R: Internal spatstat functions

spatstat-internal {spatstat} | R Documentation

## Internal spatstat functions

### Description

Internal spatstat functions.

### Usage

    ## 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[...]
    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)
    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)
    BartCalc(fY, fK)
    bbEngine(...)
    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, 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)
    checksolve(M, action, descrip, target)
    check.finespacing(r, eps, win, rmaxdefault, context, action, rname)
    check.hist.lengths(hist,breaks)
    check.mat.mul(A, B, Acols, Brows, fatal)
    check.testfun(f, f1, X)
    circticks(R, at, unit, start, clockwise, labels)
    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)
    CressieReadSymbol(lambda)
    CressieReadName(lambda)
    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, force, quadsub, sparseOK)
    Deviation(x, ref, leaveout, n, xi)
    dflt.redraw(button, name, env)
    densitycrossEngine(Xdata, Xquery, sigma, ...,
                        weights, edge, varcov,
                        diggle, sorted)
    densitypointsEngine(x, sigma, ...,
                        kernel, scalekernel,
                        weights, edge, varcov,
                        leaveoneout, diggle, sorted, spill, cutoff)
    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)
    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 '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, ...)
    do.istat(panel)
    doMultiStraussHard(iradii, hradii, types)
    dppmFixIntensity(DPP, lambda, po)
    dppmFixAlgorithm(algorithm, changealgorithm, clusters, startpar)
    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, 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, 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)
    equalpairs(U, X, marked=FALSE)
    equalpairs.quad(Q)
    equals.quad(Q)
    equalsfun.quad(Q)
    erodemask(w,r,strict)
    erode.owin(...)
    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,...,precomputed,savecomputed)
    evalInterEngine(X,P,E,interaction,correction,...,
                    Reach,precomputed,savecomputed)
    evalPairPotential(X,P,E,pairpot,potpars,R,finite)
    evalSparse3Dentrywise(expr, envir)
    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, sigma, dtt, weights, iterMax, sparse, dtx)
    fft2D(z, inverse, west)
    fftwAvailable()
    fill.coefs(coefs, required)
    findbestlegendpos(...)
    findCovariate(covname, scope, scopename=NULL)
    findcbind(root, depth, maxdepth)
    fii(interaction, coefs, Vnames, IsOffset)
    fillNA(x, value)
    flatfname(x)
    flipxypolygon(p)
    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)
    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)
    GLMpredict(fit, data, coefs, changecoef, type)
    good.correction.K(X)

    gridindex(x, y, xrange, yrange, nx, ny)
    grid1index(x, xrange, nx)
    grokIndexVector(ind, len, nama)
    grow.mask(M, xmargin=0, ymargin=xmargin)
    hackglmmPQL(fixed, random, family, data, correlation, weights,
                control, niter, verbose, subset, ..., reltol)
    hasenvelope(X, E)
    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)
    IdenticalRows(i,j,a,b)
    idorempty(w, r, caller)
    illegal.iformula(ifmla, itags, dfvarnames)
    implemented.for.K(correction, windowtype, explicit)
    impliedpresence(tags, formula, df, extranames=character(0))
    impliedcoefficients(object, tag)
    inpoint(W)
    instantiate.interact(x, par)
    interactionfamilyname(x)
    intermaker(f, blank)
    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.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.pp3(x)
    is.ppx(x)
    is.psp(x)
    is.scov(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)
    Kount(dIJ, bI, b, breaks)
    Kwtsum(dIJ, bI, wIJ, b, w, breaks)
    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)
    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, correction, verbose, rvalue)
    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, ...)
    makeLinnetTolerance
    maskLaslett(X, ..., eps, dimyx, xy, oldX, verbose, plotit)
    match2DkernelName(kernel)
    parbreak(terse)
    plan.legend.layout(B, ..., side, sep, size, sep.frac, size.frac,
                       started, map)
    PairPotentialType(pairpot)
    PDEdensityLPP(x, sigma, ..., weights, dx, dt,
                  fun, finespacing, finedata)
    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, ..., Q, keepNA, irregular)
    ## 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)
    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)
    mpl.usable(x)
    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)
    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)
    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 'lurk'
    plot(x, ..., shade)
    ## S3 method for class 'minconfit'
    plot(x, ...)
    ## S3 method for class 'parres'
    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, main, tag, coeff, xvariable,
                             col, lty, lwd, col.opt, lty.opt, lwd.opt)
    ## 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)
    ## S3 method for class 'studpermutest'
    plot(x, fmla, ...,
            lty = NULL, col = NULL, lwd = NULL,
            lty.theo = NULL, col.theo = NULL, lwd.theo = NULL,
            lwd.mean = if (meanonly) 1 else NULL, lty.mean = lty, col.mean = col,
            separately = FALSE, meanonly = FALSE,
            main = if (meanonly) "group means" else NULL,
            xlim = NULL, ylim = NULL, ylab = NULL, legend = !add,
            legendpos = "topleft", lbox = FALSE, add = FALSE)
    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,
                  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 '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 '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.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.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)
    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)
    replacementIndex(ii, stuff)
    representativeRows(x)
    resolveEinfo(x, what, fallback, warn, atomic)
    resolve.vargamma.shape(..., nu.ker, nu.pcf, default = FALSE)
    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,
               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)
    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, 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)
    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)
    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=NULL, expand=FALSE, debug=FALSE)
    second.moment.engine(x, sigma, edge, what, ...,
          kernel, 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, ...)
    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, ...)
    smoothcrossEngine(Xdata, Xquery, values, sigma, ...,
                        weights, varcov, sorted)
    smoothpointsEngine(x, values, sigma, ...,
                        weights, varcov, leaveoneout, sorted, cutoff)
    smudge(X)
    ## S3 method for class 'im'
    sort(x, ...)
    sortalongsegment(df)
    spatstat.xy.coords(x, y)
    spatstatClusterModelInfo(name, onlyPCP)
    spatstatDPPModelInfo(model)
    spatstatRmhInfo(cifname)
    spatialCDFframe(model, covariate, ...)
    spatialCDFtest(model, covariate, test, ...,
             dimyx, eps, interpolate, jitter,
             nsim, verbose, modelname, covname, dataname)
    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 'funxy'
    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 '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, ...)
    sumsymouter(x, w)
    superimposeMarks(arglist, nobj)
    symbolmaptype(x)
    ## S3 method for class 'hyperframe'
    tail(x,n,...)
    tensor1x1(A,B)
    test.crossing.psp(A,B)
    test.selfcrossing.psp(A)
    thinjump(n, p)
    tilecentroids(W, nx, ny)
    trianglediameters(iedge, jedge, edgelength, ...,
                      nvert, dmax, check)
    trim.mask(M, R, tolerant)
    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, testblurb)
    x %unit% u
    ## Default S3 method:
    unitname(x)
    ## Default S3 replacement method:
    unitname(x) <- value
    ## S3 method for class 'solist'
    unstack(x, ...)
    ## S3 method for class 'layered'
    unstack(x, ...)
    unstackFilter(x)
    ## S3 method for class 'im'
    update(object, ...)
    ## S3 method for class 'ippm'
    update(object, ..., envir)
    ## 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)

    versionstring.interact(object)
    versionstring.ppm(object)
    versionstring.spatstat()
    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)
    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)

    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)
    RelevantEmpty(x)
    isRelevantZero(x)
    unionOfSparseIndices(A,B)
    Math(x, \dots)
    Ops(e1, e2)
    Summary(\dots, 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, dbg)
    tenseur(A, B, alongA, alongB)
    marginSums(X, MARGIN)
    rbindCompatibleDataFrames(x)
    bind.sparse3Darray(A, B, along)

    spatstatDiagnostic(msg)

    as.ppplist(x, check)
    as.imlist(x, check)
    pointsAlongNetwork(L, delta)
    expandSparse(x, n, across)
    allElementsIdentical(x, entry)
    resampleNetworkDataFrame(df, template)
    sparseVectorCumul(x, i, length)

    ## S3 method for class 'lppm'
    as.ppm(object)
    ## S3 method for class 'rppm'
    as.ppm(object)
    ## S3 method for class 'profilepl'
    predict(object, ...)

### Details

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.

[Package spatstat version 1.54-0 Index]