Summary plots for clustering analysis

Produces some summary plots for clustering analysis

stdiagn(pts, stkh, stse, stmc=0,Dzero=FALSE)

Arguments

pts

A set of points, as used in Splancs

stkh

An object returned from stkhat

stse

An object returned from stsecal

stmc

An object returned from stmctest

Dzero

FALSE - default D plot, TRUE Dzero plot

Details

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.

See also

stkhat, stsecal, stvmat, stmctest

References

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: https://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.

Examples

example(stkhat)
#> 
#> stkhat> data(burkitt)
#> 
#> stkhat> bur1 <- stkhat(burpts, burkitt$t, burbdy, c(400, 5800),
#> stkhat+   seq(1,40,2), seq(100, 1500, 100))
#> 
#> stkhat> oldpar <- par(mfrow=c(2,1))
#> 
#> stkhat> plot(bur1$s, bur1$ks, type="l", xlab="distance", ylab="Estimated K",
#> stkhat+   main="spatial K function")
#> 
#> stkhat> plot(bur1$t, bur1$kt, type="l", xlab="time", ylab="Estimated K",
#> stkhat+   main="temporal K function")
#> 
#> stkhat> par(oldpar)
example(stsecal)
#> 
#> stsecl> example(stkhat)
#> 
#> stkhat> data(burkitt)
#> 
#> stkhat> bur1 <- stkhat(burpts, burkitt$t, burbdy, c(400, 5800),
#> stkhat+   seq(1,40,2), seq(100, 1500, 100))
#> 
#> stkhat> oldpar <- par(mfrow=c(2,1))
#> 
#> stkhat> plot(bur1$s, bur1$ks, type="l", xlab="distance", ylab="Estimated K",
#> stkhat+   main="spatial K function")
#> 
#> stkhat> plot(bur1$t, bur1$kt, type="l", xlab="time", ylab="Estimated K",
#> stkhat+   main="temporal K function")

#> 
#> stkhat> par(oldpar)
#> 
#> stsecl> bur1se <- stsecal(burpts, burkitt$t, burbdy, c(400, 5800),
#> stsecl+  seq(1,40,2), seq(100, 1500, 100))
example(stmctest)
#> 
#> stmcts> example(stkhat)
#> 
#> stkhat> data(burkitt)
#> 
#> stkhat> bur1 <- stkhat(burpts, burkitt$t, burbdy, c(400, 5800),
#> stkhat+   seq(1,40,2), seq(100, 1500, 100))
#> 
#> stkhat> oldpar <- par(mfrow=c(2,1))
#> 
#> stkhat> plot(bur1$s, bur1$ks, type="l", xlab="distance", ylab="Estimated K",
#> stkhat+   main="spatial K function")
#> 
#> stkhat> plot(bur1$t, bur1$kt, type="l", xlab="time", ylab="Estimated K",
#> stkhat+   main="temporal K function")
#> 
#> stkhat> par(oldpar)
#> 
#> stmcts> bur1mc <- stmctest(burpts, burkitt$t, burbdy, c(400, 5800),
#> stmcts+   seq(1,40,2), seq(100, 1500, 100), nsim=49, quiet=TRUE, returnSims=TRUE)
#> 
#> stmcts> plot(density(bur1mc$t), xlim=range(c(bur1mc$t0, bur1mc$t)))

#> 
#> stmcts> abline(v=bur1mc$t0)
#> 
#> stmcts> r0 <- attr(bur1mc, "obs")$kst-outer(attr(bur1mc, "obs")$ks, attr(bur1mc, "obs")$kt)
#> 
#> stmcts> rsimlist <- lapply(attr(bur1mc, "sims"), function(x) x$kst - outer(x$ks, x$kt))
#> 
#> stmcts> rarray <- array(do.call("cbind", rsimlist), dim=c(20, 15, 49))
#> 
#> stmcts> rmin <- apply(rarray, c(1,2), min)
#> 
#> stmcts> rmax <- apply(rarray, c(1,2), max)
#> 
#> stmcts> r0 < rmin
#>        [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9] [,10] [,11] [,12]
#>  [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
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#> [15,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
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#> [19,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [20,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>       [,13] [,14] [,15]
#>  [1,] FALSE FALSE FALSE
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#> [19,] FALSE FALSE FALSE
#> [20,] FALSE FALSE FALSE
#> 
#> stmcts> r0 > rmax
#>        [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9] [,10] [,11] [,12]
#>  [1,]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [2,] FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE
#>  [3,] FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE
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#>  [5,]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
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#>  [7,]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [8,]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [9,]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#> [10,]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE
#> [11,] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE
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#>       [,13] [,14] [,15]
#>  [1,] FALSE FALSE FALSE
#>  [2,] FALSE FALSE FALSE
#>  [3,]  TRUE  TRUE  TRUE
#>  [4,]  TRUE  TRUE  TRUE
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stdiagn(burpts, bur1, bur1se, bur1mc)