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#'
#' Header for all (concatenated) test files
#'
#' Require spatstat.core
#' Obtain environment variable controlling tests.
#'
#' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $
require(spatstat.core)
FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0)
ALWAYS <- TRUE
cat(paste("--------- Executing",
if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of",
"test code -----------\n"))
#
# tests/testaddvar.R
#
# test addvar options
#
# $Revision: 1.3 $ $Date: 2020/05/02 01:32:58 $
if(FULLTEST) {
local({
X <- rpoispp(function(x,y){exp(3+3*x)})
model <- ppm(X ~y)
addvar(model, "x", crosscheck=TRUE)
addvar(model, "x", bw.input="quad")
w <- square(0.5)
addvar(model, "x", subregion=w)
addvar(model, "x", subregion=w, bw.input="points")
Z <- as.im(function(x,y) { x }, Window(X))
addvar(model, Z)
})
}
#
# tests/testparres.R
#
# additional test of parres
#
# $Revision: 1.7 $ $Date: 2020/05/02 01:32:58 $
#
if(FULLTEST) {
local({
X <- rpoispp(function(x,y){exp(3+x+2*x^2)})
model <- ppm(X ~x+y)
# options in parres (and code blocks in print.parres)
parres(model, "x")
parres(model, "x", smooth.effect=TRUE)
parres(model, "x", bw.input="quad")
w <- square(0.5)
parres(model, "x", subregion=w)
parres(model, "x", subregion=w, bw.input="quad")
f <- function(x,y) { x + y }
parres(model, f)
# check whether 'update.ppm' has messed up internals
mod2 <- update(model, ~x)
parres(mod2, "x")
#' other kinds of covariates
mod3 <- ppm(X ~ x + offset(y))
parres(mod3, "offset(y)")
Z <- distmap(runifpoint(3))
parres(mod3, Z)
mod4 <- ppm(X ~ sin(x), data=solist(B=Z))
parres(mod4, "sin(x)")
parres(mod4, "B")
#' models with interaction
mod5 <- ppm(cells ~ x, AreaInter(0.06))
parres(mod5, "x")
dlin <- distfun(copper$SouthLines)
copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1))
parres(copfit, "dlin")
#' covariate need not be specified if there is only one.
parres(mod5)
parres(copfit)
#' infrastructure
ltuae <- evalCovariate(42, cells)
LTUAE <- evalCovariate(ltuae, cells)
fit <- ppm(amacrine ~ x * marks, nd=16)
dmat <- model.depends(fit)
check.separable(dmat, "x", c(x=FALSE, marks=FALSE), FALSE)
check.separable(dmat, "x", c(FALSE, FALSE), FALSE)
check.separable(dmat, "x", c(x=FALSE, marks=TRUE), FALSE)
})
}
#'
#' tests/threedee.R
#'
#' Tests of 3D code
#'
#' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $
#'
local({
X <- runifpoint3(30)
Y <- runifpoint3(20)
if(FULLTEST) {
A <- runifpoint3(10, nsim=2)
Z <- ppsubset(X, 2:4)
}
##
if(ALWAYS) { # includes C code
d <- pairdist(X, periodic=TRUE, squared=TRUE)
d <- crossdist(X, Y, squared=TRUE)
d <- crossdist(X, Y, squared=TRUE, periodic=TRUE)
#'
h <- has.close(X, 0.2)
h <- has.close(X, 0.2, periodic=TRUE)
h <- has.close(X, 0.2, Y=Y)
h <- has.close(X, 0.2, Y=Y, periodic=TRUE)
#' code blocks not otherwise reached
rmax <- 0.6 * max(nndist(X))
g <- G3est(X, rmax=rmax, correction="rs")
g <- G3est(X, rmax=rmax, correction="km")
g <- G3est(X, rmax=rmax, correction="Hanisch")
g <- G3est(X, rmax=rmax, sphere="ideal")
g <- G3est(X, rmax=rmax, sphere="digital")
v <- sphere.volume()
v <- digital.volume()
#' older code
co <- coords(X)
xx <- co$x
yy <- co$y
zz <- co$z
gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3")
gg2 <- g3engine(xx, yy, zz, correction="minus sampling")
ff1 <- f3engine(xx, yy, zz, correction="no")
ff2 <- f3engine(xx, yy, zz, correction="minus sampling")
}
##
if(ALWAYS) {
#'class support
X <- runifpoint3(10)
print(X)
print(X %mark% runif(10))
print(X %mark% factor(letters[c(1:5,5:1)]))
print(X %mark% data.frame(a=1:10, b=runif(10)))
da <- as.Date(paste0("2020-01-0", c(1:5,5:1)))
print(X %mark% da)
print(X %mark% data.frame(a=1:10, b=da))
}
})
#
# tests/triplets.R
#
# test code for triplet interaction and associated summary function Tstat
#
# $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $
#
if(ALWAYS) { # C code, platform dependence
local({
#' valid model
fit <- ppm(cells ~1, Triplets(0.1))
fit
suffstat(fit)
#' invalid model
fitR <- ppm(redwood ~1, Triplets(0.1))
fitR
suffstat(fitR)
#' hard core (zero triangles, coefficient is NA)
fit0 <- ppm(cells ~1, Triplets(0.05))
fit0
suffstat(fit0)
#' bug case (1 triangle in data)
fit1 <- ppm(cells ~1, Triplets(0.15))
fit1
suffstat(fit1)
#' Tstat function, all code blocks
a <- Tstat(redwood, ratio=TRUE,
correction=c("none", "border", "bord.modif", "translate"))
#' simulation
X <- simulate(fit)
mod <- list(cif="triplets",par=list(beta=50,gamma=0.2,r=0.07), w=square(1))
Xm <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5))
#' hard core
mod$par$gamma <- 0
XmHard <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5))
})
}
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