spatstat-internal {spatstat} | R Documentation |
Internal spatstat functions.
## S3 method for class 'hyperframe' x[i, j, drop=FALSE, ...] ## S3 replacement method for class 'hyperframe' x[i, j] <- value ## S3 method for class 'hyperframe' x$name ## S3 replacement method for class 'hyperframe' x$i <- value acedist.show(X, Y, n, d, timelag = 0) acedist.noshow(X, Y, n, d) adjustthinrange(ur,vstep,vr) affinexy(X, mat = diag(c(1, 1)), vec = c(0, 0), invert=FALSE) affinexypolygon(p, mat, vec, detmat) anycrossing.psp(A,B) apply23sum(x) area.xypolygon(polly) areaGain.diri(u, X, r, ..., W=as.owin(X)) areaGain.grid(u, X, r, ..., W=NULL, ngrid=spatstat.options("ngrid.disc")) areaLoss.diri(X, r, ..., W=as.owin(X), subset=NULL) areaLoss.grid(X, r, ..., W=as.owin(X), subset=NULL, ngrid=spatstat.options("ngrid.disc")) AsymmDistance.psp(X, Y, metric="Hausdorff", method="Fortran") as.breakpts(...) ## S3 method for class 'fv' as.data.frame(x, ...) as.fv(x) ## S3 method for class 'hyperframe' as.list(x, ...) ## S3 method for class 'scan.test' as.im(X, ...) ## S3 method for class 'linim' as.im(X, ...) as.listof(x) as.units(s) badprobability(x, NAvalue) beachcolours(heightrange, sealevel, monochrome, ncolours) bermantestEngine(model, covariate, which, alternative, ..., modelname, covname, dataname) bdrylength.xypolygon(polly) bdry.mask(W) blankcoefnames(x) breakpts(val, maxi, even = FALSE, npos = NULL, step = NULL) breakpts.from.r(r) bt.frame(Q, trend=~1, interaction=NULL, ..., covariates=NULL, correction="border", rbord=0, use.gam=FALSE, allcovar=FALSE) bw.optim(cv, h, iopt, ..., xlab, ylab) cartesian(pp, markset, fac = TRUE) cat.factor(..., recursive=FALSE) cellmiddles(W, nx, ny, npix, gi) censtimeCDFest(o, cc, d, breaks, ..., KM, RS, HAN, RAW, han.denom, pmax) checkfields(X,L) check.finite(x, context, xname) check.hist.lengths(hist,breaks) check.named.list(x, nam, context, namopt) check.named.vector(x, nam, context, namopt) check.named.thing(x, nam, namopt, xtitle, valid, type, context, fatal) check.nvector(v, npoints, fatal=TRUE, things="data points", naok=FALSE) check.nmatrix(m, npoints, fatal=TRUE, things="data points", naok=FALSE, squarematrix=TRUE) check.1.real(x, context, fatal) check.testfun(f, f1, X) clarkevansCalc(X, correction, clipregion, working) clip.psp(x, window, check=TRUE) cliprect.psp(x, window) clippoly.psp(s, window) closepairs(X,rmax,ordered) ## S3 method for class 'summary.ppm' coef(object, ...) ## S3 method for class 'rat' compatible(A, B, ...) complaining(whinge, fatal, value) compileK(D, r, weights, denom, check) compilepcf(D, r, weights, denom, check, endcorrect, ...) crosspairs(X,Y,rmax) crosspaircounts(X,Y,r) cobble.xy(x, y, f, fatal) codetime(x) commasep(x) conform.imagelist(X, Zlist) countingweights(id, areas, check = TRUE) damaged.ppm(object) default.clipwindow(object, epsilon) default.n.tiling(X, nd, ntile, npix, verbose) default.ntile(X) densitypointsEngine(x, sigma, ..., weights, edge, varcov, leaveoneout, diggle, sorted) diagnose.ppm.engine(object, ..., type="eem", typename, opt, sigma=NULL, rbord = reach(object), compute.sd=TRUE, compute.cts=TRUE, rv=NULL, oldstyle=FALSE) digital.volume(range, nval, vside) dilate.owin(...) ## 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 'fasp' dimnames(x) ## S3 replacement method for class 'fasp' dimnames(x) <- value ## S3 method for class 'msr' dimnames(x) distpl(p, l) distppl(p, l) distppll(p, l, mintype, method, listit) distppllmin(p, l, big) distributecbind(x) dist2dpath(dist, method="C") divisors(n) do.as.im(x, action, ..., W, eps, dimyx, xy, na.replace) do.call.matched(fun, arglist, funargs, extrargs) do.iplot(panel) do.istat(panel) edge.Ripley(X, r, W, method) edge.Trans(X, Y, W, exact, paired, trim) edge.Trans.modif(X, Y, WX, WY, exact, paired, trim) emptywindow(w) ensure2vector(x) envelopeEngine(X, fun, simul, nsim=99, nrank=1, ..., verbose=TRUE, clipdata=TRUE, transform=NULL, global=FALSE, ginterval=NULL, savefuns=FALSE, savepatterns=FALSE, nsim2=nsim, VARIANCE=FALSE, nSD=2, Yname=NULL, maxnerr=nsim, internal=NULL, cl=NULL, envir.user=envir.user) ## S3 method for class 'matrix' envelope(Y, ..., rvals, observed, theory, funX, nsim, nsim2, jsim, jsim.mean, type, csr, use.theory, nrank, ginterval, nSD, check, Yname) equalpairs(U, X, marked=FALSE) equalpairs.quad(Q) equals.quad(Q) equalsfun.quad(Q) eratosthenes(nmax) erodemask(w,r,strict) erode.owin(...) evalCovar(model, covariate, ..., dimyx, eps, jitter, modelname, covname, dataname) evalCovariate(covariate, locations) evalInteraction(X,P,E,interaction,correction,...,precomputed,savecomputed) evalInterEngine(X,P,E,interaction,correction,...,precomputed,savecomputed) even.breaks.owin(w) evenly.spaced(x, tol) exactdt(X, ...) exactPdt(w) explain.ifnot(expr, context) ## S3 method for class 'slrm' extractAIC(fit, scale = 0, k = 2, ...) 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) findCovariate(covname, scope, scopename=NULL) findcbind(root, depth, maxdepth) findmarktype(x) firstfactor(x) fii(interaction, coefs, Vnames, IsOffset) fillNA(x, value) flipxypolygon(p) forbidNA(x, context, xname) FormatFaspFormulae(f, argname) fvlabels(x, expand=FALSE) fvlabels(x) <- value fvlabelmap(x, dot=TRUE) fvlegend(object, elang) fvnames(X, a) fvnames(X, a) <- value g3engine(x, y, z, box, rmax, nrval, correction) g3Cengine(x, y, z, box, rmax, nrval) gpcmethod(fname, signature) greatest.common.divisor(n,m) getdataname(defaultvalue, ..., dataname) getfields(X, L, fatal = TRUE) getglmdata(object, drop=FALSE) getglmfit(object) getglmsubset(object) geyercounts(U,X,r,sat,Xcounts,EqualPairs) GLMpredict(fit, data, coefs, changecoef) good.names(nama, defaults, suffices) gridindex(x, y, xrange, yrange, nx, ny) grid1index(x, xrange, nx) grow.rectangle(W, xmargin=0, ymargin=xmargin) handle.r.b.args(r = NULL, breaks = NULL, window, eps = NULL, rmaxdefault) handle.rshift.args(W, ..., radius, width, height, edge, clip, edgedefault) ho.engine(model, ..., nsim, nrmh, start, control, verb) hsvNA(h, s, v, ...) identical.formulae(x,y) idorempty(w, r, caller) implemented.for.K(correction, windowtype, explicit) inpoint(W) inside.triangle(x, y, xx, yy) inside.xypolygon(pts, polly, test01, method) instantiate.interact(x, par) intersect.ranges(a,b,fatal) intX.owin(w) intX.xypolygon(polly) intY.owin(w) intY.xypolygon(polly) is.cadlag(s) is.data(Q) is.fv(x) is.hole.xypolygon(polly) is.hyperframe(x) is.infline(x) is.interact(x) ## Default S3 method: is.marked(...) ## S3 method for class 'psp' is.marked(X, ...) ## S3 method for class 'quad' is.marked(X, na.action="warn", ...) is.mask(w) ## Default S3 method: is.multitype(...) ## S3 method for class 'quad' is.multitype(X, na.action="warn", ...) is.parseable(x) is.pp3(x) is.ppx(x) is.prime(n) is.psp(x) is.slrm(x) is.tess(x) k3engine(x, y, z, box, rmax, nrval, correction) Kborder.engine(X, rmax, nr, correction, weights, ratio) Kount(dIJ, bI, b, breaks) Kwtsum(dIJ, bI, wIJ, b, w, breaks) Kmulti.inhom(X, I, J, lambdaI=NULL, lambdaJ=NULL, ..., r=NULL, breaks=NULL, correction = c("border", "isotropic", "Ripley", "translate") , lambdaIJ=NULL, sigma=NULL, varcov=NULL, Iname = "points satisfying condition I", Jname = "points satisfying condition J") Kpcf.kppm(model, what) killinteraction(model) km.rs.opt(o, cc, d, breaks, KM, RS) ## S3 method for class 'ppm' labels(object, ...) least.common.multiple(n,m) ## S3 method for class 'im' levels(x) ## S3 replacement method for class 'im' levels(x) <- value lhs.of.formula(x) licence.polygons() license.polygons() linequad(X, Y, ..., eps, nd) linearKengine(X, ..., r, reweight, denom, correction, showworking) linearpcfengine(X, ..., r, reweight, denom, correction) listof(...) localKengine(X, ..., wantL, lambda, correction, verbose, rvalue) localpcfengine(X, ..., delta, rmax, nr, stoyan, lambda) localpcfmatrix(X, i, ..., lambda, delta, rmax, nr, stoyan) paste.expr(x) ## S3 method for class 'localpcfmatrix' print(x, ...) ## S3 method for class 'localpcfmatrix' plot(x, ...) ## S3 method for class 'localpcfmatrix' x[i, ...] lookup.im(Z, x, y, naok, strict) majorminorversion(v) make.even.breaks(bmax, npos, bstep) make.parseable(x) makeunits(sing, plur, mul) markappend(...) markcbind(...) markformat(x) ## S3 method for class 'ppp' markformat(x) ## S3 method for class 'psp' markformat(x) ## Default S3 method: markformat(x) mark.scale.default(marx, w, markscale=NULL, maxsize=NULL) markspace.integral(X) ## Default S3 method: marks(x, ...) ## S3 method for class 'quad' marks(x, dfok=FALSE, ...) markappendop(x, y) marksubset(x, index, format) marksubsetop(x, i) markreplicateop(x, n) mask2df(w) matcolall(x) matcolany(x) matcolsum(x) matrixsample(mat, newdim, phase, scale, na.value) matrowall(x) matrowany(x) matrowsum(x) maxflow(costm) meanlistfv(z) meanX.owin(w) meanY.owin(w) ## S3 method for class 'slrm' model.matrix(object, ..., keepNA = TRUE) model.se.image(fit, W, ..., what) mpl.engine(Q, trend, interaction, ..., covariates, covfunargs, correction, rbord, use.gam, gcontrol, famille, forcefit, nd, allcovar, callstring, precomputed, savecomputed, preponly, rename.intercept) mpl.get.covariates(covariates, locations, type, covfunargs) mpl.prepare(Q, X, P, trend, interaction, covariates, want.trend, want.inter, correction, rbord, Pname, callstring, ..., covfunargs, allcovar, precomputed, savecomputed, vnamebase, vnameprefix) MultiPair.checkmatrix(mat, n, matname, naok, zerook) multiply.only.finite.entries(x, a) na.handle.im(X, na.replace) ## S3 method for class 'hyperframe' names(x) ## S3 replacement method for class 'hyperframe' names(x) <- value nearest.pixel(x, y, im) nearest.valid.pixel(x, y, im) newstyle.coeff.handling(object) nncleanEngine(kthNND, k, d, ..., tol, plothist, verbose, maxit) nndcumfun(X, ..., r) no.trend.ppm(x) nobjects(x) ## S3 method for class 'ppp' nobjects(x) ## S3 method for class 'ppx' nobjects(x) ## S3 method for class 'psp' nobjects(x) n.quad(Q) numalign(i, nmax, zero) numeric.columns(M, logical, others) nzpaste(..., sep, collapse) offsetsinformula(x) onecolumn(m) ordinal(k) outdated.interact(object) overlap.owin(A,B) overlap.trapezium(xa, ya, xb, yb, verb = FALSE) overlap.xypolygon(P, Q) oversize.quad(Q, ..., nU, nX) owinpolycheck(W, verbose=TRUE) owinpoly2mask(w, rasta, check=TRUE) ## S3 method for class 'listof' pairs(..., plot=TRUE) param.quad(Q) paren(x, type) 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) ploterodewin(W1, W2, col.edge, col.inside, ...) ploterodeimage(W, Z, ..., Wcol, rangeZ, colsZ) ## S3 method for class 'barplotdata' plot(x, ...) ## S3 method for class 'bw.optim' plot(x, ..., add) ## S3 method for class 'fii' plot(x, ...) ## S3 method for class 'minconfit' plot(x, ...) ## S3 method for class 'pppmatching' plot(x, addmatch = NULL, main = NULL, ...) ## S3 method for class 'plotpairsim' plot(x, ...) ## S3 method for class 'profilepl' plot(x, ..., add=FALSE, main=NULL, tag=TRUE, coeff=NULL, xvariable=NULL) ## S3 method for class 'qqppm' plot(x, ..., limits=TRUE, monochrome=FALSE, limcol=if(monochrome) "black" else "red") ## S3 method for class 'quadratcount' plot(x, ..., add, entries, dx, dy, show.tiles) ## S3 method for class 'quadrattest' plot(x, ...) ## S3 method for class 'scan.test' plot(x, ..., do.window) polynom(x, ...) ppllengine(X, Y, action="project", check=FALSE) ppmCovariates(model) ppm.influence(fit, what = c("leverage","influence","dfbetas","derivatives"), ..., iScore = NULL, iHessian = NULL, iArgs=list(), drop = FALSE, method=c("C", "interpreted")) pppdist.mat(X, Y, cutoff = 1, q = 1, matching = TRUE, precision = 9, approximation = 10) pppdist.prohorov(X, Y, n, dfix, type, cutoff = 1, matching = TRUE, ccode = TRUE, precision = 9, approximation = 10) prange(x) prefixfv(x, tagprefix, descprefix, lablprefix, whichtags) primefactors(n, prmax) ## S3 method for class 'bt.frame' print(x, ...) ## S3 method for class 'bw.optim' print(x, ...) ## S3 method for class 'colourmap' print(x, ...) ## S3 method for class 'diagppm' print(x, ...) ## S3 method for class 'envelope' print(x, ...) ## S3 method for class 'fasp' print(x, ...) ## S3 method for class 'fii' print(x, ...) ## S3 method for class 'fv' print(x, ...) ## S3 method for class 'hyperframe' print(x, ...) ## S3 method for class 'interact' print(x, ..., family=TRUE, brief=FALSE) ## S3 method for class 'isf' print(x, ...) ## S3 method for class 'layered' print(x, ...) ## S3 method for class 'linim' print(x, ...) ## S3 method for class 'lut' print(x, ...) ## S3 method for class 'minconfit' print(x, ...) ## S3 method for class 'msr' 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 'rmhmodel' print(x, ...) ## S3 method for class 'rmhstart' print(x, ...) ## S3 method for class 'rmhInfoList' print(x, ...) ## S3 method for class 'splitppp' print(x, ...) ## S3 method for class 'summary.fii' print(x, ...) ## S3 method for class 'summary.hyperframe' print(x, ...) ## S3 method for class 'summary.listof' print(x, ...) ## S3 method for class 'summary.owin' print(x, ...) ## S3 method for class 'summary.ppp' print(x, ..., dp=3) ## S3 method for class 'summary.psp' print(x, ...) ## S3 method for class 'summary.splitppp' print(x, ...) ## S3 method for class 'summary.units' print(x, ...) ## S3 method for class 'tess' print(x, ..., brief=FALSE) prolongseq(x, newrange) quad(data, dummy, w, param) rectquadrat.breaks(xr, yr, nx = 5, ny = nx, xbreaks = NULL, ybreaks = NULL) rectquadrat.countEngine(x, y, xbreaks, ybreaks, weights) rgbNA(red, green, blue, ...) rhs.of.formula(x) quadrat.testEngine(X, nx, ny, ..., Xcount, xbreaks, ybreaks, tess=NULL, fit=NULL, Xname=NULL, fitname=NULL) quadscheme.replicated(data, dummy, method = "grid", ...) quadscheme.spatial(data, dummy, method = "grid", ...) pointgrid(W, ngrid) rastersample(X, Y) rasterx.im(x) rastery.im(x) ## S3 method for class 'fii' reach(x, ..., epsilon) rebadge.fv(x, new.ylab, new.fname, tags, new.desc, new.labl, new.yexp, new.dotnames, new.preferred, new.formula, new.tags) 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(...) repair.old.factor.image(x) reincarnate.interact(object) resid4plot(RES, plot.neg="image", plot.smooth="imagecontour", spacing=0.1, srange=NULL,monochrome=FALSE, main=NULL, ...) resid1plot(RES, opt, plot.neg="image", plot.smooth="imagecontour", srange=NULL, monochrome=FALSE, main=NULL, ...) resid1panel(observedX, observedV, theoreticalX, theoreticalV, theoreticalSD, xlab,ylab, ...) resolve.defaults(..., .StripNull=FALSE) resolve.2D.kernel(..., sigma, varcov, x, mindist, adjust, bwfun) restrict.mask(M, W) reverse.xypolygon(p, adjust=FALSE) revcumsum(x) rmax.rule(fun, W, lambda) rotxy(X, angle = pi/2) rotxypolygon(p, angle = pi/2) rmhResolveControl(control, model) rmhResolveExpansion(win, control, imagelist, itype) rmhResolveTypes(model, start, control) ## S3 method for class 'rmhcontrol' rmhcontrol(...) ## S3 method for class 'list' rmhcontrol(...) rmhEngine(InfoList, ..., verbose, track, kitchensink, preponly) ## 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=NULL, marks = NULL, win = unit.square(), giveup = 1000, verbose = FALSE) runifpoispp(lambda, win = owin(c(0, 1), c(0, 1))) runifpoisppOnLines(lambda, L) runifrect(n, win = owin(c(0, 1), c(0, 1))) safelookup(Z, X, factor, warn) samefunction(f, g) scanmeasure(X, ...) ## S3 method for class 'ppp' scanmeasure(X, r, ...) ## S3 method for class 'im' scanmeasure(X, r, ...) scanPoisLRTS(nZ, nG, muZ, muG, alternative) scanBinomLRTS(nZ, nG, muZ, muG, alternative) scanLRTS(X, r, ..., method, baseline, case, alternative) second.moment.calc(x, sigma=NULL, edge=TRUE, what="Kmeasure", debug=FALSE, ..., varcov=NULL, expand=FALSE) second.moment.engine(x, sigma=NULL, edge=TRUE, what="Kmeasure", debug=FALSE, ..., obswin=as.owin(x), varcov=NULL, npts=NULL) sensiblevarname(guess, fallback, maxlen) sewpcf(d, w, denargs, lambda2area) sewsmod(d, ff, wt, Ef, rvals, method="smrep", ..., nwtsteps=500) shiftxy(X, vec = c(0, 0)) shiftxypolygon(p, vec = c(0, 0)) simplify.xypolygon(p, dmin) simulrecipe(type, expr, envir, csr, pois) singlestring(s, coll) slr.prepare(CallInfo, envir, data, dataAtPoints, splitby, clip) slrAssemblePixelData(Y, Yname, W, covimages, dataAtPoints, pixelarea) smoothpointsEngine(x, values, sigma, ..., weights, varcov, leaveoneout, sorted) ## S3 method for class 'im' sort(x, ...) spatstat.rawdata.location(...) spatialCDFframe(model, covariate, ...) spatialCDFtest(model, covariate, test, ..., dimyx, eps, jitter, modelname, covname, dataname) sphere.volume(range, nval = 10) sp.foundclass(cname, inlist, formalname, argsgiven) sp.foundclasses(cnames, inlist, formalname, argsgiven) stratrand(window, nx, ny, k = 1) strausscounts(U,X,r,EqualPairs) suffloc(object) suffstat.generic(model, X, callstring) suffstat.poisson(model, X, callstring) ## S3 method for class 'envelope' summary(object,...) ## S3 method for class 'fii' summary(object,...) ## S3 method for class 'hyperframe' summary(object, ..., brief=FALSE) ## S3 method for class 'profilepl' summary(object, ...) ## S3 method for class 'pppmatching' summary(object, ...) ## S3 method for class 'ppx' summary(object, ...) superimposeMarks(arglist, nobj) sympoly(x, y, n) termsinformula(x) test.crossing.psp(A,B) test.selfcrossing.psp(A) tilecentroids(W, nx, ny) tilenames(x) trianglediameters(iedge, jedge, edgelength, ..., nvert, check) trim.mask(M, R, tolerant) tweak.fv.entry(x, current.tag, new.labl=NULL, new.desc=NULL, new.tag=NULL) ## Default S3 method: unitname(x) ## Default S3 replacement method: unitname(x) <- value ## S3 method for class 'interact' update(object, ...) ## S3 method for class 'slrm' update(object, ..., evaluate = TRUE, env = parent.frame()) validradius(r, caller) validate.mask(w, fatal=TRUE) validate.quad(Q, fatal, repair, announce) validposint(n, caller, fatal) vanilla.fv(x) variablesinformula(x) ## S3 method for class 'slrm' vcov(object, ...) verbalogic(x, op) versionstring.interact(object) versionstring.ppm(object) versionstring.spatstat() verifyclass(X, C, N = deparse(substitute(X)), fatal = TRUE) verify.xypolygon(p, fatal=TRUE) warn.ignored.args(..., context) ## S3 method for class 'msr' with(data, expr, ...) w.quad(Q) x.quad(Q) y.quad(Q) ## S3 method for class 'im' xtfrm(x) xypolyselfint(p, eps, proper, yesorno, checkinternal) xypolygon2psp(p, w, check)
These are usually not to be called by the user.