spatstat-internal {spatstat} | R Documentation |
Internal spatstat functions.
## S3 method for class 'splitppx' x[...] ## S3 replacement method for class 'splitppx' x[...] <- value ## S3 method for class 'diagramobj' x[...] ## S3 method for class 'rat' x[...] accumulateStatus(x, stats) acedist.show(X, Y, n, d, timelag) acedist.noshow(X, Y, n, d) active.interactions(object) adaptcoef(new.coef, fitcoef, drop) adjust.ratfv(f, columns, numfactor, denfactor) affinexy(X, mat, vec, invert) affinexypolygon(p, mat, vec, detmat) ## S3 method for class 'msr' affine(X, mat, vec, ...) ang2rad(ang, unit, start, clockwise) anycrossing.psp(A,B) ApplyConnected(X, Engine, r, ..., rule, auxdata) applytolayers(L, FUN, ...) applyPolyclipArgs(x, p) areadelta2(X, r, ..., sparseOK) areaGain.diri(u, X, r, ..., W, verbose) areaGain.grid(u, X, r, ..., W, ngrid) areaLoss.diri(X, r, ..., W, subset) areaLoss.grid(X, r, ..., W, subset, method = c("count", "distmap"), ngrid = spatstat.options("ngrid.disc"), exact = FALSE) areaLoss.poly(X, r, ..., W, subset, splitem) assemble.plot.objects(xlim, ylim, ..., lines, polygon) AsymmDistance.psp(X, Y, metric, method) as.breakpts(...) ## S3 method for class 'unitname' as.character(x, ...) ## S3 method for class 'bw.optim' as.data.frame(x, ...) ## S3 method for class 'fv' as.data.frame(x, ...) ## S3 method for class 'im' as.double(x, ...) ## S3 method for class 'linfun' as.linfun(X, ...) ## S3 method for class 'hyperframe' as.list(x, ...) as.listof(x) ## S3 method for class 'lintess' as.owin(W, ...) as.unitname(s) augment.msr(x, ..., sigma, recompute) avenndist(X) bandwidth.is.infinite(sigma) BartCalc(fY, fK) bbEngine(...) bermantestCalc(fram, which, alternative, ...) bermantestEngine(model, covariate, which, alternative, ..., modelname, covname, dataname) bdry.mask(W) bind.ratfv(x, numerator, denominator, labl, desc, preferred, ratio, quotient) blankcoefnames(x) bounding.box3(...) break.holes(x, splitby, depth, maxdepth) breakpts(val, maxi, even = FALSE, npos = NULL, step = NULL) breakpts.from.r(r) bt.frame(Q, trend, interaction, ..., covariates, correction, rbord, use.gam, allcovar) bw.optim(cv, h, iopt, ..., cvname, hname, criterion, optimum, warnextreme, hargnames, unitname) calc.DR(COV, z, Dim) calc.NNIR(COV, z, pos, Dim) calc.SAVE(COV, z, Dim) calc.SIR(COV, z) calc.TSE(COV, z, pos, Dim1, Dim2) cannot.update(...) cartesian(pp, markset, fac = TRUE) cellmiddles(W, nx, ny, npix, distances) censtimeCDFest(o, cc, d, breaks, ..., KM, RS, HAN, RAW, han.denom, tt, pmax) change.default.expand(x, newdefault) checkbigmatrix(n, m, fatal, silent) checkfields(X,L) check.arc(arc, fatal) check.finespacing(r, eps, win, rmaxdefault, context, action, rname) check.hist.lengths(hist,breaks) check.separable(dmat, covname, isconstant, fatal) check.testfun(f, f1, X) circticks(R, at, unit, start, clockwise, labels) circunion(arcs) clarkevansCalc(X, correction, clipregion, working) clip.psp(x, window, check, fragments) cliprect.psp(x, window, fragments) clippoly.psp(s, window, fragments) closethresh(X,R,S,twice,...) ## S3 method for class 'summary.kppm' coef(object, ...) ## S3 method for class 'summary.ppm' coef(object, ...) ## S3 method for class 'vblogit' coef(object, ...) coerce.marks.numeric(X, warn) ## S3 method for class 'rat' compatible(A, B, ...) compileCDF(D, B, r, ..., han.denom, check) conform.ratfv(x) crosspairquad(Q,rmax,what) cobble.xy(x, y, f, fatal, ...) codetime(x, hms, what) col.args.to.grey(x, ...) commonPolyclipArgs(..., p) conform.imagelist(X, Zlist) countingweights(id, areas, check = TRUE) CressieReadStatistic(OBS,EXP,lambda,normalise,named) CressieReadSymbol(lambda) CressieReadName(lambda) cutoff2Dkernel(kernel, sigma, varcov, ..., scalekernel, cutoff, fatal) CVforPCF(bw, stuff) damaged.ppm(object) data.mppm(x) datagen.runifpointOnLines(n, L) datagen.runifpoisppOnLines(lambda, L) datagen.rpoisppOnLines(lambda, L, lmax, ..., check) default.clipwindow(object, epsilon) default.linnet.tolerance(L) default.n.tiling(X, nd, ntile, npix, eps, random, quasi, verbose) default.ntile(X) deltasuffstat(model, ..., restrict, dataonly, sparseOK, quadsub, force, warn.forced, verbose, use.special) ## S3 method for class 'hyperframe' dimnames(x) ## S3 replacement method for class 'hyperframe' dimnames(x) <- value DoCountEnds(X, D, toler) DoCountCrossEnds(X, I, J, DIJ, toler) Deviation(x, ref, leaveout, n, xi) ## S3 method for class 'ppmInfluence' dfbetas(model, ...) dflt.redraw(button, name, env) densitycrossEngine(Xdata, Xquery, sigma, ..., kernel, scalekernel, weights, edge, varcov, diggle, sorted, cutoff) densitypointsEngine(x, sigma, ..., kernel, scalekernel, weights, edge, varcov, leaveoneout, diggle, sorted, spill, cutoff) densitypointsLPP(x, sigma, ..., weights, nsigma, leaveoneout, fast, fastmethod, floored, dx, dt, iterMax, verbose, debug) diagnose.ppm.engine(object, ..., type, typename, opt, sigma, rbord, compute.sd, compute.cts, envelope, nsim, nrank, rv, oldstyle, splineargs, verbose) diagramobj(X, ...) digestCovariates(..., W) digital.volume(range, nval, vside) ## S3 method for class 'fasp' dim(x) ## S3 method for class 'hyperframe' dim(x) ## S3 method for class 'im' dim(x) ## S3 method for class 'msr' dim(x) ## S3 method for class 'owin' dim(x) ## S3 method for class 'fasp' dimnames(x) ## S3 replacement method for class 'fasp' dimnames(x) <- value ## S3 method for class 'msr' dimnames(x) distributecbind(x) dist2dpath(dist, method="C") do.as.im(x, action, ..., W, eps, dimyx, xy, na.replace) do.call.plotfun(fun, arglist, ...) doMultiStraussHard(iradii, hradii, types) dppmFixIntensity(DPP, lambda, po) dppmFixAlgorithm(algorithm, changealgorithm, clusters, startpar) drawSignedPoly(x,y,pars,sgn) emptywindow(w) envelopeEngine(X, fun, simul, nsim, nrank, ..., funargs, funYargs, verbose, clipdata, transform, global, ginterval, use.theory, alternative, scale, clamp, savefuns, savepatterns, saveresultof, weights, nsim2, VARIANCE, nSD, Yname, maxnerr, rejectNA, silent, maxerr.action, internal, cl, envir.user, expected.arg, do.pwrong, foreignclass, collectrubbish) envelopeProgressData(X, fun, ..., exponent, alternative, leaveout, scale, clamp, normalize, deflate, rmin, save.envelope, savefuns, savepatterns) envelopeTest(X, ..., exponent, alternative, rinterval, leaveout, scale, clamp, tie.rule, interpolate, save.interpolant, save.envelope, savefuns, savepatterns, Xname, badXfatal, verbose) ## S3 method for class 'hasenvelope' envelope(Y, ..., Yname) ## S3 method for class 'matrix' envelope(Y, ..., rvals, observed, theory, funX, nsim, nsim2, jsim, jsim.mean, type, alternative, scale, clamp, csr, use.theory, nrank, ginterval, nSD, savefuns, check, Yname, do.pwrong, weights, precomputed, gaveup) equalpairs(U, X, marked=FALSE) equalpairs.quad(Q) equals.quad(Q) equalsfun.quad(Q) erodemask(w,r,strict) evalCovar(model, covariate, ...) ## S3 method for class 'ppm' evalCovar(model, covariate, ..., lambdatype, dimyx, eps, interpolate, jitter, modelname, covname, dataname, subset) ## S3 method for class 'lppm' evalCovar(model, covariate, ..., lambdatype, eps, nd, interpolate, jitter, modelname, covname, dataname, subset) evalCovariate(covariate, locations) evalInteraction(X,P,E,interaction,correction,splitInf,..., precomputed,savecomputed) evalInterEngine(X,P,E,interaction,correction,splitInf,..., Reach,precomputed,savecomputed) evalPairPotential(X,P,E,pairpot,potpars,R) evaluate2Dkernel(kernel, x, y, sigma, varcov, ..., scalekernel) even.breaks.owin(w) exactdt(X, ...) exactPdt(w) existsSpatstatVariable(name) expandSpecialLists(x, special) expandwinPerfect(W, expand, amount) ExpSmoothLog(X, ..., at, weights) ## S3 method for class 'slrm' extractAIC(fit, scale = 0, k = 2, ...) extractAtomicQtests(x) fakemaintitle(bb, main, ...) ## S3 method for class 'vblogit' family(object, ...) f3engine(x, y, z, box, vside, range, nval, correction) f3Cengine(x, y, z, box, vside, rmax, nrval) fasp(fns, which, formulae, dataname, title, rowNames, colNames, checkfv) FDMKERNEL(lppobj, dtt, dtx, M, nsave, weights, stepnames, setuponly, verbose) fft2D(z, inverse, west) fftwAvailable() fill.coefs(coefs, required) findbestlegendpos(...) findCovariate(covname, scope, scopename=NULL) findcbind(root, depth, maxdepth) fii(interaction, coefs, Vnames, IsOffset, vnameprefix) fillNA(x, value) flatdensityfunlpp(X, ..., disconnect, weights, what) flatdensityatpointslpp(X, ..., leaveoneout, disconnect, weights, what) flatfname(x) flipxypolygon(p) ## S3 method for class 'msr' flipxy(X) forbid.logi(object) ## S3 method for class 'numberwithunit' format(x, ..., collapse, modifier) FormatFaspFormulae(f, argname) framebottomleft(w) fvexprmap(x) fvlabels(x, expand=FALSE) fvlabels(x) <- value fvlabelmap(x, dot=TRUE) fvlegend(object, elang) gammabreaks(ra, n, gamma) g3engine(x, y, z, box, rmax, nrval, correction) g3Cengine(x, y, z, box, rmax, nrval) genericNNdistBy(X, by, k) getdataname(defaultvalue, ..., dataname) getfields(X, L, fatal = TRUE) getglmdata(object, drop=FALSE) getglmfit(object) getglmsubset(object) getlambda.lpp(lambda, X, subset, ..., update, leaveoneout, loo.given, lambdaname) getlastshift(X) getppmdatasubset(object) getppmOriginalCovariates(object) getRandomFieldsModelGen(model) getSpatstatVariable(name) getSumFun(abbreviation, classname, ismarked, fatal) geyercounts(U,X,r,sat,Xcounts,EqualPairs) geyerdelta2(X,r,sat,...,sparseOK, correction) GLMpredict(fit, data, coefs, changecoef, type) good.correction.K(X) gridindex(x, y, xrange, yrange, nx, ny) grid1index(x, xrange, nx) grow.mask(M, xmargin=0, ymargin=xmargin) hackglmmPQL(fixed, random, family, data, correlation, weights, control, niter, verbose, subset, ..., reltol) hasenvelope(X, E) hasglmfit(object) HermiteCoefs(order) handle.r.b.args(r = NULL, breaks = NULL, window, pixeps = NULL, rmaxdefault) handle.rshift.args(W, ..., radius, width, height, edge, clip, edgedefault) ## S3 method for class 'hyperframe' head(x,n,...) hierarchicalordering(i, s) hiermat(x, h) ho.engine(model, ..., nsim, nrmh, start, control, verb) hsvNA(h, s, v, alpha) IdenticalRowPair(i,j,a,b) IdenticalRows(i,j,a,b) idorempty(w, r, caller) illegal.iformula(ifmla, itags, dfvarnames) imageOp(e1, e2, op) imagelistOp(e1, e2, op) implemented.for.K(correction, windowtype, explicit) impliedpresence(tags, formula, df, extranames=character(0)) impliedcoefficients(object, tag) ## S3 method for class 'ppmInfluence' influence(model, ...) inpoint(W) inside.arc(theta, arc) instantiate.interact(x, par) ## S3 method for class 'leverage.ppm' integral(f, domain, ...) ## S3 method for class 'influence.ppm' integral(f, domain, ...) interactionfamilyname(x) intermaker(f, blank) interpretAsOrigin(x, W) intX.owin(w) intX.xypolygon(polly) intY.owin(w) intY.xypolygon(polly) invokeColourmapRule(colfun, x, ..., zlim, colargs) is.atomicQtest(x) is.cadlag(s) is.col.argname(x) is.data(Q) is.expandable(x) ## S3 method for class 'ppm' is.expandable(x) ## S3 method for class 'rmhmodel' is.expandable(x) is.fv(x) is.hyperframe(x) is.imlist(x) is.infline(x) is.interact(x) ## Default S3 method: is.marked(...) ## S3 method for class 'msr' is.marked(X, ...) ## S3 method for class 'psp' is.marked(X, ...) ## S3 method for class 'quad' is.marked(X, na.action="warn", ...) is.mppm(x) ## Default S3 method: is.multitype(X, ...) ## S3 method for class 'msr' is.multitype(X, ...) ## S3 method for class 'quad' is.multitype(X, na.action="warn", ...) ## S3 method for class 'mppm' is.poisson(x) is.ppplist(x) is.pp3(x) is.ppx(x) is.psp(x) is.quad(x) is.scov(x) is.solist(x) is.sob(x) is.tess(x) is.vanilla(u) k3engine(x, y, z, box, rmax, nrval, correction) Kborder.engine(X, rmax, nr, correction, weights, ratio) Knone.engine(X, rmax, nr, weights, ratio) Krect.engine(X, rmax, nr, correction, weights, ratio, fname, use.integers) Kount(dIJ, bI, b, breaks) Kwtsum(dIJ, bI, wIJ, b, w, breaks, fatal) Kpcf.kppm(model, what) killinteraction(model) km.rs.opt(o, cc, d, breaks, KM, RS) kppmComLik(X, Xname, po, clusters, control, weightfun, rmax, algorithm, DPP, ...) kppmMinCon(X, Xname, po, clusters, control, statistic, statargs, algorithm, DPP, ...) kppmPalmLik(X, Xname, po, clusters, control, weightfun, rmax, algorithm, DPP, ...) kraever(package, fatal) kraeverRandomFields() ## S3 method for class 'ppm' labels(object, ...) ldtEngine(nv, ns, from, to, seglen, huge, coUXord, vnndist, vnnwhich, vnnlab) ## S3 method for class 'im' levels(x) ## S3 replacement method for class 'im' levels(x) <- value levelsAsFactor(x) ## S3 method for class 'ppmInfluence' leverage(model, ...) linearKengine(X, ..., r, reweight, denom, correction, ratio, showworking) linearKmulti(X, I, J, r, ..., correction) linearKmulti.inhom(X, I, J, lambdaI, lambdaJ, r, ..., correction, normalise) linearpcfengine(X, ..., r, reweight, denom, correction, ratio) linearpcfmulti(X, I, J, r, ..., correction) linearpcfmulti.inhom(X, I, J, lambdaI, lambdaJ, r, ..., correction, normalise) linearKmultiEngine(X, I, J, ..., r, reweight, denom, correction, showworking) linearPCFmultiEngine(X, I, J, ..., r, reweight, denom, correction, showworking) listof(...) localKengine(X, ..., wantL, lambda, rmax, correction, verbose, rvalue) localKmultiEngine(X, from, to, lambdaFrom, lambdaTo, ..., rmax, wantL, correction, verbose, rvalue, sigma, varcov, lambdaX, update, leaveoneout, Iexplain, Jexplain, Ikey, Jkey, miss.update, miss.leave) localpcfengine(X, ..., delta, rmax, nr, stoyan, lambda) localpcfmatrix(X, i, ..., lambda, delta, rmax, nr, stoyan) local2lpp(L, seg, tp, X, df.only) logicalIndex(i, nama, len) logi.dummy(X, dummytype, nd, mark.repeat, ...) logi.engine(Q, trend, interaction, ..., covariates, subsetexpr, clipwin, correction, rbord, covfunargs, allcovar, vnamebase, vnameprefix, justQ, savecomputed, precomputed, VB) ## S3 method for class 'vblogit' logLik(object, ...) looHeatLPP(U0, Amatrix, npts, niter, nsave, lixelweight, lixelmap, verbose) looVoronoiLPP(X) makeLinnetTolerance(toler) maskLaslett(X, ..., eps, dimyx, xy, oldX, verbose, plotit) markvaluetype(x) match2DkernelName(kernel) packupNNdata(NND, NNW, what, k) parbreak(terse) plan.legend.layout(B, ..., side, sep, size, sep.frac, size.frac, started, map) PairPotentialType(pairpot) plotWidthMap(bb.leg, zlim, phys.scale, leg.scale, leg.side, leg.args, grafpar) pointweights(X, ..., weights, parent) PoisSaddle(beta, fi) PoisSaddleArea(beta, fi) PoisSaddleGeyer(beta, fi) PoisSaddlePairwise(beta, fi) polyLaslett(X, ..., oldX, verbose, plotit) polytileareaEngine(P, xrange, yrange, nx, ny, DivideByPixelArea) positiveIndex(i, nama, len) PPMmodelmatrix(object, data, ..., subset, Q, keepNA, irregular, splitInf) ## S3 method for class 'localpcfmatrix' print(x, ...) ## S3 method for class 'localpcfmatrix' plot(x, ...) putSpatstatVariable(name, value) ## S3 method for class 'localpcfmatrix' x[i, ...] ## S3 method for class 'pp3' x[i, drop, ...] lookup.im(Z, x, y, naok, strict) lookup2DkernelInfo(kernel) majorminorversion(v) make.even.breaks(bmax, npos, bstep) makefvlabel(op, accent, fname, sub, argname) makeunitname(sing, plur, mul) markappend(...) markcbind(...) markformat(x) ## S3 method for class 'ppp' markformat(x) ## S3 method for class 'ppx' markformat(x) ## S3 method for class 'psp' markformat(x) ## Default S3 method: markformat(x) mark.scale.default(marx, w, ..., markscale, maxsize, meansize, characters) markspace.integral(X) ## Default S3 method: marks(x, ...) ## S3 method for class 'quad' marks(x, dfok=FALSE, ...) markappendop(x, y) x %mapp% y marksubset(x, index, format) marksubsetop(x, i) x %msub% i markreplicateop(x, n) x %mrep% n mask2df(w) match.kernel(kernel) maxflow(costm) mctestSigtraceEngine(R, devdata, devsim, ..., interpolate, confint, alpha, exponent, unitname) ## S3 method for class 'leverage.ppm' mean(x, ...) meanlistfv(z, ...) meanX.owin(w) meanY.owin(w) model.se.image(fit, W, ..., what) modelFrameGam(formula, ...) mpl.engine(Q, trend, interaction, ..., covariates, subsetexpr, clipwin, covfunargs, correction, rbord, use.gam, gcontrol, GLM, GLMfamily, GLMcontrol, famille, forcefit, nd, eps, allcovar, callstring, precomputed, savecomputed, preponly, rename.intercept, justQ, weightfactor) mpl.get.covariates(covariates, locations, type, covfunargs, need.deriv) mpl.prepare(Q, X, P, trend, interaction, covariates, want.trend, want.inter, correction, rbord, Pname, callstring, ..., subsetexpr, covfunargs, allcovar, precomputed, savecomputed, vnamebase, vnameprefix, warn.illegal, warn.unidentifiable, weightfactor, skip.border, clip.interaction, splitInf) mpl.usable(x) MinimalTess(W, ...) MultiPair.checkmatrix(mat, n, matname, naok, zerook, asymmok) multiplicityNumeric(x) multiply.only.finite.entries(x, a) na.handle.im(X, na.replace) ## S3 replacement method for class 'fv' names(x) <- value ## S3 method for class 'hyperframe' names(x) ## S3 replacement method for class 'hyperframe' names(x) <- value nearest.pixel(x, y, Z) nearest.valid.pixel(x, y, Z, method, nsearch) newformula(old, change, eold, enew) newstyle.coeff.handling(object) nncleanEngine(kthNND, k, d, ..., tol, maxit, plothist, lineargs, verbose, Xname) nndcumfun(X, ..., r) no.trend.ppm(x) n.quad(Q) numberwithunit(x, u) numeric.columns(M, logical, others) objsurfEngine(objfun, optpar, objargs, ..., dotargs, objname, ngrid, ratio, verbose) onecolumn(m) optimStatus(x, call) printStatus(x, errors.only) printStatusList(stats) signalStatus(x, errors.only) outdated.interact(object) oversize.quad(Q, ..., nU, nX, p) owinpolycheck(W, verbose=TRUE) owinpoly2mask(w, rasta, check=TRUE) owin2polypath(w) ## S3 method for class 'listof' pairs(..., plot=TRUE) ## S3 method for class 'solist' pairs(..., plot=TRUE) param.quad(Q) partialModelMatrix(X,D,model,callstring,...) pcf3engine(x, y, z, box, rmax, nrval, correction, delta) pcfmulti.inhom(X, I, J, lambdaI = NULL, lambdaJ = NULL, ..., r = NULL, breaks = NULL, kernel = "epanechnikov", bw = NULL, stoyan = 0.15, correction = c("translate", "Ripley"), sigma = NULL, varcov = NULL, Iname = "points satisfying condition I", Jname = "points satisfying condition J") pickoption(what="option", key, keymap, ..., exact=FALSE, list.on.err=TRUE, die=TRUE, multi=FALSE, allow.all=TRUE) plotEachLayer(x, ..., main, plotargs, add, show.all, do.plot) ploterodewin(W1, W2, col.edge, col.inside, do.plot, ...) ploterodeimage(W, Z, ..., Wcol, rangeZ, colsZ, do.plot) plot3Dpoints(xyz, eye, org, ..., type, xlim, ylim, zlim, add, box, main, cex, box.back, box.front) plotPolygonBdry(x, ...) ## S3 method for class 'addvar' plot(x, ..., do.points=FALSE) ## S3 method for class 'barplotdata' plot(x, ...) ## S3 method for class 'bw.frac' plot(x, ...) ## S3 method for class 'bw.optim' plot(x, ..., showopt, optargs) ## S3 method for class 'indicfun' plot(x, W, ..., main) ## S3 method for class 'lurk' plot(x, ..., shade) ## S3 method for class 'minconfit' plot(x, ...) ## S3 method for class 'parres' plot(x, ...) ## S3 method for class 'plotpairsim' plot(x, ...) ## S3 method for class 'qqppm' plot(x, ..., limits=TRUE, monochrome=spatstat.options('monochrome'), limcol=if(monochrome) "black" else "red") ## S3 method for class 'spatialcdf' plot(x, ..., xlab, ylab) ppllengine(X, Y, action="project", check=FALSE) ## Default S3 method: ppm(Q, trend, interaction, ..., covariates, data, covfunargs, subset, clipwin, correction, rbord, use.gam, method, forcefit, emend, project, prior.mean, prior.var, nd, eps, gcontrol, nsim, nrmh, start, control, verb, callstring) ppmCovariates(model) ppmDerivatives(fit, what, Dcovfun, loc, covfunargs) ppmInfluenceEngine(fit, what, ..., iScore, iHessian, iArgs, drop, method, fine, precomputed, sparseOK, fitname, multitypeOK, entrywise, matrix.action, dimyx, eps, geomsmooth) pppdist.mat(X, Y, cutoff = 1, q = 1, matching = TRUE, precision = 9, approximation = 10) pppdist.prohorov(X, Y, n, dfix, type, cutoff, matching, ccode, auction, precision, approximation) ppsubset(X, I, Iname, fatal) ## S3 method for class 'vblogit' predict(object, newdata, type, se.fit, dispersion, terms, na.action, ...) prefixfv(x, tagprefix, descprefix, lablprefix, whichtags) prepareTitle(main) ## S3 method for class 'addvar' print(x, ...) ## S3 method for class 'anylist' print(x, ...) ## S3 method for class 'autoexec' print(x, ...) ## S3 method for class 'bt.frame' print(x, ...) ## S3 method for class 'bugtable' print(x, ...) ## S3 method for class 'bw.frac' print(x, ...) ## S3 method for class 'bw.optim' print(x, ...) ## S3 method for class 'colourmap' print(x, ...) ## S3 method for class 'densityfun' print(x, ...) ## S3 method for class 'diagppm' print(x, ...) ## S3 method for class 'distfun' print(x, ...) ## S3 method for class 'detpointprocfamily' print(x, ...) ## S3 method for class 'detpointprocfamilyfun' print(x, ...) ## S3 method for class 'envelope' print(x, ...) ## S3 method for class 'ewcdf' print(x, digits, ...) ## S3 method for class 'fasp' print(x, ...) ## S3 method for class 'funxy' print(x, ...) ## S3 method for class 'fv' print(x, ..., tight) ## S3 method for class 'fvfun' print(x, ...) ## S3 method for class 'hasenvelope' print(x, ...) ## S3 method for class 'hierarchicalordering' print(x, ...) ## S3 method for class 'hyperframe' print(x, ...) ## S3 method for class 'indicfun' print(x, ...) ## S3 method for class 'influence.ppm' print(x, ...) ## S3 method for class 'interact' print(x, ..., family, brief, banner) ## S3 method for class 'intermaker' print(x, ...) ## S3 method for class 'isf' print(x, ...) ## S3 method for class 'laslett' print(x, ...) ## S3 method for class 'layered' print(x, ...) ## S3 method for class 'leverage.ppm' print(x, ...) ## S3 method for class 'lintess' print(x, ...) ## S3 method for class 'lurk' print(x, ...) ## S3 method for class 'lut' print(x, ...) ## S3 method for class 'minconfit' print(x, ...) ## S3 method for class 'mppm' print(x, ...) ## S3 method for class 'msr' print(x, ...) ## S3 method for class 'nnfun' print(x, ...) ## S3 method for class 'numberwithunit' print(x, ...) ## S3 method for class 'onearrow' print(x, ...) ## S3 method for class 'parres' print(x, ...) ## S3 method for class 'plotppm' print(x, ...) ## S3 method for class 'plotpairsim' print(x, ...) ## S3 method for class 'pppmatching' print(x, ...) ## S3 method for class 'profilepl' print(x, ...) ## S3 method for class 'quadrattest' print(x, ...) ## S3 method for class 'qqppm' print(x, ...) ## S3 method for class 'rat' print(x, ...) ## S3 method for class 'rmhcontrol' print(x, ...) ## S3 method for class 'rmhexpand' print(x, ..., prefix=TRUE) ## S3 method for class 'rmhmodel' print(x, ...) ## S3 method for class 'rmhstart' print(x, ...) ## S3 method for class 'rmhInfoList' print(x, ...) ## S3 method for class 'rppm' print(x, ...) ## S3 method for class 'simplepanel' print(x, ...) ## S3 method for class 'Smoothfun' print(x, ...) ## S3 method for class 'solist' print(x, ...) ## S3 method for class 'splitppp' print(x, ...) ## S3 method for class 'splitppx' print(x, ...) ## S3 method for class 'summary.distfun' print(x, ...) ## S3 method for class 'summary.funxy' print(x, ...) ## S3 method for class 'summary.hyperframe' print(x, ...) ## S3 method for class 'summary.linim' print(x, ...) ## S3 method for class 'summary.linnet' print(x, ...) ## S3 method for class 'summary.lintess' print(x, ...) ## S3 method for class 'summary.listof' print(x, ...) ## S3 method for class 'summary.logiquad' print(x, ..., dp=3) ## S3 method for class 'summary.lut' print(x, ...) ## S3 method for class 'summary.mppm' print(x, ..., brief) ## S3 method for class 'summary.owin' print(x, ...) ## S3 method for class 'summary.ppp' print(x, ..., dp) ## S3 method for class 'summary.psp' print(x, ...) ## S3 method for class 'summary.rmhexpand' print(x, ...) ## S3 method for class 'summary.ssf' print(x, ...) ## S3 method for class 'summary.splitppp' print(x, ...) ## S3 method for class 'summary.solist' print(x, ...) ## S3 method for class 'summary.splitppx' print(x, ...) ## S3 method for class 'summary.unitname' print(x, ...) ## S3 method for class 'symbolmap' print(x, ...) ## S3 method for class 'textstring' print(x, ...) ## S3 method for class 'texturemap' print(x, ...) ## S3 method for class 'tess' print(x, ..., brief=FALSE) ## S3 method for class 'timed' print(x, ...) ## S3 method for class 'vblogit' print(x, ...) ## S3 method for class 'yardstick' print(x, ...) project3Dhom(xyz, eye, org, vert) putlastshift(X, vec) qkdeEngine(X, sigma, ..., at, what, leaveoneout, diggle, raw, edge2D, edge, weights, varcov, positive, shortcut, precomputed, savecomputed) qtPrepareCoordinate(covname, W, origin) quad(data, dummy, w, param) quad.mppm(x) quadBlockSizes(nX, nD, p, nMAX, announce) RandomFieldsSafe() rasterfilter(X, f) ratfv(df, numer, denom, ..., ratio) recognise.spatstat.type(x) rectquadrat.breaks(xr, yr, nx = 5, ny = nx, xbreaks = NULL, ybreaks = NULL) rectquadrat.countEngine(x, y, xbreaks, ybreaks, weights) reduceformula(fmla, deletevar, verbose) reheat(model, invtemp) RelevantDeviation(x, alternative, clamp, scaling) repair.image.xycoords(x) ## S3 method for class 'msr' rescale(X, s, unitname) resolveEinfo(x, what, fallback, warn, atomic) resolve.foxall.window(X, Y, W, warn.trim) resolve.heat.steps(sigma, ..., dx, dt, niter, iterMax, nsave, seglengths, maxdegree, AMbound, L, finespacing, fineNsplit, fineNlixels, W, eps, dimyx, xy, allow.adjust, warn.adjust, verbose, stepnames) resolve.lambda(X, lambda, ..., sigma, varcov, leaveoneout, update) resolve.lambda.cross(X, I, J, lambdaI, lambdaJ, ..., lambdaX, sigma, varcov, leaveoneout, update, lambdaIJ, Iexplain, Jexplain, miss.update, miss.leave, caller) resolve.vargamma.shape(..., nu.ker, nu.pcf, default) rgbNA(red, green, blue, alpha, maxColorValue) rhohatEngine(model, covariate, reference, volume, ..., subset, weights, method, horvitz, smoother, resolution, n, bw, adjust, from, to, bwref, covname, covunits, confidence, modelcall, callstring) rhohatCalc(ZX, Zvalues, lambda, denom, ..., weights, lambdaX, method, horvitz, smoother, n, bw, adjust, from, to, bwref, covname, confidence, positiveCI, markovCI, covunits, modelcall, callstring, savestuff) rMaternInhibition(type, kappa, r, win, stationary, ..., nsim, drop) RmhExpandRule(nama) rocData(covariate, nullmodel, ..., high) rocModel(lambda, nullmodel, ..., high) rmhsnoop(..., Wsim, Wclip, R, xcoords, ycoords, mlevels, mcodes, irep, itype, proptype, proplocn, propmark, propindx, numerator, denominator, panel.only) roseContinuous(ang, rad, unit, ..., start, clockwise, main, labels, at, do.plot) ruletextline(ch, n, terse) quadrat.testEngine(X, nx, ny, alternative, method, conditional, CR, ..., nsim, Xcount, xbreaks, ybreaks, tess, fit, df.est, Xname, fitname) quadscheme.replicated(data, dummy, method, ...) quadscheme.spatial(data, dummy, method, ...) pointgrid(W, ngrid) rastersample(X, Y) rasterx.mask(w, drop) rastery.mask(w, drop) rasterxy.mask(w, drop) rasterx.im(x) rastery.im(x) rasterxy.im(x, drop) rebadge.fv(x, new.ylab, new.fname, tags, new.desc, new.labl, new.yexp, new.dotnames, new.preferred, new.formula, new.tags) rebadge.as.crossfun(x, main, sub, i, j) rebadge.as.dotfun(x, main, sub, i) rebound(x, rect) ## S3 method for class 'im' rebound(x, rect) ## S3 method for class 'ppp' rebound(x, rect) ## S3 method for class 'psp' rebound(x, rect) ## S3 method for class 'owin' rebound(x, rect) reconcile.fv(...) rename.fv(x, fname, ylab, yexp) repair.old.factor.image(x) reincarnate.interact(object) resid4plot(RES, plot.neg, plot.smooth, spacing, outer, srange, monochrome, main, xlab, ylab, rlab, col.neg, col.smooth, ...) resid1plot(RES, opt, plot.neg, plot.smooth, srange, monochrome, main, add, show.all, do.plot, col.neg, col.smooth, ...) resid1panel(observedX, observedV, theoreticalX, theoreticalV, theoreticalSD, xlab,ylab, ..., do.plot) resolve.2D.kernel(..., sigma, varcov, x, mindist, adjust, bwfun, allow.zero) restrict.mask(M, W) reversePolyclipArgs(x, p) rmax.Rigid(X, g) rmax.rule(fun, W, lambda) ## S3 method for class 'msr' rotate(X, angle, ..., centre) rotxy(X, angle = pi/2) rotxypolygon(p, angle = pi/2) rmhResolveControl(control, model) rmhResolveExpansion(win, control, imagelist, itype) rmhResolveTypes(model, start, control) rmhSnoopEnv(Xinit, Wclip, R) ## S3 method for class 'rmhcontrol' rmhcontrol(...) ## S3 method for class 'list' rmhcontrol(...) rmhEngine(InfoList, ..., verbose, kitchensink, preponly, snoop, overrideXstart, overrideclip) ## S3 method for class 'rmhmodel' rmhmodel(model, ...) ## S3 method for class 'rmhstart' rmhstart(start, ...) ## S3 method for class 'list' rmhstart(start, ...) rmpoint.I.allim(n, f, types) ## S3 method for class 'hyperframe' row.names(x) ## S3 replacement method for class 'hyperframe' row.names(x) <- value rpoint.multi(n, f, fmax, marks, win, giveup, verbose, warn, nsim, drop) runifpoispp(lambda, win, ..., nsim, drop) runifpoisppOnLines(lambda, L, nsim, drop) runifrect(n, win, nsim, drop) safedeldir(X) safelookup(Z, x, factor, warn) ## S3 method for class 'breakpts' scalardilate(X, f, ...) ## S3 method for class 'diagramobj' scalardilate(X, f, ...) ## S3 method for class 'msr' scalardilate(X, f, ...) scanmeasure(X, ...) ## S3 method for class 'ppp' scanmeasure(X, r, ..., method) ## S3 method for class 'im' scanmeasure(X, r, ...) scanPoisLRTS(nZ, nG, muZ, muG, alternative) scanBinomLRTS(nZ, nG, muZ, muG, alternative) second.moment.calc(x, sigma, edge, what, ..., varcov, expand, obswin, npts, debug) second.moment.engine(x, sigma, edge, what, ..., kernel, scalekernel, obswin, varcov, npts, debug) sewpcf(d, w, denargs, lambda2area, divisor) sewsmod(d, ff, wt, Ef, rvals, method="smrep", ..., nwtsteps=500) ## S3 method for class 'diagramobj' shift(X, ...) ## S3 method for class 'influence.ppm' shift(X, ...) ## S3 method for class 'leverage.ppm' shift(X, ...) ## S3 method for class 'msr' shift(X, ...) ## S3 method for class 'quadratcount' shift(X, ...) ## S3 method for class 'quadrattest' shift(X, ...) shiftxy(X, vec = c(0, 0)) shiftxypolygon(p, vec = c(0, 0)) ## S3 method for class 'profilepl' simulate(object, ...) simulationresult(resultlist, nsim, drop, NameBase) simulrecipe(type, expr, envir, csr, pois, constraints) slr.prepare(CallInfo, envir, data, dataAtPoints, splitby, clip) slrAssemblePixelData(Y, Yname, W, covimages, dataAtPoints, pixelarea) ## S3 method for class 'solist' Smooth(X, ...) ## S3 method for class 'leverage.ppm' Smooth(X, ...) ## S3 method for class 'influence.ppm' Smooth(X, ...) smoothcrossEngine(Xdata, Xquery, values, sigma, ..., weights, varcov, kernel, scalekernel, sorted, cutoff) smoothpointsEngine(x, values, sigma, ..., kernel, scalekernel, weights, varcov, leaveoneout, sorted, cutoff) smudge(X) ## S3 method for class 'im' sort(x, ...) sortalongsegment(df) spatstat.deldir.setopt(use.trigrafS, use.trigraf, debug.delaunay) spatstat.xy.coords(x, y) spatstatClusterModelInfo(name, onlyPCP) spatstatDPPModelInfo(model) spatstatRmhInfo(cifname) spatialCDFframe(model, covariate, ..., jitter) spatialCDFtest(model, covariate, test, ..., dimyx, eps, interpolate, jitter, nsim, verbose, modelname, covname, dataname) spatialCDFtestCalc(fra, test, ..., details) sphere.volume(range, nval = 10) splitHybridInteraction(coeffs, inte) sp.foundclass(cname, inlist, formalname, argsgiven) sp.foundclasses(cnames, inlist, formalname, argsgiven) store.versionstring.spatstat() ## S3 method for class 'hyperframe' str(object, ...) strausscounts(U,X,r,EqualPairs) suffloc(object) suffstat.generic(model, X, callstring) suffstat.poisson(model, X, callstring) summarise.trend(trend, w, a) ## S3 method for class 'envelope' summary(object,...) ## S3 method for class 'hyperframe' summary(object, ..., brief=FALSE) ## S3 method for class 'lintess' summary(object, ...) ## S3 method for class 'logiquad' summary(object, ..., checkdup=FALSE) ## S3 method for class 'lut' summary(object, ...) ## S3 method for class 'mppm' summary(object, ..., brief=FALSE) ## S3 method for class 'msr' summary(object, ...) ## S3 method for class 'profilepl' summary(object, ...) ## S3 method for class 'pppmatching' summary(object, ...) ## S3 method for class 'ppx' summary(object, ...) ## S3 method for class 'rmhexpand' summary(object, ...) ## S3 method for class 'splitppx' summary(object, ...) ## S3 method for class 'vblogit' summary(object, ...) superimposeMarks(arglist, nobj) symbolmapdomain(x) symbolmaptype(x) ## S3 method for class 'hyperframe' tail(x,n,...) thinjump(n, p) tilecentroids(W, nx, ny) trianglediameters(iedge, jedge, edgelength, ..., nvert, dmax, check) trim.mask(M, R, tolerant) tweak.closepairs(cl, rmax, i, deltax, deltay, deltaz) tweak.fv.entry(x, current.tag, new.labl, new.desc, new.tag) tweak.ratfv.entry(x, ...) tweak.coefs(model, new.coef) twostage.test(X, ..., exponent, nsim, nsimsub, alternative, reuse, leaveout, interpolate, savefuns, savepatterns, verbose, badXfatal, testblurb) twostage.envelope(X, ..., nsim, nsimsub, nrank, alternative, reuse, leaveout, interpolate, savefuns, savepatterns, verbose, badXfatal, testlabel) x %unit% u ## Default S3 method: unitname(x) ## Default S3 replacement method: unitname(x) <- value ## S3 method for class 'msr' unitname(x) ## S3 replacement method for class 'msr' unitname(x) <- value unstackFilter(x) ## S3 method for class 'im' update(object, ...) ## S3 method for class 'ippm' update(object, ..., envir) ## S3 method for class 'msr' update(object, ...) ## S3 method for class 'rmhstart' update(object, ...) validradius(r, caller) validate2Dkernel(kernel, fatal) validate.angles(angles, unit, guess) validate.lpp.coords(X, fatal, context) validate.mask(w, fatal=TRUE) validate.quad(Q, fatal, repair, announce) validate.weights(x, recip, how, allowzero, allowinf) vanilla.fv(x) varcountEngine(g, B, lambdaB, f) versioncurrency.spatstat(today, checkR) versionstring.interact(object) versionstring.ppm(object) versionstring.spatstat() veryunique(z) verifyclass(X, C, N = deparse(substitute(X)), fatal = TRUE) vnnFind(seg, tp, ns, nv, from, to, seglen, huge, tol, kmax) ## S3 method for class 'lintess' Window(X, ...) ## S3 replacement method for class 'linnet' Window(X, ..., check=TRUE) <- value ## S3 replacement method for class 'lpp' Window(X, ..., check=TRUE) <- value warn.once(key, ...) waxlyrical(type, terse) weightedclosepairs(X, r, correction, what) windows.mppm(x) w.quad(Q) x.quad(Q) y.quad(Q) xy.grid(xr, yr, nx, ny, dx, dy) X2testEngine(OBS, EXP, ..., method, CR, df, nsim, conditional, alternative, testname, dataname) ## S3 method for class 'im' xtfrm(x) xypolyselfint(p, eps, proper, yesorno, checkinternal) xypolygon2psp(p, w, check) ZeroValue(x) ## S3 method for class 'im' fullIndexSequenceZeroValue(g) grokIndexVector(ind, len, nama) replacementIndex(ii, stuff) representativeRows(x) strictIndexSequence(g) checksolve(M, action, descrip, target) check.mat.mul(A, B, Acols, Brows, fatal) sumsymouter(x, w, distinct) sparse3Darray(i,j,k,x,dims,dimnames,strict,nonzero) as.sparse3Darray(x, ...) ## S3 method for class 'sparse3Darray' dim(x) ## S3 replacement method for class 'sparse3Darray' dim(x) <- value ## S3 method for class 'sparse3Darray' dimnames(x) ## S3 replacement method for class 'sparse3Darray' dimnames(x) <- value ## S3 method for class 'sparse3Darray' print(x, ...) ## S3 method for class 'sparse3Darray' aperm(a, perm, resize, ...) ## S3 method for class 'sparse3Darray' as.array(x, ...) ## S3 method for class 'sparse3Darray' x[i, j, k, drop, ...] ## S3 replacement method for class 'sparse3Darray' x[i, j, k, ...] <- value ## S3 method for class 'sparse3Darray' anyNA(x, recursive) RelevantZero(x) RelevantNA(x) RelevantEmpty(x) isRelevantZero(x) unionOfSparseIndices(A,B) Complex(z) Math(x, ...) Ops(e1, e2) Summary(..., na.rm = FALSE) inside3Darray(d, i, j, k) SparseEntries(x) SparseIndices(x) EntriesToSparse(df, dims) mapSparseEntries(x, margin, values, conform, across) applySparseEntries(x, f, ...) sumsymouterSparse(x, w, distinct, dbg) tensorSparse(A, B, alongA, alongB) marginSumsSparse(X, MARGIN) rbindCompatibleDataFrames(x) bind.sparse3Darray(A, B, along) check.anySparseVector(v, npoints, fatal, things, naok, warn, vname, oneok) evalSparse3Dentrywise(expr, envir) expandSparse(x, n, across) sparseVectorCumul(x, i, length) tensor1x1(A,B) spatstatDiagnostic(msg) as.ppplist(x, check) as.imlist(x, check) pointsAlongNetwork(L, delta) allElementsIdentical(x, entry) resampleNetworkDataFrame(df, template) ## S3 method for class 'lppm' as.ppm(object) ## S3 method for class 'rppm' as.ppm(object) ## S3 method for class 'profilepl' predict(object, ...)
These internal spatstat functions are not usually called directly by the user. Their names and capabilities may change without warning from one version of spatstat to the next.