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Type 'q()' to quit R. > #' > #' Header for all (concatenated) test files > #' > #' Require spatstat.model > #' Obtain environment variable controlling tests. > #' > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ > > require(spatstat.model) Loading required package: spatstat.model Loading required package: spatstat.data Loading required package: spatstat.geom spatstat.geom 3.2-8 Loading required package: spatstat.random spatstat.random 3.2-2 Loading required package: spatstat.explore Loading required package: nlme spatstat.explore 3.2-6 Loading required package: rpart spatstat.model 3.2-9 > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) > ALWAYS <- TRUE > cat(paste("--------- Executing", + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", + "test code -----------\n")) --------- Executing **RESTRICTED** subset of test code ----------- > # > # tests/ppmBadData.R > # > # $Revision: 1.6 $ $Date: 2020/04/30 05:23:52 $ > > # Testing robustness of ppm and support functions > # when data are rubbish > > local({ + if(ALWAYS) { + ## from Rolf: very large proportion of data is NA + SEED <- 42 + K <- 101 + A <- 500 + X <- seq(0, A, length=K) + G <- expand.grid(x=X, y=X) + FOO <- function(x,y) { sin(x)^2 + cos(y)^2 } + M1 <- im(matrix(FOO(G$x, G$y), K, K), xcol=X, yrow=X) + M <- im(matrix(FOO(G$x, G$y), K, K)) + BAR <- function(x) { exp(-6.618913 + 5.855337 * x - 8.432483 * x^2) } + V <- im(BAR(M$v), xcol=X, yrow=X) + # V <- eval.im(exp(-6.618913 + 5.855337 * M - 8.432483 * M^2)) + set.seed(SEED) + Y <- rpoispp(V) + fY <- ppm(Y ~cv + I(cv^2), data=list(cv=M), correction="translate") + diagnose.ppm(fY) + lurking(fY, covariate=as.im(function(x,y){x}, square(A)), type="raw") + } + + if(ALWAYS) { + ## from Andrew Bevan: numerical overflow, ill-conditioned Fisher information + SEED <- 42 + nongranite<- owin(poly = list(x = c(0, 8500, 7000, 6400, 6400, 6700, 7000, 7200, 7300, 8000, 8100, 8800, 9500, 10000, 10000, 0), y = c(0, 0, 2000, 3800, 4000, 5000, 6500, 7400, 7500, 8000, 8100, 9000, 9500, 9600, 10000, 10000))) + ## Trend on raster grid + rain <- as.im(X=function(x,y) { x^2 + y^2 }, W=nongranite, dimyx=100) + ## Generate a point pattern via a Lennard-Jones process + set.seed(SEED) + mod4<- rmhmodel(cif="lennard", + par=list(beta=1, sigma=250, epsilon=2.2), + trend=rain, w=nongranite) + ljtr<- rmh(mod4, start=list(n.start=80), control=list(p=1, nrep=1e5)) + + ## Fit a point process model to the pattern with rain as a covariate + ## NOTE INCORRECT TREND FORMULA + ljtrmod <- ppm(ljtr, trend= ~ Z, interaction=NULL, data=list(Z=rain)) + ss <- summary(ljtrmod) + } + + if(FULLTEST) { + ## From Ege + ## Degenerate but non-null argument 'covariates' + xx <- list() + names(xx) <- character(0) + fit <- ppm(cells ~x, covariates = xx) + st <- summary(fit) + } + + }) Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. Error in solve.default(M) : system is computationally singular: reciprocal condition number = 5.72218e-18 In addition: Warning messages: 1: Values of the covariate 'cv' were NA or undefined at 96% (1774 out of 1845) of the quadrature points. Occurred while executing: ppm.ppp(Q = Y, trend = ~cv + I(cv^2), data = list(list(c(1, 1.91953576453823, 2: Some infinite, NA or NaN increments were removed 3: Numerical underflow detected: sigma is probably too small 4: Some infinite, NA or NaN increments were removed Error in solve.default(M) : system is computationally singular: reciprocal condition number = 5.72218e-18 In addition: Warning message: Cannot compute variance: Fisher information matrix is singular Warning message: Cannot compute variance: Fisher information matrix is singular > > > > #' tests/ppmclass.R > #' > #' Class support for ppm > #' > #' $Revision: 1.9 $ $Date: 2022/03/07 03:26:09 $ > > if(FULLTEST) { + local({ + #' (1) print.ppm, summary.ppm, print.summary.ppm + Z <- as.im(function(x,y){x}, Window(cells)) + fitZ <- ppm(cells ~ Z) + print(fitZ) + print(summary(fitZ)) + #' logistic + fitl <- ppm(swedishpines ~ x+y, method="logi") + print(fitl) + print(summary(fitl)) + #' Model with covariate arguments + f <- function(x,y,b) { x+b } + fitf <- ppm(cells ~ f, covfunargs=list(b=1)) + print(fitf) + print(summary(fitf)) + #' Invalid model + fitN <- ppm(redwood ~ 1, Strauss(0.1)) + print(fitN) + print(summary(fitN)) + #' standard errors in output + fat <- ppm(cells ~ x, Strauss(0.12)) + op <- spatstat.options(print.ppm.SE='always') + print(fat) + spatstat.options(print.ppm.SE='never') + print(fat) + print(fitZ) + spatstat.options(op) + + ## (2) plot.ppm + plot(fitZ) + plot(fat, trend=FALSE, cif=FALSE, se=FALSE) + + ## (3) emend.ppm + fitZe <- emend(fitZ, trace=TRUE) + ZZ <- Z + fitZZ <- ppm(cells ~ Z + ZZ) + fitZZe <- emend(fitZZ, trace=TRUE) + fitOK <- ppm(redwood ~1, Strauss(0.1), emend=TRUE) + print(fitOK) + fitNot <- ppm(redwood ~1, Strauss(0.1)) + fitSlow <- emend(fitNot, trace=TRUE) + print(fitSlow) + op <- spatstat.options(project.fast=TRUE) + fitFast <- emend(fitNot, trace=TRUE) + print(fitFast) + fitZZe <- emend(fitZZ, trace=TRUE) + spatstat.options(op) + + #' (4) methods for other generics + logLik(fitZ, absolute=TRUE) + unitname(fitZ) + unitname(fat) <- c("metre", "metres") + is.expandable(fitf) + fit0 <- update(fitZ, . ~ 1) + anova(fit0, fitZ, override=TRUE) + interactionfamilyname(fat) + interactionorder(fat) + hardcoredist(fat) + + #' (5) miscellaneous + + ## example from Robert Aue - handling offsets + X <- demohyper$Points[[1]] + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) + fit <- ppm(X ~ 1, GH) + valid.ppm(fit) + + #' hard core distance of hybrid + hardcoredist(fit) + #' interaction order of hybrid + interactionorder(fit) + + #' case of boundingbox + boundingbox(cells, ppm(cells ~ 1)) + }) + + reset.spatstat.options() + } > # > # tests/ppmgam.R > # > # Test ppm with use.gam=TRUE > # > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ > # > > if(FULLTEST) { + local({ + fit <- ppm(nztrees ~s(x,y), use.gam=TRUE) + mm <- model.matrix(fit) + mf <- model.frame(fit) + v <- vcov(fit) + prd <- predict(fit) + }) + } > #' > #' tests/ppmlogi.R > #' > #' Tests of ppm(method='logi') > #' and related code (predict, leverage etc) > #' > #' $Revision: 1.15 $ $Date: 2020/04/30 05:23:52 $ > #' > > local({ + if(FULLTEST) { + fit <- ppm(cells ~x, method="logi") + f <- fitted(fit) + p <- predict(fit) + u <- summary(fit) + fitS <- ppm(cells ~x, Strauss(0.12), method="logi") + fS <- fitted(fitS) + pS <- predict(fitS) + uS <- summary(fitS) + print(uS) + + plot(leverage(fit)) + plot(influence(fit)) + plot(dfbetas(fit)) + plot(leverage(fitS)) + plot(influence(fitS)) + plot(dfbetas(fitS)) + } + + if(FULLTEST) { + #' same with hard core - A1 is singular + fitH <- ppm(cells ~x, Strauss(0.08), method="logi") + print(fitH) + fH <- fitted(fitH) + pH <- predict(fitH) + uH <- summary(fitH) + print(uH) + plot(leverage(fitH)) + plot(influence(fitH)) + plot(dfbetas(fitH)) + } + + if(FULLTEST) { + #' logistic fit to data frame of covariates + z <- c(rep(TRUE, 5), rep(FALSE, 5)) + df <- data.frame(A=z + 2* runif(10), + B=runif(10)) + Y <- quadscheme.logi(runifpoint(5), runifpoint(5)) + fut <- ppm(Y ~ A+B, data=df, method="logi") + sf <- summary(fut) + print(sf) + } + + if(FULLTEST) { + #' vblogit code, just to check that it runs. + fee <- ppm(cells ~ x, method="VBlogi", nd=21) + print(fee) + summary(fee) + logLik(fee) + AIC(fee) + extractAIC(fee) + Z <- predict(fee) + summary(Z) + print(fee$internal$glmfit) # print.vblogit + } + }) > > # > # tests/ppmmarkorder.R > # > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ > # > # Test that predict.ppm, plot.ppm and plot.fitin > # tolerate marks with levels that are not in alpha order > # > if(ALWAYS) { # locale-dependent? + local({ + X <- amacrine + levels(marks(X)) <- c("ZZZ", "AAA") + fit <- ppm(X ~marks, MultiStrauss(c("ZZZ","AAA"), matrix(0.06, 2, 2))) + aa <- predict(fit, type="trend") + bb <- predict(fit, type="cif") + plot(fit) + plot(fitin(fit)) + }) + } > > > # > # tests/ppmscope.R > # > # Test things that might corrupt the internal format of ppm objects > # > # $Revision: 1.7 $ $Date: 2022/01/19 09:18:20 $ > # > > if(ALWAYS) { # dependent on R version? + local({ + + ## (1) Scoping problem that can arise when ppm splits the data + fit <- ppm(bei ~elev, data=bei.extra) + mm <- model.matrix(fit) + + ## (2) Fast update mechanism + fit1 <- ppm(cells ~x+y, Strauss(0.07)) + fit2 <- update(fit1, ~y) + fit3 <- update(fit2, ~x) + + ## (3) New formula-based syntax + attach(bei.extra) + slfit <- ppm(bei ~ grad) + sl2fit <- update(slfit, ~grad + I(grad^2)) + slfitup <- update(slfit, use.internal=TRUE) + sl2fitup <- update(sl2fit, use.internal=TRUE) + + ## (4) anova.ppm + fut1 <- ppm(cells ~ 1, Strauss(0.1)) + futx <- ppm(cells ~ x, Strauss(0.1)) + anova(fut1, test="Chi") + anova(futx, test="Chi") + fut1a <- ppm(cells ~ 1, Strauss(0.1), rbord=0) + anova(fut1a, futx, test="Chi") + fut1d <- ppm(cells ~ 1, Strauss(0.1), nd=23) + anova(fut1d, futx, test="Chi") + ## This now works! + futxyg <- ppm(cells ~ x + s(y), Strauss(0.1), use.gam=TRUE) + anova(futx, futxyg) + ## marked + fatP <- ppm(amacrine ~ marks) + fatM <- ppm(amacrine ~ marks, MultiStrauss(matrix(0.07, 2, 2))) + anova(fatP, fatM, test="Chi") + + ## (5) expansion of "." in update.ppm + fitb <- ppm(bei ~ . , data=bei.extra) + step(fitb) + }) + } Start: AIC=42295.11 ~elev + grad Df AIC 42295 - elev 1 42383 - grad 1 42760 Nonstationary Poisson process Fitted to point pattern dataset 'bei' Log intensity: ~elev + grad Fitted trend coefficients: (Intercept) elev grad -8.56355220 0.02143995 5.84646680 Estimate S.E. CI95.lo CI95.hi Ztest Zval (Intercept) -8.56355220 0.341113849 -9.23212306 -7.89498134 *** -25.104675 elev 0.02143995 0.002287866 0.01695581 0.02592408 *** 9.371155 grad 5.84646680 0.255781018 5.34514522 6.34778838 *** 22.857313 Warning messages: 1: anova.ppm now computes the *adjusted* deviances when the models are not Poisson processes. 2: Models were re-fitted using a common value of 'rbord' 3: Models were re-fitted using a common quadrature scheme 4: Models were re-fitted with use.gam=TRUE 5: Deviance adjustment is not available for gam fits; unadjusted composite deviance calculated. 6: Models were re-fitted using a common value of 'rbord' > grep# function (pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE, fixed = FALSE, useBytes = FALSE, invert = FALSE) { pattern <- as.character(pattern) if (is.factor(x) && length(levx <- levels(x)) < length(x) && !is.na(pattern[1L])) { value <- is.character(idxna <- suppressWarnings(grep(pattern, NA_character_, ignore.case, perl, value, fixed, useBytes, invert))) idx <- logical(length(levx)) idx[grep(pattern, levx, ignore.case, perl, FALSE, fixed, useBytes, invert)] <- TRUE idx <- idx[x] if (length(idxna)) idx[is.na(x)] <- TRUE idx <- which(idx) if (value) { idx <- x[idx] structure(as.character(idx), names = names(idx)) } else idx } else { if (!is.character(x)) x <- structure(as.character(x), names = names(x)) .Internal(grep(pattern, x, ignore.case, value, perl, fixed, useBytes, invert)) } } > # tests/ppmtricks.R > # > # Test backdoor exits, hidden options, internals and tricks in ppm > # > # $Revision: 1.19 $ $Date: 2020/04/30 05:23:52 $ > # > local({ + + ## (1) skip.border + if(ALWAYS) { # needed below + fit <- ppm(cells, ~1, Strauss(0.1), skip.border=TRUE) + } + + ## (2) subset arguments of different kinds + if(FULLTEST) { + fut <- ppm(cells ~ x, subset=(x > 0.5)) + fot <- ppm(cells ~ x, subset=(x > 0.5), method="logi") + W <- owin(c(0.4, 0.8), c(0.2, 0.7)) + fut <- ppm(cells ~ x, subset=W) + fot <- ppm(cells ~ x, subset=W, method="logi") + V <- as.im(inside.owin, Window(cells), w=W) + fet <- ppm(cells ~ x, subset=V) + fet <- ppm(cells ~ x, subset=V, method="logi") + } + + ## (3) profilepl -> ppm + ## uses 'skip.border' and 'precomputed' + ## also tests scoping for covariates + if(FULLTEST) { + splants <- split(ants) + mess <- splants[["Messor"]] + cats <- splants[["Cataglyphis"]] + ss <- data.frame(r=seq(60,120,by=20),hc=29/6) + dM <- distmap(mess,dimyx=256) + mungf <- profilepl(ss, StraussHard, cats ~ dM) + mungp <- profilepl(ss, StraussHard, trend=~dM, Q=cats) + } + + ## (4) splitting large quadschemes into blocks + if(FULLTEST) { + mop <- spatstat.options(maxmatrix=5000) + qr <- quadBlockSizes(quadscheme(cells)) + pr <- predict(ppm(cells ~ x, AreaInter(0.05))) + spatstat.options(mop) + qr <- quadBlockSizes(quadscheme(cells)) + } + + ## (5) shortcuts in summary.ppm + ## and corresponding behaviour of print.summary.ppm + if(FULLTEST) { + print(summary(fit, quick=TRUE)) + print(summary(fit, quick="entries")) + print(summary(fit, quick="no prediction")) + print(summary(fit, quick="no variances")) + } + + ## (6) suffstat.R + if(ALWAYS) { + fitP <- update(fit, Poisson()) + suffstat.poisson(fitP, cells) + fit0 <- killinteraction(fit) + suffstat.poisson(fit0, cells) + } + + ## (7) various support for class ppm + if(FULLTEST) { + fut <- kppm(redwood ~ x) + A <- quad.ppm(fut) + Z <- as.im(function(x,y){x}, Window(cells)) + fitZ <- ppm(cells ~ Z) + U <- getppmOriginalCovariates(fitZ) + } + + ## (8) support for class profilepl + if(FULLTEST) { + rr <- data.frame(r=seq(0.05, 0.15, by=0.02)) + ps <- profilepl(rr, Strauss, cells) + ## plot(ps) ## covered in plot.profilepl.Rd + simulate(ps, nrep=1e4) + parameters(ps) + fitin(ps) + predict(ps, type="cif") + } + + ## (9) class 'plotppm' + if(FULLTEST) { + fut <- ppm(amacrine ~ marks + polynom(x,y,2), Strauss(0.07)) + p <- plot(fut, plot.it=FALSE) + print(p) + plot(p, how="contour") + plot(p, how="persp") + } + + ## (10) ppm -> mpl.engine -> mpl.prepare + if(ALWAYS) { # includes C code + fit <- ppm(cells, NULL) + fit <- ppm(cells ~ x, clipwin=square(0.7)) + fit <- ppm(cells ~ x, subset=square(0.7)) + DG <- as.im(function(x,y){x+y < 1}, square(1)) + fit <- ppm(cells ~ x, subset=DG) + fit <- ppm(cells ~ x, GLM=glm) + fit <- ppm(cells ~ x, famille=quasi(link='log', variance='mu')) + fit <- ppm(cells ~ x, Hardcore(0.07), skip.border=TRUE, splitInf=TRUE) + } + + ## (11) unidentifiable model (triggers an error in ppm) + if(FULLTEST) { + Q <- quadscheme(cells) + M <- mpl.prepare(Q, cells, as.ppp(Q), trend=~1, covariates=NULL, + interaction=Hardcore(0.3), correction="none") + } + }) > > reset.spatstat.options() > # > # tests/prediction.R > # > # Things that might go wrong with predict() > # > # $Revision: 1.20 $ $Date: 2020/04/30 05:41:59 $ > # > > local({ + if(ALWAYS) { + ## test of 'covfunargs' - platform dependent? + f <- function(x,y,a){ y - a } + fit <- ppm(cells ~x + f, covariates=list(f=f), covfunargs=list(a=1/2)) + p <- predict(fit) + + ## prediction involving 0 * NA + qc <- quadscheme(cells, nd=10) + r <- minnndist(as.ppp(qc))/10 + fit <- ppm(qc ~ 1, Strauss(r)) # model has NA for interaction coefficient + p1 <- predict(fit) + p2 <- predict(fit, type="cif", ngrid=10) + stopifnot(all(is.finite(as.matrix(p1)))) + stopifnot(all(is.finite(as.matrix(p2)))) + } + + if(FULLTEST) { + ## test of 'new.coef' mechanism + fut <- ppm(cells ~ x, Strauss(0.15), rbord=0) + p0 <- predict(fut, type="cif") + pe <- predict(fut, type="cif", new.coef=coef(fut)) + pn <- predict(fut, type="cif", new.coef=unname(coef(fut))) + if(max(abs(pe-p0)) > 0.01) + stop("new.coef mechanism is broken!") + if(max(abs(pn-p0)) > 0.01) + stop("new.coef mechanism gives wrong answer, for unnamed vectors") + #' adaptcoef + a <- c(A=1,B=2,Z=42) + b <- c(B=41,A=0) + ab <- adaptcoef(a, b, drop=TRUE) + } + + if(FULLTEST) { + ## tests of relrisk.ppm + fut <- ppm(amacrine ~ x * marks) + a <- relrisk(fut, control=2, relative=TRUE) + a <- relrisk(fut, se=TRUE) + a <- relrisk(fut, relative=TRUE, se=TRUE) + fut <- ppm(sporophores ~ marks + x) + a <- relrisk(fut, control=2, relative=TRUE) + a <- relrisk(fut, se=TRUE) + a <- relrisk(fut, relative=TRUE, se=TRUE) + + ## untested cases of predict.ppm + fit0 <- ppm(cells) + a <- predict(fit0, interval="confidence") + a <- predict(fit0, interval="confidence", type="count") + fit <- ppm(cells ~ x) + b <- predict(fit, se=TRUE, locations=cells) + b <- predict(fit, se=TRUE, interval="confidence") + b <- predict(fit, type="count", se=TRUE) + b <- predict(fit, type="count", window=square(0.5), se=TRUE) + b <- predict(fit, type="count", window=quadrats(cells, 3), se=TRUE) + d <- predict(fit, type="count", interval="prediction", se=TRUE) + d <- predict(fit, type="count", interval="confidence", se=TRUE) + d <- predict(fit, interval="confidence", se=TRUE) + foot <- ppm(cells ~ x, StraussHard(0.12)) + d <- predict(foot, ignore.hardcore=TRUE) + dX <- predict(foot, ignore.hardcore=TRUE, locations=cells) + + ## superseded usages + b <- predict(fit, type="se", getoutofjail=TRUE) + b <- predict(fit, type="se", locations=cells) # warning + b <- predict(fit, total=TRUE) + b <- predict(fit, total=square(0.5)) + b <- predict(fit, total=quadrats(cells, 3)) + + ## supporting code + u <- model.se.image(fit, square(0.5)) + u <- model.se.image(fit, square(0.5), what="cv") + u <- model.se.image(fit, square(0.5), what="ce") + co <- c(Intercept=5, slope=3, kink=2) + re <- c("Intercept", "slope") + a <- fill.coefs(co, re) # warning + b <- fill.coefs(co, rev(names(co))) + d <- fill.coefs(co, letters[1:3]) + ## model matrix etc + v <- model.frame(ppm(cells)) + fut <- ppm(cells ~ x, Strauss(0.1)) + v <- model.matrix(fut, subset=(x<0.5), keepNA=FALSE) + df <- data.frame(x=runif(10), y=runif(10), + Interaction=sample(0:1, 10, TRUE)) + m10 <- PPMmodelmatrix(fut, data=df) + mmm <- PPMmodelmatrix(fut, Q=quad.ppm(fut)) + #' effectfun for Gibbs + effectfun(fut, "x") + effectfun(fut, "x", se.fit=TRUE) + #' implicit covariate when there is only one + effectfun(fut) + effectfun(fut, se.fit=TRUE) + #' given covariate + dlin <- distfun(copper$SouthLines) + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) + effectfun(copfit, "dlin") + effectfun(copfit) + #' covariate that is not used in model + effectfun(fut, "y", x=0) + futS <- ppm(cells ~ 1, Strauss(0.1)) + effectfun(futS, "x") + effectfun(futS, "y") + #' factor covariate + fot <- ppm(amacrine~x+marks) + effectfun(fot, "marks", x=0.5, se.fit=TRUE) + #' covariate retained but not used + W <- Window(swedishpines) + a <- solist(A=funxy(function(x,y){x < 20}, W), + B=funxy(function(x,y){factor(x < 20)}, W)) + fvt <- ppm(swedishpines ~ A, data=a, allcovar=TRUE) + effectfun(fvt, "A", se.fit=TRUE) + effectfun(fvt, "B", A=TRUE, se.fit=TRUE) + + ## ppm with covariate values in data frame + X <- rpoispp(42) + Q <- quadscheme(X) + weirdfunction <- function(x,y){ 10 * x^2 + 5 * sin(10 * y) } + Zvalues <- weirdfunction(x.quad(Q), y.quad(Q)) + fot <- ppm(Q ~ y + Z, data=data.frame(Z=Zvalues)) + effectfun(fot, "y", Z=0) + effectfun(fot, "Z", y=0) + + #' multitype + modX <- ppm(amacrine ~ polynom(x,2)) + effectfun(modX) + effectfun(modX, "x") + modXM <- ppm(amacrine ~ marks*polynom(x,2)) + effectfun(modXM, "x", marks="on") + modXYM <- ppm(amacrine ~ marks*polynom(x,y,2)) + effectfun(modXYM, "x", y=0, marks="on") + + df <- as.data.frame(simulate(modXM, drop=TRUE)) + df$marks <- as.character(df$marks) + dfpr <- predict(modXM, locations=df) + } + }) > > # > # tests/project.ppm.R > # > # $Revision: 1.7 $ $Date: 2020/04/30 05:41:59 $ > # > # Tests of projection mechanism > # > > local({ + chk <- function(m) { + if(!valid.ppm(m)) stop("Projected model was still not valid") + return(invisible(NULL)) + } + + if(FULLTEST) { + ## a very unidentifiable model + fit <- ppm(cells ~Z, Strauss(1e-06), covariates=list(Z=0)) + chk(emend(fit)) + ## multitype + r <- matrix(1e-06, 2, 2) + fit2 <- ppm(amacrine ~1, MultiStrauss(types=c("off", "on"), radii=r)) + chk(emend(fit2)) + ## complicated multitype + fit3 <- ppm(amacrine ~1, MultiStraussHard(types=c("off", "on"), + iradii=r, hradii=r/5)) + chk(emend(fit3)) + + #' code coverage + op <- spatstat.options(project.fast=TRUE) + fut <- emend(fit, trace=TRUE) + chk(fut) + spatstat.options(op) + + #' hierarchical + ra <- r + r[2,1] <- NA + fit4 <- ppm(amacrine ~1, HierStrauss(types=c("off", "on"), radii=r)) + chk(emend(fit4)) + #' complicated hierarchical + fit5 <- ppm(amacrine ~1, HierStraussHard(types=c("off", "on"), + iradii=r, hradii=r/5)) + chk(emend(fit5)) + + ## hybrids + r0 <- min(nndist(redwood)) + ra <- 1.25 * r0 + rb <- 0.8 * r0 + f1 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Geyer(0.1, 2)), project=TRUE) + chk(f1) + f2 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Geyer(0.1, 2)), project=TRUE) + chk(f2) + f3 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Strauss(0.1)), project=TRUE) + chk(f3) + f4 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Strauss(0.1)), project=TRUE) + chk(f4) + f5 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Strauss(0.1)), project=TRUE) + chk(f5) + f6 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Geyer(0.1, 2)), project=TRUE) + chk(f6) + f7 <- ppm(redwood ~1, Hybrid(A=Geyer(rb, 1), B=Strauss(0.1)), project=TRUE) + chk(f7) + } + }) > > reset.spatstat.options() > > proc.time() user system elapsed 8.42 2.20 10.59