2[inout(ds2,ds1.poly,bound=FALSE),], col="green", pch=20) points(ds2[!inout(ds2,ds1.poly,bound=FALSE),], col="orange", pch=20) points(ds1[inout(ds1,ds1.poly,bound=FALSE),], col="black", pch=20) points(ds1[!inout(ds1,ds1.poly,bound=FALSE),], col="red", pch=20)data(uganda) suganda <- sbox(uganda$poly) ruganda <- csr(suganda, 1000) polymap(suganda) polymap(uganda$poly, add=TRUE) def <- inout(ruganda, uganda$poly, bound=NULL) pointmap(as.points(ruganda[def,1], ruganda[def,2]), add=TRUE, col="black") pointmap(as.points(ruganda[!def,1], ruganda[!def,2]), add=TRUE, col="red") tru <- inout(ruganda, uganda$poly, bound=TRUE, quiet=FALSE) which(tru & !def) ds1 <- as.points(expand.grid(x=seq(-1.5,1.5,0.5), y=seq(-1.5,1.5,0.5))) ds1.poly <- ds1[chull(ds1),] ds2 <- as.points(rnorm(300),rnorm(300)) plot(ds2, type="n", asp=1) polymap(ds1.poly, add=TRUE, border="lightblue", col="lightblue", lwd=1) points(ds2[inout(ds2,ds1.poly),], col="green", pch=20) points(ds2[!inout(ds2,ds1.poly),], col="orange", pch=20) points(ds1[inout(ds1,ds1.poly),], col="black", pch=20) points(ds1[!inout(ds1,ds1.poly),], col="red", pch=20) plot(ds2, type="n", asp=1) polymap(ds1.poly, add=TRUE, border="lightblue", col="lightblue", lwd=1) points(ds2[inout(ds2,ds1.poly,bound=TRUE),], col="green", pch=20) points(ds2[!inout(ds2,ds1.poly,bound=TRUE),], col="orange", pch=20) points(ds1[inout(ds1,ds1.poly,bound=TRUE),], col="black", pch=20) points(ds1[!inout(ds1,ds1.poly,bound=TRUE),], col="red", pch=20) plot(ds2, type="n", asp=1) polymap(ds1.poly, add=TRUE, border="lightblue", col="lightblue", lwd=1) points(ds2[inout(ds2,ds1.poly,bound=FALSE),], col="green", pch=20) points(ds2[!inout(ds2,ds1.poly,bound=FALSE),], col="orange", pch=20) points(ds1[inout(ds1,ds1.poly,bound=FALSE),], col="black", pch=20) points(ds1[!inout(ds1,ds1.poly,bound=FALSE),], col="red", pch=20)
Select points inside a polygon
inpip(pts,poly,bound=NULL,quiet=TRUE)inpip(pts,poly,bound=NULL,quiet=TRUE)
pts |
A points data set |
poly |
A polygon data set |
bound |
If points fall exactly on polygon boundaries, the default NULL gives arbitrary assignments. If TRUE, then all points "on" boundaries are set as within the polygon, if FALSE, outside. |
quiet |
Do not report which points are on boundary for non-NULL bound |
inpip returns a vector of indices of the points in pts that are located
in the polygon. Note that "in" is an arbitrary concept for points "on" the polygon boundary.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Tests for data in spatial point format.
is.points(p)is.points(p)
p |
any object. |
is.points returns TRUE if p is a points object, FALSE otherwise.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculates an estimate of the bivariate K-function
k12hat(pts1,pts2,poly,s)k12hat(pts1,pts2,poly,s)
pts1, pts2
|
Two points data sets |
poly |
A polygon containing the points |
s |
A vector of distances at which to estimate the K12 function |
The bivariate K function is defined as the expected number of points of pattern 1 within a distance s of an arbitrary point of pattern 2, divided by the overall density of the points in pattern 1. To estimate this function, the approximately unbiased estimator given by Lotwick and Silverman (1982) is used.
A vector like s containing the value of K12hat at the points in s.
Lotwick, H.W. and Silverman B.W. (1982) Methods for Analysing Spatial Processes of Several types of Points. J. R. Statist Soc B44 406-13; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) plot(seq(5,80,5), sqrt(k12hat(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), seq(5,80,5))/pi) - seq(5,80,5), xlab="distance", ylab=expression(hat(L)[12]), ylim=c(-20,20), type="l")data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) plot(seq(5,80,5), sqrt(k12hat(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), seq(5,80,5))/pi) - seq(5,80,5), xlab="distance", ylab=expression(hat(L)[12]), ylim=c(-20,20), type="l")
Compute envelope of Khat from simulations of complete spatial randomness.
Kenv.csr(nptg,poly,nsim,s,quiet=FALSE)Kenv.csr(nptg,poly,nsim,s,quiet=FALSE)
nptg |
Number of points to generate in each simulation. |
poly |
Polygon in which to generate the points. |
nsim |
Number of simulations to do. |
s |
Vector of distances at which to calculate the envelope. |
quiet |
If FALSE, print a message after every simulation for progress monitoring. If TRUE, print no messages. |
A list with two components, called $upper and $lower. Each
component is a vector like s. The two components contain the upper
and lower bound of the Khat envelope.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(cardiff) UL.khat <- Kenv.csr(length(cardiff$x), cardiff$poly, nsim=29, seq(2,30,2)) plot(seq(2,30,2), sqrt(khat(as.points(cardiff), cardiff$poly, seq(2,30,2))/pi)-seq(2,30,2), type="l", xlab="Splancs - polygon boundary", ylab="Estimated L", ylim=c(-1,1.5)) lines(seq(2,30,2), sqrt(UL.khat$upper/pi)-seq(2,30,2), lty=2) lines(seq(2,30,2), sqrt(UL.khat$lower/pi)-seq(2,30,2), lty=2)data(cardiff) UL.khat <- Kenv.csr(length(cardiff$x), cardiff$poly, nsim=29, seq(2,30,2)) plot(seq(2,30,2), sqrt(khat(as.points(cardiff), cardiff$poly, seq(2,30,2))/pi)-seq(2,30,2), type="l", xlab="Splancs - polygon boundary", ylab="Estimated L", ylim=c(-1,1.5)) lines(seq(2,30,2), sqrt(UL.khat$upper/pi)-seq(2,30,2), lty=2) lines(seq(2,30,2), sqrt(UL.khat$lower/pi)-seq(2,30,2), lty=2)
Compute envelope of K1hat-K2hat from random labelling of two point patterns
Kenv.label(pts1,pts2,poly,nsim,s,quiet=FALSE)Kenv.label(pts1,pts2,poly,nsim,s,quiet=FALSE)
pts1 |
First point data set. |
pts2 |
Second point data set. |
poly |
Polygon containing the points. |
nsim |
Number of random labellings to do. |
s |
Vector of distances at which to calculate the envelope. |
quiet |
If FALSE, print a message after every simulation for progress monitoring. If TRUE, print no messages. |
The two point data sets are randomly labelled using rLabel, then
Khat is called to estimate the K-function for each resulting set
at the distances in s. The difference between these two estimates
is then calculated.
The maximum and minimum values of this difference at each distance,over
the nlab
labellings is returned.
A list with two components, called $upper and $lower. Each
component is a vector like s.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) K1.hat <- khat(as.points(okwhite), bboxx(bbox(as.points(okpoly))), seq(5,80,5)) K2.hat <- khat(as.points(okblack), bboxx(bbox(as.points(okpoly))), seq(5,80,5)) K.diff <- K1.hat-K2.hat plot(seq(5,80,5), K.diff, xlab="distance", ylab=expression(hat(K)[1]-hat(K)[2]), ylim=c(-11000,7000), type="l", main="Simulation envelopes, random labelling") env.lab <- Kenv.label(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), nsim=29, s=seq(5,80,5)) lines(seq(5,80,5), env.lab$upper, lty=2) lines(seq(5,80,5), env.lab$lower, lty=2)data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) K1.hat <- khat(as.points(okwhite), bboxx(bbox(as.points(okpoly))), seq(5,80,5)) K2.hat <- khat(as.points(okblack), bboxx(bbox(as.points(okpoly))), seq(5,80,5)) K.diff <- K1.hat-K2.hat plot(seq(5,80,5), K.diff, xlab="distance", ylab=expression(hat(K)[1]-hat(K)[2]), ylim=c(-11000,7000), type="l", main="Simulation envelopes, random labelling") env.lab <- Kenv.label(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), nsim=29, s=seq(5,80,5)) lines(seq(5,80,5), env.lab$upper, lty=2) lines(seq(5,80,5), env.lab$lower, lty=2)
This function computes the envelope of Khat from simulations of a Poisson Cluster Process for a given polygon
Kenv.pcp(rho, m, s2, region.poly, larger.region=NULL, nsim, r, vectorise.loop=TRUE)Kenv.pcp(rho, m, s2, region.poly, larger.region=NULL, nsim, r, vectorise.loop=TRUE)
rho |
intensity of the parent process |
m |
average number of offsprings per parent |
s2 |
variance of location of offsprings relative to their parent |
region.poly |
a polygon defining the region in which the process is to be generated |
larger.region |
a rectangle containing the region of interest given in the form (xl,xu,yl,yu), defaults to |
nsim |
number of simulations required |
r |
vector of distances at which the K function has to be estimated |
vectorise.loop |
if TRUE, use new vectorised code, if FALSE, use loop as before |
ave |
mean of simulations |
upper |
upper bound of envelope |
lower |
lower bound of envelope |
Giovanni Petris <[email protected]>, [email protected]
Diggle, P. J. (1983) Statistical analysis of spatial point patterns, London: Academic Press, pp. 55-57 and 78-81; Bailey, T. C. and Gatrell, A. C. (1995) Interactive spatial data analysis, Harlow: Longman, pp. 106-109.
data(cardiff) polymap(cardiff$poly) pointmap(as.points(cardiff), add=TRUE) title("Locations of homes of 168 juvenile offenders") pcp.fit <- pcp(as.points(cardiff), cardiff$poly, h0=30, n.int=30) pcp.fit m <- npts(as.points(cardiff))/(areapl(cardiff$poly)*pcp.fit$par[2]) r <- seq(2,30,by=2) K.env <- Kenv.pcp(pcp.fit$par[2], m, pcp.fit$par[1], cardiff$poly, nsim=20, r=r) L.env <- lapply(K.env, FUN=function(x) sqrt(x/pi)-r) limits <- range(unlist(L.env)) plot(r, sqrt(khat(as.points(cardiff),cardiff$poly,r)/pi)-r, ylim=limits, main="L function with simulation envelopes and average", type="l", xlab="distance", ylab="") lines(r, L.env$lower, lty=5) lines(r, L.env$upper, lty=5) lines(r, L.env$ave, lty=6) abline(h=0)data(cardiff) polymap(cardiff$poly) pointmap(as.points(cardiff), add=TRUE) title("Locations of homes of 168 juvenile offenders") pcp.fit <- pcp(as.points(cardiff), cardiff$poly, h0=30, n.int=30) pcp.fit m <- npts(as.points(cardiff))/(areapl(cardiff$poly)*pcp.fit$par[2]) r <- seq(2,30,by=2) K.env <- Kenv.pcp(pcp.fit$par[2], m, pcp.fit$par[1], cardiff$poly, nsim=20, r=r) L.env <- lapply(K.env, FUN=function(x) sqrt(x/pi)-r) limits <- range(unlist(L.env)) plot(r, sqrt(khat(as.points(cardiff),cardiff$poly,r)/pi)-r, ylim=limits, main="L function with simulation envelopes and average", type="l", xlab="distance", ylab="") lines(r, L.env$lower, lty=5) lines(r, L.env$upper, lty=5) lines(r, L.env$ave, lty=6) abline(h=0)
Compute envelope of K12hat from random toroidal shifts of two point patterns.
Kenv.tor(pts1,pts2,poly,nsim,s,quiet=FALSE)Kenv.tor(pts1,pts2,poly,nsim,s,quiet=FALSE)
pts1 |
First point data set. |
pts2 |
Second point data set. |
poly |
Polygon containing the points. |
nsim |
Number of random toroidal shifts to do. |
s |
Vector of distances at which to calculate the envelope. |
quiet |
If FALSE, print a message after every simulation for progress monitoring. If true, print no messages. |
The second point data set is randomly shifted using rtor.shift
in the rectangle defined by poly. Then k12hat is called
to compute K12hat for the two patterns.
The upper and lower values of K12hat over the ntor
toroidal shifts are returned.
A list with two components, called $upper and $lower. Each
component is a vector like s.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) plot(seq(5,80,5), sqrt(k12hat(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), seq(5,80,5))/pi) - seq(5,80,5), xlab="distance", ylab=expression(hat(L)[12]), ylim=c(-35,35), type="l", main="Simulation envelopes, random toroidal shifts") env.ok <- Kenv.tor(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), nsim=29, s=seq(5,80,5)) lines(seq(5,80,5), sqrt(env.ok$upper/pi)-seq(5,80,5), lty=2) lines(seq(5,80,5), sqrt(env.ok$lower/pi)-seq(5,80,5), lty=2)data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) plot(seq(5,80,5), sqrt(k12hat(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), seq(5,80,5))/pi) - seq(5,80,5), xlab="distance", ylab=expression(hat(L)[12]), ylim=c(-35,35), type="l", main="Simulation envelopes, random toroidal shifts") env.ok <- Kenv.tor(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), nsim=29, s=seq(5,80,5)) lines(seq(5,80,5), sqrt(env.ok$upper/pi)-seq(5,80,5), lty=2) lines(seq(5,80,5), sqrt(env.ok$lower/pi)-seq(5,80,5), lty=2)
Modification of Kenv.tor() to allow the assignment of a p value to the
goodness of fit, following the method outlined in Peter Diggle's 1986
paper (J Neurosci methods 18:115-125) and in his 2002 book.
Kenv.tor1(pts1, pts2, poly, nsim, s, quiet = FALSE)Kenv.tor1(pts1, pts2, poly, nsim, s, quiet = FALSE)
pts1 |
First point data set |
pts2 |
Second point data set |
poly |
Polygon containing the points |
nsim |
Number of random toroidal shifts to do |
s |
Vector of distances at which to calculate the envelope |
quiet |
If FALSE, print a message after every simulation for progress monitoring. If TRUE, print no messages |
A list with components: $upper, $lower, real, u, ksim, and rank. The first three
components are vectors like s, the next two contain results passed back from the simulations, and the final is a one-element vector with the rank of the observed data set.
Stephen Eglen <[email protected]>
data(amacrines) ama.a <- rbind(amacrines.on, amacrines.off) ama.bb <- bboxx(bbox(as.points(ama.a))) ama.t <- seq(from = 0.002, to=.250, by=0.002) nsim=999 plot(amacrines.on, asp=1, pch=19, main="Data set, match figure 1.4 of Diggle(2002)?") points(amacrines.off, pch=1) # k12 <- k12hat(amacrines.on, amacrines.off, ama.bb, ama.t) # k11 <- khat(amacrines.on, ama.bb, ama.t) k22 <- khat(amacrines.off, ama.bb, ama.t) k00 <- khat(ama.a, ama.bb, ama.t) theor <- pi * (ama.t^2) # plot(ama.t, k12-theor, ylim=c(min( c(k12, k11, k22, k00) - theor), max( c(k12, k11, k22, k00) - theor)), main="2nd order properties, match figure 4.8 of Diggle (2002)", type="l") lines(ama.t, -theor) lines(ama.t, k11-theor, lty=2) lines(ama.t, k22-theor, lty=3) lines(ama.t, k00-theor, lty=5) # k12.tor <- Kenv.tor(amacrines.on, amacrines.off, ama.bb, nsim, ama.t, quiet=TRUE) plot(ama.t, k12-theor, type="l", main="Output from Kenv.tor") lines(ama.t, k12.tor$upper-theor, type="l", col="red") lines(ama.t, k12.tor$lower-theor, type="l", col="red") # k12.sims <- Kenv.tor1(amacrines.on, amacrines.off, ama.bb, nsim, ama.t, quiet=TRUE) plot(ama.t, sqrt(k12.sims$real/pi), type="l", asp=1, bty="n", main=paste("K12 versus toroidal sims; rank ", k12.sims$rank, "of", length(k12.sims$u))) lines(ama.t, sqrt(k12.sims$upper/pi), col="red") lines(ama.t, sqrt(k12.sims$lower/pi), col="red")data(amacrines) ama.a <- rbind(amacrines.on, amacrines.off) ama.bb <- bboxx(bbox(as.points(ama.a))) ama.t <- seq(from = 0.002, to=.250, by=0.002) nsim=999 plot(amacrines.on, asp=1, pch=19, main="Data set, match figure 1.4 of Diggle(2002)?") points(amacrines.off, pch=1) # k12 <- k12hat(amacrines.on, amacrines.off, ama.bb, ama.t) # k11 <- khat(amacrines.on, ama.bb, ama.t) k22 <- khat(amacrines.off, ama.bb, ama.t) k00 <- khat(ama.a, ama.bb, ama.t) theor <- pi * (ama.t^2) # plot(ama.t, k12-theor, ylim=c(min( c(k12, k11, k22, k00) - theor), max( c(k12, k11, k22, k00) - theor)), main="2nd order properties, match figure 4.8 of Diggle (2002)", type="l") lines(ama.t, -theor) lines(ama.t, k11-theor, lty=2) lines(ama.t, k22-theor, lty=3) lines(ama.t, k00-theor, lty=5) # k12.tor <- Kenv.tor(amacrines.on, amacrines.off, ama.bb, nsim, ama.t, quiet=TRUE) plot(ama.t, k12-theor, type="l", main="Output from Kenv.tor") lines(ama.t, k12.tor$upper-theor, type="l", col="red") lines(ama.t, k12.tor$lower-theor, type="l", col="red") # k12.sims <- Kenv.tor1(amacrines.on, amacrines.off, ama.bb, nsim, ama.t, quiet=TRUE) plot(ama.t, sqrt(k12.sims$real/pi), type="l", asp=1, bty="n", main=paste("K12 versus toroidal sims; rank ", k12.sims$rank, "of", length(k12.sims$u))) lines(ama.t, sqrt(k12.sims$upper/pi), col="red") lines(ama.t, sqrt(k12.sims$lower/pi), col="red")
Perform kernel smoothing of a point pattern
kernel2d(pts,poly,h0,nx=20,ny=20,kernel='quartic',quiet=FALSE) spkernel2d(pts, poly, h0, grd, kernel = "quartic")kernel2d(pts,poly,h0,nx=20,ny=20,kernel='quartic',quiet=FALSE) spkernel2d(pts, poly, h0, grd, kernel = "quartic")
pts |
A points data set, or in function spkernel2d an object with a coordinates method from the sp package |
poly |
A splancs polygon data set |
h0 |
The kernel width parameter |
nx |
Number of points along the x-axis of the returned grid. |
ny |
Number of points along the y-axis of the returned grid. |
kernel |
Type of kernel function to use. Currently only the quartic kernel is implemented. |
quiet |
If TRUE, no debugging output is printed. |
grd |
a GridTopology object from the sp package |
The kernel estimate, with a correction for edge effects, is computed for
a grid of points that span the
input polygon. The kernel function for points in the grid that are outside the polygon are returned
as NA's.
The output list is in a format that can be read into image() directly,
for display and superposition onto other plots.
kernel2d returns a list with the following components:
x |
List of x-coordinates at which the kernel function has been evaluated. |
y |
List of y-coordinates at which the kernel function has been evaluated. |
z |
A matrix of dimension |
h0, kernel
|
containing the values input to |
spkernel2d returns a numeric vector with the value of the kernel function stored in the order required by sp package SpatialGridDataFrame objects
Berman M. and Diggle P.J. (1989) Estimating Weighted Integrals of the Second-Order Intensity of Spatial Point Patterns. J. R. Statist Soc B51 81-92; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655, (Barry Rowlingson ); the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(bodmin) plot(bodmin$poly, asp=1, type="n") image(kernel2d(as.points(bodmin), bodmin$poly, h0=2, nx=100, ny=100), add=TRUE, col=terrain.colors(20)) pointmap(as.points(bodmin), add=TRUE) polymap(bodmin$poly, add=TRUE) bodmin.xy <- coordinates(bodmin[1:2]) apply(bodmin$poly, 2, range) grd1 <- GridTopology(cellcentre.offset=c(-5.2, -11.5), cellsize=c(0.2, 0.2), cells.dim=c(75,100)) k100 <- spkernel2d(bodmin.xy, bodmin$poly, h0=1, grd1) k150 <- spkernel2d(bodmin.xy, bodmin$poly, h0=1.5, grd1) k200 <- spkernel2d(bodmin.xy, bodmin$poly, h0=2, grd1) k250 <- spkernel2d(bodmin.xy, bodmin$poly, h0=2.5, grd1) df <- data.frame(k100=k100, k150=k150, k200=k200, k250=k250) kernels <- SpatialGridDataFrame(grd1, data=df) spplot(kernels, checkEmptyRC=FALSE, col.regions=terrain.colors(16), cuts=15)data(bodmin) plot(bodmin$poly, asp=1, type="n") image(kernel2d(as.points(bodmin), bodmin$poly, h0=2, nx=100, ny=100), add=TRUE, col=terrain.colors(20)) pointmap(as.points(bodmin), add=TRUE) polymap(bodmin$poly, add=TRUE) bodmin.xy <- coordinates(bodmin[1:2]) apply(bodmin$poly, 2, range) grd1 <- GridTopology(cellcentre.offset=c(-5.2, -11.5), cellsize=c(0.2, 0.2), cells.dim=c(75,100)) k100 <- spkernel2d(bodmin.xy, bodmin$poly, h0=1, grd1) k150 <- spkernel2d(bodmin.xy, bodmin$poly, h0=1.5, grd1) k200 <- spkernel2d(bodmin.xy, bodmin$poly, h0=2, grd1) k250 <- spkernel2d(bodmin.xy, bodmin$poly, h0=2.5, grd1) df <- data.frame(k100=k100, k150=k150, k200=k200, k250=k250) kernels <- SpatialGridDataFrame(grd1, data=df) spplot(kernels, checkEmptyRC=FALSE, col.regions=terrain.colors(16), cuts=15)
Compute the space-time kernel
kernel3d(pts, times, xgr, ygr, zgr, hxy, hz)kernel3d(pts, times, xgr, ygr, zgr, hxy, hz)
pts |
A matrix of event coodinates x,y. |
times |
A vector of event times, t. |
xgr |
The values of x at which to compute the kernel function. |
ygr |
The values of y at which to compute the kernel function. |
zgr |
The values of time at which to compute the kernel function. |
hxy |
The quartic kernel width in the x and y direction. |
hz |
The quartic kernel width in the temporal direction. |
A list is returned. Most of the components are just copies of the
input parameters, except for the $v parameter.
This is a three dimensional array containing the kernel-smoothed
values. Its dimension is
[length(xgr),length(ygr),length(tgr)].
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(burkitt) b3d <- kernel3d(burpts, burkitt$t, seq(250,350,10), seq(250, 400, 10), seq(365,5800,365), 30, 200) brks <- quantile(b3d$v, seq(0,1,0.05)) cols <- heat.colors(length(brks)-1) oldpar <- par(mfrow=c(3,5)) for (i in 1:15) image(seq(250,350,10), seq(250, 400, 10), b3d$v[,,i], asp=1, xlab="", ylab="", main=1960+i, breaks=brks, col=cols) par(oldpar)data(burkitt) b3d <- kernel3d(burpts, burkitt$t, seq(250,350,10), seq(250, 400, 10), seq(365,5800,365), 30, 200) brks <- quantile(b3d$v, seq(0,1,0.05)) cols <- heat.colors(length(brks)-1) oldpar <- par(mfrow=c(3,5)) for (i in 1:15) image(seq(250,350,10), seq(250, 400, 10), b3d$v[,,i], asp=1, xlab="", ylab="", main=1960+i, breaks=brks, col=cols) par(oldpar)
Return the ratio of two kernel smoothings
kernrat(pts1,pts2,poly,h1,h2,nx=20,ny=20,kernel='quartic')kernrat(pts1,pts2,poly,h1,h2,nx=20,ny=20,kernel='quartic')
pts1, pts2
|
Point data sets |
poly |
A polygon data set |
h1, h2
|
The kernel width parameters, |
nx |
Number of points along the x-axis of the returned grid. |
ny |
Number of points along the y-axis of the returned grid. |
kernel |
Type of kernel function to use. Currently only the quartic kernel is implemented. |
A list with the following components:
x |
List of x-coordinates at which the kernel function has been evaluated. |
y |
List of y-coordinates at which the kernel function has been evaluated. |
z |
A matrix of dimension |
h |
A vector of length 2 containing |
kernel |
a character string containing the kernel name. |
Berman M. and Diggle P.J. (1989) Estimating Weighted Integrals of the Second-Order Intensity of Spatial Point Patterns. J. R. Statist Soc B51 81-92; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) kr <- kernrat(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), h1=50, h2=50) image(kr, asp=1) brks <- quantile(c(kr$z), seq(0,1,1/10), na.rm=TRUE) lbrks <- formatC(brks, 3, 6, "g", " ") cols <- heat.colors(length(brks)-1) def.par <- par(no.readonly = TRUE) layout(matrix(c(1,0,1,2), 2, 2, byrow = TRUE), c(2.5,1.5), c(1,3), TRUE) image(kr, breaks=brks, col=cols, asp=1) plot.new() legend(c(0,1), c(0,1), legend=paste(lbrks[-length(lbrks)], lbrks[-1], sep=":"), fill=cols, bty="n") par(def.par)data(okwhite) data(okblack) okpoly <- list(x=c(okwhite$x, okblack$x), y=c(okwhite$y, okblack$y)) kr <- kernrat(as.points(okwhite), as.points(okblack), bboxx(bbox(as.points(okpoly))), h1=50, h2=50) image(kr, asp=1) brks <- quantile(c(kr$z), seq(0,1,1/10), na.rm=TRUE) lbrks <- formatC(brks, 3, 6, "g", " ") cols <- heat.colors(length(brks)-1) def.par <- par(no.readonly = TRUE) layout(matrix(c(1,0,1,2), 2, 2, byrow = TRUE), c(2.5,1.5), c(1,3), TRUE) image(kr, breaks=brks, col=cols, asp=1) plot.new() legend(c(0,1), c(0,1), legend=paste(lbrks[-length(lbrks)], lbrks[-1], sep=":"), fill=cols, bty="n") par(def.par)
A linked-window system for browsing space-time data.
kerview(pts, times, k3, map=TRUE, addimg=TRUE, ncol=1)kerview(pts, times, k3, map=TRUE, addimg=TRUE, ncol=1)
pts |
A matrix of event x,y coordinates. |
times |
A vector of event times. |
k3 |
An object returned from |
map |
If false, don't plot the map display. |
addimg |
If true, overwrite successive images in the image display, else make a fresh image plot each time. |
ncol |
Number of columns and rows for multiple images and maps. |
This function displays three linked views of the data. In the current graphics window a temporal slice from the kernel smoothing is displayed. Another graphics device is started to display a map of the data that contributed to that time-slice. A third graphics device shows a histogram of the times of the events. Clicking with the mouse in this window with button 1 sets the time for the other displays to the time on the x-axis of the histogram at the clicked point.
In this way the 3-dimensional kernel smoothed function can be browsed, and the corresponding map of the data compared.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculates an estimate of the K-function
khat(pts,poly,s,newstyle=FALSE,checkpoly=TRUE) ## S3 method for class 'khat' print(x, ...) ## S3 method for class 'khat' plot(x, ...)khat(pts,poly,s,newstyle=FALSE,checkpoly=TRUE) ## S3 method for class 'khat' print(x, ...) ## S3 method for class 'khat' plot(x, ...)
pts |
A points data set |
poly |
A polygon containing the points - must be a perimeter ring of points |
s |
A vector of distances at which to calculate the K function |
newstyle |
if TRUE, the function returns a khat object |
checkpoly |
if TRUE compare polygon area and polygon bounding box and convex hull areas to see whether the polygon object is malformed; may be set to FALSE if the polygon is known to be a ring of points |
x |
a |
... |
other arguments passed to plot and print functions |
The K function is defined as the expected number of further points within a distance s of an arbitrary point, divided by the overall density of the points. In practice an edge-correction is required to avoid biasing the estimation due to non-recording of points outside the polygon.
The newstyle argument and khat object were introduced in collaboration with Thomas de Cornulier to permit the mapping of counts or khats for chosen distance values, as in ftp://pbil.univ-lyon1.fr/pub/mac/ADE/ADE4/DocThemPDFUS/Thema81.pdf, p.18.
If newstyle is FALSE,
a vector like s containing the value of K at the points in s.
else a khat object list with:
khat |
the value of K at the points in |
counts |
integer matrix of counts of points within the vector of
distances |
khats |
matrix of values of K within the vector of distances |
s |
|
Ripley, B.D. 1976 The second-order analysis of stationary point processes, J. Appl. Prob, 13 255-266; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(cardiff) s <- seq(2,30,2) plot(s, sqrt(khat(as.points(cardiff), cardiff$poly, s)/pi) - s, type="l", xlab="Splancs - polygon boundary", ylab="Estimated L", ylim=c(-1,1.5)) newstyle <- khat(as.points(cardiff), cardiff$poly, s, newstyle=TRUE) str(newstyle) newstyle apply(newstyle$khats, 2, sum) plot(newstyle)data(cardiff) s <- seq(2,30,2) plot(s, sqrt(khat(as.points(cardiff), cardiff$poly, s)/pi) - s, type="l", xlab="Splancs - polygon boundary", ylab="Estimated L", ylim=c(-1,1.5)) newstyle <- khat(as.points(cardiff), cardiff$poly, s, newstyle=TRUE) str(newstyle) newstyle apply(newstyle$khats, 2, sum) plot(newstyle)
Calculate the covariance matrix for the difference between two K-functions. Also return the contribution to the variance for each of the two point patterns,
khvc(pts1, pts2, poly, s)khvc(pts1, pts2, poly, s)
pts1 |
An object containing the case locations. |
pts2 |
An object containing the control locations. |
poly |
A polygon enclosing the locations in |
s |
A vector of distances at which the calculation is to be made. |
A list with four components:
varmat |
The upper triangle of the covariance matrix. |
k11 |
The variance of Khat for the cases |
k22 |
The variance of Khat for the controls |
k12 |
The covariance of Khat for the cases and Khat for controls. |
Note that the diagonal of the covariance matrix is
$k11 - 2 * $k12 + $k22
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculate the covariance matrix for the difference between two K-functions under random labelling of the corresponding two sets of points.
khvmat(pts1, pts2, poly, s)khvmat(pts1, pts2, poly, s)
pts1 |
An object containing the case locations. |
pts2 |
An object containing the control locations. |
poly |
Polygon enclosing the points in pts1 and pts2. |
s |
A vector of distances at which the calculation is to be made. |
A matrix containing the covariances, with the variances on the diagonal.
Diggle P.J and Chetwynd A.C (1991) Second order analysis of spatial clustering Biometrics 47 1155-63; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Overlay a number of point patterns.
mpoint(...,cpch,add=FALSE,type="p")mpoint(...,cpch,add=FALSE,type="p")
... |
At least one argument consisting of a points data set must be specified. |
cpch |
A vector of characters for plotting symbols |
add |
if |
type |
plot data as points if |
mpoint enables several point or polygon datasets to be overlayed. The plot
region is calculated so that all the specified datasets fit in the region.
The parameter cpch specifies the characters to use for each set of points. The
default cpch consists of the numbers 1 to 9 followed by the uppercase
letters A to Z. If cpch is shorter than the number of point sets to
plot, then it is repeated.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Estimate the Mean Square Error for a Kernel Smoothing.
mse2d(pts,poly,nsmse, range)mse2d(pts,poly,nsmse, range)
pts |
A set of points. |
poly |
A polygon containng the points. |
nsmse |
Number of steps of |
range |
Maximum value of |
A list with two components, $h and $mse. These vectors store
corresponding values of the mean square error at values of the kernel
smoothing parameter, h.
The value of h corresponding to the minimum value of $mse
can be passed to kernel2d as the optimum smoothing parameter.
Berman M. \& Diggle P.J. (1989) Estimating Weighted Integrals of the Second-Order Intensity of a Spatial Point Pattern. J. R. Statist Soc B 51 81–92; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(bodmin) Mse2d <- mse2d(as.points(bodmin), bodmin$poly, nsmse=50, range=8) plot(Mse2d$h[5:50],Mse2d$mse[5:50], type="l")data(bodmin) Mse2d <- mse2d(as.points(bodmin), bodmin$poly, nsmse=50, range=8) plot(Mse2d$h[5:50],Mse2d$mse[5:50], type="l")
Calculate nearest neighbours for two point patterns
n2dist(pts1,pts2)n2dist(pts1,pts2)
pts1, pts2
|
Point data sets |
Returns a list with components $dists and $neighs.
$dists[i] is the distance
of the nearest neighbour of point pts2[i,]
in pts1 and $neighs[i]
is the index in pts1 of the point nearest to pts2[i,]. Documentation and example by Alun Pope, 2007-08-23.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
(test1 <- matrix(c(151.1791, -33.86056, 151.1599, -33.88729, 151.1528, -33.90685, 151.1811, -33.85937),nrow=4,byrow=TRUE)) (test2 <- as.points(151.15, -33.9)) n2dist(test1,test2) n2dist(test2,test1)(test1 <- matrix(c(151.1791, -33.86056, 151.1599, -33.88729, 151.1528, -33.90685, 151.1811, -33.85937),nrow=4,byrow=TRUE)) (test2 <- as.points(151.15, -33.9)) n2dist(test1,test2) n2dist(test2,test1)
Calculate nearest neighbour distances as used by Fhat()
nndistF(pts1,pts2)nndistF(pts1,pts2)
pts1 |
A points data set |
pts2 |
A points data set |
The set of distances from each of the points in pts2 to the nearest
point in pts1 is returned as a vector.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(uganda) boxplot(nndistF(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))))) plot(ecdf(nndistF(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))))), main="Fhat ecdf Uganda volcano data")data(uganda) boxplot(nndistF(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))))) plot(ecdf(nndistF(as.points(uganda), as.points(csr(uganda$poly, length(uganda$x))))), main="Fhat ecdf Uganda volcano data")
Calculate nearest neighbour distances as used by Ghat().
nndistG(pts)nndistG(pts)
pts |
A points data set |
Returns a list with components $dists and $neighs.
$dists[i] is the distance
to the nearest neighbour of point i in pts, and $neighs[i]
is the index
of the neighbour of point i.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(uganda) boxplot(nndistG(as.points(uganda))$dists) plot(ecdf(nndistG(as.points(uganda))$dists))data(uganda) boxplot(nndistG(as.points(uganda))$dists) plot(ecdf(nndistG(as.points(uganda))$dists))
return number of points in data set
npts(pts)npts(pts)
pts |
A points data set |
The number of points in the data set.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Locations of theft from property offences committed by black offenders in Oklahoma City
data(okblack)data(okblack)
A list corresponding to a Venables and Ripley point object with 147 observations
| x | numeric | grid eastings |
| y | numeric | grid northings |
| area | list | bounding box with xl, xu, yl, yu |
Carter and Hill, 1979, - Bailey and Gatrell 1995, ch. 3.
Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow.
Locations of theft from property offences committed by white offenders in Oklahoma City
data(okwhite)data(okwhite)
A list corresponding to a Venables and Ripley point object with 104 observations
| x | numeric | grid eastings |
| y | numeric | grid northings |
| area | list | bounding box with xl, xu, yl, yu |
Carter and Hill, 1979, - Bailey and Gatrell 1995, ch. 3.
Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow.
The function fits a Poisson cluster process to point data for a given enclosing polygon and fit parameters
pcp(point.data, poly.data, h0=NULL, expo=0.25, n.int=20)pcp(point.data, poly.data, h0=NULL, expo=0.25, n.int=20)
point.data |
a points object |
poly.data |
a polygon enclosing the study region |
h0 |
upper bound of integration in the criterion function |
expo |
exponent in the criterion function |
n.int |
number of intervals used to approximate the integral in the criterion function with a sum |
The function returns an object as returned by optim, including:
par |
The best set of parameters s2 and rho found |
value |
The value of the fit corresponding to ‘par’ |
convergence |
‘0’ indicates successful convergence |
Giovanni Petris <[email protected]>, [email protected]
Diggle, P. J. (1983) Statistical analysis of spatial point patterns, London: Academic Press, pp. 55-57 and 78-81; Bailey, T. C. and Gatrell, A. C. (1995) Interactive spatial data analysis, Harlow: Longman, pp. 106-109.
optim, pcp.sim, Kenv.pcp, khat
data(cardiff) polymap(cardiff$poly) pointmap(as.points(cardiff), add=TRUE) title("Locations of homes of 168 juvenile offenders") pcp.fit <- pcp(as.points(cardiff), cardiff$poly, h0=30, n.int=30) pcp.fitdata(cardiff) polymap(cardiff$poly) pointmap(as.points(cardiff), add=TRUE) title("Locations of homes of 168 juvenile offenders") pcp.fit <- pcp(as.points(cardiff), cardiff$poly, h0=30, n.int=30) pcp.fit
The function generates a Poisson cluster process for a given polygon within a larger bounding region and given process parameters
pcp.sim(rho, m, s2, region.poly, larger.region=NULL, vectorise.loop=TRUE)pcp.sim(rho, m, s2, region.poly, larger.region=NULL, vectorise.loop=TRUE)
rho |
intensity of the parent process |
m |
average number of offsprings per parent |
s2 |
variance of location of offsprings relative to their parent |
region.poly |
a polygon defining the region in which the process is to be generated |
larger.region |
a rectangle containing the region of interest given in the form (xl,xu,yl,yu), defaults to |
vectorise.loop |
if TRUE, use new vectorised code, if FALSE, use loop as before |
The function generates the parents in the larger bounding region, generates their children also in the larger bounding region, and then returns those inside the given polygon.
A point object with the simulated pattern
Giovanni Petris <[email protected]>, [email protected]
Diggle, P. J. (1983) Statistical analysis of spatial point patterns, London: Academic Press, pp. 55-57 and 78-81; Bailey, T. C. and Gatrell, A. C. (1995) Interactive spatial data analysis, Harlow: Longman, pp. 106-109.
data(cardiff) polymap(cardiff$poly) pointmap(as.points(cardiff), add=TRUE) title("Locations of homes of 168 juvenile offenders") pcp.fit <- pcp(as.points(cardiff), cardiff$poly, h0=30, n.int=30) pcp.fit m <- npts(as.points(cardiff))/(areapl(cardiff$poly)*pcp.fit$par[2]) sims <- pcp.sim(pcp.fit$par[2], m, pcp.fit$par[1], cardiff$poly) pointmap(as.points(sims), add=TRUE, col="red")data(cardiff) polymap(cardiff$poly) pointmap(as.points(cardiff), add=TRUE) title("Locations of homes of 168 juvenile offenders") pcp.fit <- pcp(as.points(cardiff), cardiff$poly, h0=30, n.int=30) pcp.fit m <- npts(as.points(cardiff))/(areapl(cardiff$poly)*pcp.fit$par[2]) sims <- pcp.sim(pcp.fit$par[2], m, pcp.fit$par[1], cardiff$poly) pointmap(as.points(sims), add=TRUE, col="red")
Calculate overall density for a point pattern.
pdense(pts,poly)pdense(pts,poly)
pts |
A points data set |
poly |
A polygon data set |
The density of the points in the polygon. i.e. the number of points per unit area.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Return points inside or outside a polygon.
pip(pts,poly,out=FALSE,bound=NULL,quiet=TRUE)pip(pts,poly,out=FALSE,bound=NULL,quiet=TRUE)
pts |
A points data set |
poly |
A polygon data set |
out |
If |
bound |
If points fall exactly on polygon boundaries, the default NULL gives arbitrary assignments. If TRUE, then all points "on" boundaries are set as within the polygon, if FALSE, outside. |
quiet |
Do not report which points are on boundary for non-NULL bound |
pip calls inout, then selects the appropriate sub-set of points.
pip returns the points of pts that lie inside (or outside with
out=TRUE)
the polygon poly. Compare this with inpip, which returns
the indices of
the points in the polygon, and inout which returns a logical vector
indicating whether points are inside or outside.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
bins nearest neighbour distances
plt(data, value)plt(data, value)
data |
nearest neighbour distances |
value |
breaks for binning distances |
binned values
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Plots point and polygon data sets on the current graphics device.
pointmap(pts,add=FALSE,axes=TRUE,xlab="",ylab="", asp,...)pointmap(pts,add=FALSE,axes=TRUE,xlab="",ylab="", asp,...)
pts |
a points data set. |
add |
if FALSE, start a new plot. If TRUE, superimpose on current plot. |
axes |
if true, display axes with labelling. If false, do not display any axes on the plot. |
xlab, ylab
|
Label strings for x and y axes. |
asp |
aspect parameter for plot |
... |
Graphical arguments may be entered, and these are passed to the
standard S |
The specified data set is plotted on the current graphics device, either
as points or polygons. For polymap, the last point in the data set
is drawn connected to the first point.
pointmap and polymap preserve
the aspect ratio in the data by using the asp=1 plot argument.
Graphical parameters can also be supplied to these routines, and are passed
through to plot. Some useful parameters include pch to change the plotting
character for points, lty to change the line type for polygons, and
type="n" to set up axes for the plot without plotting anything.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(bodmin) plot(bodmin$poly, asp=1, type="n") pointmap(as.points(bodmin), add=TRUE) polymap(bodmin$poly, add=TRUE)data(bodmin) plot(bodmin$poly, asp=1, type="n") pointmap(as.points(bodmin), add=TRUE) polymap(bodmin$poly, add=TRUE)
Plots point and polygon data sets on the current graphics device.
polymap(poly,add=FALSE,xlab="",ylab="",axes=TRUE, asp,...)polymap(poly,add=FALSE,xlab="",ylab="",axes=TRUE, asp,...)
poly |
a polygon. |
add |
if FALSE, start a new plot. If TRUE, superimpose on current plot. |
xlab, ylab
|
Label strings for x and y axes. |
axes |
if true, display axes with labelling. If false, do not display any axes on the plot. |
asp |
aspect parameter for plot |
... |
Graphical arguments may be entered, and these are passed to the
standard S |
The specified data set is plotted on the current graphics device, either
as points or polygons. For polymap, the last point in the data set
is drawn connected to the first point.
pointmap and polymap preserve
the aspect ratio in the data by using the asp=1 plot argument.
Graphical parameters can also be supplied to these routines, and are passed
through to plot. Some useful parameters include pch to change the plotting
character for points, lty to change the line type for polygons, and
type="n" to just set up axes for the plot without plotting anything.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
data(bodmin) plot(bodmin$poly, asp=1, type="n") pointmap(as.points(bodmin), add=TRUE) polymap(bodmin$poly, add=TRUE)data(bodmin) plot(bodmin$poly, asp=1, type="n") pointmap(as.points(bodmin), add=TRUE) polymap(bodmin$poly, add=TRUE)
Display the fit from tribble
## S3 method for class 'ribfit' print(x, ...)## S3 method for class 'ribfit' print(x, ...)
x |
An object returned from |
... |
optional arguments to pass through to |
The parameter estimates and log-likelihood for the raised incidence
model are displayed. The likelihood ratio, D = 2*(L-Lo), is also given.
This function is called whenever print operates on an object
with class ribfit.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
adjust number of random points in polygon
ranpts(pts, poly, nprq)ranpts(pts, poly, nprq)
pts |
points object |
poly |
polygon object |
nprq |
required number of points |
points object with required number of random points
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Randomly label two or more point sets. (function name changed from rlabel to rLabel to avoid collision with spatstat)
rLabel(...)rLabel(...)
... |
Any number of points data sets |
The output data sets are a random labelling of the input data sets, i.e. all the points in the input data sets are randomly assigned to the output sets. The number of points in each output set is the same as its corresponding input set.
A list of points data sets. There are as many elements in the list as arguments.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Perform a random toroidal shift on a point data set
rtor.shift(pts,rect)rtor.shift(pts,rect)
pts |
The point data set to shift |
rect |
A rectangle defining the region for the toroidal map. If not given,
the bounding box of |
The planar region defined by rect
is assumed connected at its top and bottom edges, and at its left and
right sides. A random shift is applied to the
points and the resulting set of points returned.
A point data set like pts, but after application of a random toroidal
shift along the x and y axes.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Generate a box surrounding a point object
sbox(pts, xfrac = .1, yfrac = .1)sbox(pts, xfrac = .1, yfrac = .1)
pts |
A points data set |
xfrac |
The fraction of the width of the point pattern by which the box will surround the point pattern to the left and right. |
yfrac |
The fraction of the height of the point pattern by which the box will surround the point pattern to the top and bottom. |
A points data set of four points giving the coordinates of the surrounding box
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculate standard errors for the difference between two K-functions under random labelling of the corresponding two sets of points.
secal(pts1,pts2,poly,s)secal(pts1,pts2,poly,s)
pts1, pts2
|
Two point data sets |
poly |
Polygon enclosing the points in |
s |
A vector of distances at which to calculate the standard error. |
To compare two point patterns, one can calculate the difference between
their K-functions. The function secal gives the pointwise standard
errors for the estimated differences, under the random labelling hypothesis.
A vector like s containing the value of the standard error at each of the
distances in s
Diggle P.J. and Chetwynd A.G. (1991) Second-order analysis of spatial clustering Biometrics 47 1155–63; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Shift a point data set (function name changed from shift to Shift to avoid collision with spatstat)
Shift(pts,xsh=0.0,ysh=0.0)Shift(pts,xsh=0.0,ysh=0.0)
pts |
The point data set to shift |
xsh |
Amount to shift along the x-axis |
ysh |
Amount to shift along the y-axis |
A point data set like pts, but with xsh added to its
x-coordinates, and ysh added to its y-coordinates.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Locations of cases of cancer of lung and larynx in
Chorley-Ribble, Lancashire. The data set is split into a points object southlancs.pts and a
case/control 0/1 vector southlancs.cc. There are 917 controls and 57
cases in this data set - these numbers differ from 978 and 58 in Diggle (1990)
and Diggle and Rowlingson (1994). The data set also includes the approximate
location of an old incinerator old.incinerator, as well as
southlancs.bdy, the study area boundary.
data(southlancs)data(southlancs)
A data frame with 974 observations
| [,1] | x | numeric | grid eastings (metres) |
| [,2] | y | numeric | grid northings (metres) |
| [,3] | cc | numeric | case/control, lung=0, larynx=1 |
Diggle, Gatrell and Lovett, 1990, - Bailey and Gatrell 1995, ch. 3.
Bailey and Gatrell 1995, ch. 3; Diggle, P. (1990) A point process modelling approach to raised incidence of a rare phenomenon in the viscinity of a prespecified point. Journal of the Royal Statistical Society, A, 153, 349-362; Diggle, P. and Rowlingson, B. (1994) A conditional approach to point process modelling of elevated risk. Journal of the Royal Statistical Society, A, 157, 433-440.
data(southlancs) op <- par(mfrow=c(2,1)) pointmap(southlancs.pts[southlancs.cc == 0,]) pointmap(old.incinerator, add=TRUE, col="red", pch=19) title("Lung cancer controls") pointmap(southlancs.pts[southlancs.cc == 1,]) pointmap(old.incinerator, add=TRUE, col="red", pch=19) title("Larynx cancer cases") par(op) polymap(southlancs.bdy,border="grey") contour(kernel2d(southlancs.pts[southlancs.cc == 0,], southlancs.bdy, h=500, nx=100, ny=100), nlevels=20, add=TRUE,drawlabels=FALSE) pointmap(southlancs.pts[southlancs.cc == 1,], add=TRUE, pch=19, col="green") pointmap(old.incinerator, add=TRUE, pch=19, col="red") title(xlab="h=500, quartic kernel") title("Density map of control, green case points, red old incinerator")data(southlancs) op <- par(mfrow=c(2,1)) pointmap(southlancs.pts[southlancs.cc == 0,]) pointmap(old.incinerator, add=TRUE, col="red", pch=19) title("Lung cancer controls") pointmap(southlancs.pts[southlancs.cc == 1,]) pointmap(old.incinerator, add=TRUE, col="red", pch=19) title("Larynx cancer cases") par(op) polymap(southlancs.bdy,border="grey") contour(kernel2d(southlancs.pts[southlancs.cc == 0,], southlancs.bdy, h=500, nx=100, ny=100), nlevels=20, add=TRUE,drawlabels=FALSE) pointmap(southlancs.pts[southlancs.cc == 1,], add=TRUE, pch=19, col="green") pointmap(old.incinerator, add=TRUE, pch=19, col="red") title(xlab="h=500, quartic kernel") title("Density map of control, green case points, red old incinerator")
Return version number and author information
splancs()splancs()
The version string is returned. This is a number of the format x.yy, where x is the major version number and yy is the minor version number.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Creates and tests for data in spatial point format.
spoints(data,npoints)spoints(data,npoints)
data |
vector containing the data values for the points in order (x1,y1),(x2,y2),... |
npoints |
number of points to generate, if missing, set to length(data)/2. |
spoints returns an object suitable for use as a point data
object. If npoints is given, the vector data is either truncated
or repeated until sufficient data values are generated.
The returned object is a two-column matrix, where the first column stores the
x-coordinate, and the second column stores the y-coordinate.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Produces some summary plots for clustering analysis
stdiagn(pts, stkh, stse, stmc=0,Dzero=FALSE)stdiagn(pts, stkh, stse, stmc=0,Dzero=FALSE)
pts |
A set of points, as used in Splancs |
stkh |
An object returned from |
stse |
An object returned from |
stmc |
An object returned from |
Dzero |
FALSE - default D plot, TRUE Dzero plot |
Four plots are produced on the current graphics device. The first plot is simply a map of the data. The second is a perspective plot of the difference between space-time K-function and the product of spatial and temporal K-functions. The third plot is of the standardised residuals against the product of spatial and temporal K-functions. If the Monte-Carlo data is given the fourth plot is a a histogram of the test statistics, with the value for the data indicated with a vertical line. See Diggle, Chetwynd, Haggkvist, and Morris (1995) for details.
Diggle, P., Chetwynd, A., Haggkvist, R. and Morris, S. 1995 Second-order analysis of space-time clustering. Statistical Methods in Medical Research, 4, 124-136;Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow, pp. 122-125; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
stkhat, stsecal, stvmat, stmctest
example(stkhat) example(stsecal) example(stmctest) stdiagn(burpts, bur1, bur1se, bur1mc)example(stkhat) example(stsecal) example(stmctest) stdiagn(burpts, bur1, bur1se, bur1mc)
Compute the space-time K-functions
stkhat(pts, times, poly, tlimits, s, tm)stkhat(pts, times, poly, tlimits, s, tm)
pts |
A set of points as defined in Splancs |
times |
A vector of times, the same length as the number of points in |
poly |
A polygon enclosing the points |
tlimits |
A vector of length 2 specifying the upper and lower temporal domain. |
s |
A vector of spatial distances for the analysis. |
tm |
A vector of times for the analysis |
A list with the following components is returned:
s, t
|
The spatial and temporal scales |
ks |
The spatial K-function |
kt |
The temporal K-function |
kst |
The space-time K-function |
For details see Diggle, Chetwynd, Haggkvist, and Morris (1995)
Diggle, P., Chetwynd, A., Haggkvist, R. and Morris, S. 1995 Second-order analysis of space-time clustering. Statistical Methods in Medical Research, 4, 124-136;Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow, pp. 122-125; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
stsecal, stvmat, stmctest, stdiagn
data(burkitt) bur1 <- stkhat(burpts, burkitt$t, burbdy, c(400, 5800), seq(1,40,2), seq(100, 1500, 100)) oldpar <- par(mfrow=c(2,1)) plot(bur1$s, bur1$ks, type="l", xlab="distance", ylab="Estimated K", main="spatial K function") plot(bur1$t, bur1$kt, type="l", xlab="time", ylab="Estimated K", main="temporal K function") par(oldpar)data(burkitt) bur1 <- stkhat(burpts, burkitt$t, burbdy, c(400, 5800), seq(1,40,2), seq(100, 1500, 100)) oldpar <- par(mfrow=c(2,1)) plot(bur1$s, bur1$ks, type="l", xlab="distance", ylab="Estimated K", main="spatial K function") plot(bur1$t, bur1$kt, type="l", xlab="time", ylab="Estimated K", main="temporal K function") par(oldpar)
Perform a Monte-Carlo test of space-time clustering.
stmctest(pts, times, poly, tlimits, s, tt, nsim, quiet=FALSE, returnSims=FALSE)stmctest(pts, times, poly, tlimits, s, tt, nsim, quiet=FALSE, returnSims=FALSE)
pts |
A set of points as used by Splancs. |
times |
A vector of times, the same length as the number of points in |
poly |
A polygon enclosing the points. |
tlimits |
A vector of length 2, specifying the upper and lower temporal domain. |
s |
A vector of spatial distances for the analysis. |
tt |
A vector of times for the analysis. |
nsim |
The number of simulations to do. |
quiet |
If |
returnSims |
default FALSE, if TRUE, return the |
The function uses a sum of residuals as a test statistic, randomly permutes the times of the set of points and recomputes the test statistic for a number of simulations. See Diggle, Chetwynd, Haggkvist and Morris (1995) for details.
A list with components:
t0 |
The observed value of the statistic |
t |
A single column matrix with |
The example of using returned simulated values is included only to show how the values might be used, not to indicate that this constitutes a way of examining which observed values of the space-time measure are exceptional.
Diggle, P., Chetwynd, A., Haggkvist, R. and Morris, S. 1995 Second-order analysis of space-time clustering. Statistical Methods in Medical Research, 4, 124-136;Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow, pp. 122-125; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
stkhat, stsecal, stvmat, stdiagn
example(stkhat) bur1mc <- stmctest(burpts, burkitt$t, burbdy, c(400, 5800), seq(1,40,2), seq(100, 1500, 100), nsim=49, quiet=TRUE, returnSims=TRUE) plot(density(bur1mc$t), xlim=range(c(bur1mc$t0, bur1mc$t))) abline(v=bur1mc$t0) r0 <- attr(bur1mc, "obs")$kst-outer(attr(bur1mc, "obs")$ks, attr(bur1mc, "obs")$kt) rsimlist <- lapply(attr(bur1mc, "sims"), function(x) x$kst - outer(x$ks, x$kt)) rarray <- array(do.call("cbind", rsimlist), dim=c(20, 15, 49)) rmin <- apply(rarray, c(1,2), min) rmax <- apply(rarray, c(1,2), max) r0 < rmin r0 > rmaxexample(stkhat) bur1mc <- stmctest(burpts, burkitt$t, burbdy, c(400, 5800), seq(1,40,2), seq(100, 1500, 100), nsim=49, quiet=TRUE, returnSims=TRUE) plot(density(bur1mc$t), xlim=range(c(bur1mc$t0, bur1mc$t))) abline(v=bur1mc$t0) r0 <- attr(bur1mc, "obs")$kst-outer(attr(bur1mc, "obs")$ks, attr(bur1mc, "obs")$kt) rsimlist <- lapply(attr(bur1mc, "sims"), function(x) x$kst - outer(x$ks, x$kt)) rarray <- array(do.call("cbind", rsimlist), dim=c(20, 15, 49)) rmin <- apply(rarray, c(1,2), min) rmax <- apply(rarray, c(1,2), max) r0 < rmin r0 > rmax
Computes the standard error for space-time clustering.
stsecal(pts, times, poly, tlim, s, tm)stsecal(pts, times, poly, tlim, s, tm)
pts |
A set of points, as defined in Splancs. |
times |
A vector of times, the same length as the number of points in |
poly |
A polygon enclosing the points |
tlim |
A vector of length 2 specifying the upper and lower temporal domain. |
s |
A vector of spatial distances for the analysis |
tm |
A vector of times for the analysis |
A matrix of dimension [length(s),length(t)] is returned. Element
[i,j] is the standard error at s[i],t[j].
See Diggle Chetwynd Haggkvist and Morris (1995) for details.
Diggle, P., Chetwynd, A., Haggkvist, R. and Morris, S. 1995 Second-order analysis of space-time clustering. Statistical Methods in Medical Research, 4, 124-136;Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow, pp. 122-125; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
stkhat, stsecal, stvmat, stdiagn
example(stkhat) bur1se <- stsecal(burpts, burkitt$t, burbdy, c(400, 5800), seq(1,40,2), seq(100, 1500, 100))example(stkhat) bur1se <- stsecal(burpts, burkitt$t, burbdy, c(400, 5800), seq(1,40,2), seq(100, 1500, 100))
Compute the variance matrix for space-time clustering
stvmat(pts, times, poly, tlim, s, tm)stvmat(pts, times, poly, tlim, s, tm)
pts |
A set of points. |
times |
A vector of times, the same length as the number of points in |
poly |
A polygon that encloses the points |
tlim |
A vector of length 2 specifying the upper and lower temporal domain. |
s |
A vector of spatial distances for the analysis |
tm |
A vector of times for the analysis |
A four-dimensional matrix is returned. The covariance between space-time
t1,s1 and t2,s2 is given by the corresponding element [t1,s1,t2,s2]
For full details, see Diggle, Chetwynd, Haggkvist and Morris (1995)
Diggle, P., Chetwynd, A., Haggkvist, R. and Morris, S. 1995 Second-order analysis of space-time clustering. Statistical Methods in Medical Research, 4, 124-136; Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
stkhat, stsecal, stmctest, stdiagn
Randomly thin a point data set.
thin(pts,n)thin(pts,n)
pts |
a points data set. |
n |
the number of points to return |
Returns a point data set consisting of n points selected randomly
from the set pts.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Perform a toroidal shift on a point data set
tor.shift(pts,xsh=0.0,ysh=0.0,rect)tor.shift(pts,xsh=0.0,ysh=0.0,rect)
pts |
The point data set to shift |
xsh |
Amount to shift along the x-axis |
ysh |
Amount to shift along the y-axis |
rect |
A rectangle defining the region for the toroidal map. If not given,
the bounding box of |
The planar region defined by rect
is assumed connected at its top and bottom edges, and at its left and
right sides. A shift of xsh and ysh is applied to the
points and the resulting set of points returned.
A point data set like pts, but after application of a toroidal
shift along the x and y axes.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Fits the Diggle-Rowlingson Raised Incidence Model.
tribble(ccflag, vars=NULL, alphas=NULL, betas=NULL, rho, which=1:length(alphas), covars=NULL, thetas=NULL, steps=NULL, reqmin=0.001, icount=50, hessian=NULL)tribble(ccflag, vars=NULL, alphas=NULL, betas=NULL, rho, which=1:length(alphas), covars=NULL, thetas=NULL, steps=NULL, reqmin=0.001, icount=50, hessian=NULL)
ccflag |
Case-control flag : a vector of ones and zeroes. |
vars |
A matrix where |
alphas |
Initial value of the |
betas |
Initial value of the |
rho |
Initial value of the |
which |
Defines the mapping from sources to parameters. |
covars |
A matrix of covariates to be modelled as log-linear terms. The element
|
thetas |
Initial values of covariate parameters. |
steps |
Step sizes for the Nelder-Mead simplex algorithm. |
reqmin |
Tolerance for simplex algorithm |
icount |
Iteration count for simplex algorithm |
hessian |
by default NULL, any other value causes hessian to be computed and returned |
The return value is a list with many components, and class ribfit.
alphas |
A vector of the alpha parameters at the maximum |
betas |
A vector of the beta values at the maximum |
rho |
The value of rho at the maximum |
logl |
The maximised log-likelihood |
null.logl |
The null log-likelihood |
call |
The function call to |
For further information see Diggle and Rowlingson (1993).
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Calculates the log-likelihood for the Diggle-Rowlingson raised incidence model.
triblik(ccflag, vars=NULL, alphas=NULL, betas=NULL, rho, which=1:length(alphas), covars=NULL, thetas=NULL)triblik(ccflag, vars=NULL, alphas=NULL, betas=NULL, rho, which=1:length(alphas), covars=NULL, thetas=NULL)
ccflag |
Case-control flag : a vector of ones and zeroes. |
vars |
A matrix where |
alphas |
The |
betas |
The |
rho |
The |
which |
Defines the mapping from sources to parameters. |
covars |
A matrix of covariates to be modelled as log-linear terms. The element
|
thetas |
The covariate parameters. |
The log-likelihood for the given parameters and the given distances and optional covariates is returned.
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.
Locations of craters in a volcanic field in Uganda
data(uganda)data(uganda)
A list corresponding to a Venables and Ripley point object with 120 observations
| x | numeric | grid eastings |
| y | numeric | grid northings |
| area | list | bounding box with xl, xu, yl, yu |
| poly | array | polygon boundary with columns x and y |
Tinkler, 1971, - Bailey and Gatrell 1995, ch. 3.
Bailey, T. C. and Gatrell, A. C. 1995, Interactive spatial data analysis. Longman, Harlow.
Interactively specify a region of a plot for expansion
zoom(quiet=FALSE,out=FALSE,...)zoom(quiet=FALSE,out=FALSE,...)
quiet |
If false, prompt the user to enter two coordinates. If true, say nothing. |
out |
If true, expand the limits of the current plot by a factor of three, centred on the current plot. |
... |
Other arguments are passed through to pointmap. |
A prompt is optionally displayed, and the user selects two points
forming the diagonal of a rectangle. A new, empty plot is created that has its
axis limits set to the bounding square of the selected rectangle.
If out=TRUE, no prompt is displayed, and a new blank plot is created with
its limits in x and y set to span an area three times the height and width
centred on the current centre.
None
Rowlingson, B. and Diggle, P. 1993 Splancs: spatial point pattern analysis code in S-Plus. Computers and Geosciences, 19, 627-655; the original sources can be accessed at: http://www.maths.lancs.ac.uk/~rowlings/Splancs/. See also Bivand, R. and Gebhardt, A. 2000 Implementing functions for spatial statistical analysis using the R language. Journal of Geographical Systems, 2, 307-317.