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[...]
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, ...)

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 1.64-1 Index]