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# test.fac.R: test factor plotting in plotmo. This also tests swapxy, xflip, and yflip
# Stephen Milborrow, Berea Mar 2011
source("test.prolog.R")
library(plotmo)
library(earth)
library(rpart)
data(ozone1)
data(etitanic)
cat("==test plotmo with factors==\n")
test.fac.with.rpart <- function(ngrid2=20)
{
et <- etitanic
col.response <- as.numeric(et$sex)+2
et$pclass.fac <- et$pclass
et$parch.int <- et$parch
parch.fac <- et$parch
parch.fac[parch.fac >= 3] <- 3
# use non alphabetically sorted factor levels
et$parch.fac <- factor(parch.fac, labels=c( "levz", "lev1", "lev2", "levf"))
et$pclass.num <- as.numeric(et$pclass)
et$pclass <- et$sex <- et$age <- et$sibsp <- et$parch <- NULL
cat("names(et):", names(et), "\n") # survived pclass.fac parch.int parch.fac pclass.num
old.par <- par(no.readonly=TRUE)
on.exit(par(old.par))
par(mfrow=c(4,5))
par(mar = c(2, 2, 3, 0.5), cex=.6)
# numeric x numeric
a2 <- rpart(survived ~ pclass.num+parch.int, data=et)
set.seed(145)
plotmo(a2, do.par=F, type2="im", degree1=2,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a2, do.par=F, type2="con", degree1=NA,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a2, do.par=F, type2="persp", degree1=NA,
ngrid2=40, persp.theta=NA, persp.ticktype="d", cex.lab=.8, persp.ntick=2)
# factor x numeric
a3 <- rpart(survived ~ pclass.fac+parch.int, data=et)
set.seed(145)
plotmo(a3, do.par=F, type2="im",
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a3, do.par=F, type2="con", degree1=NA,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a3, do.par=F, type2="persp", degree1=NA,
ngrid2=40, persp.theta=NA, persp.ticktype="d", persp.border=NA, cex.lab=.8, persp.ntick=2)
# numeric x factor
a4 <- rpart(survived ~ pclass.num+parch.fac, data=et)
set.seed(145)
plotmo(a4, do.par=F, type2="im", tra=1,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a4, do.par=F, type2="con", degree1=NA,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a4, do.par=F, type2="persp", degree1=NA,
ngrid2=40, persp.theta=NA, persp.ticktype="d", persp.border=NA, cex.lab=.8, persp.ntick=2)
# factor x factor
a5 <- rpart(survived ~ pclass.fac+parch.fac, data=et)
set.seed(145)
plotmo(a5, do.par=F, type2="im", nrug=TRUE,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a5, do.par=F, type2="con", degree1=NA,
col.response=col.response, pt.cex=.3)
set.seed(145)
plotmo(a5, do.par=F, type2="persp", degree1=NA,
ngrid2=40, persp.theta=NA, persp.ticktype="d", persp.border=NA, cex.lab=.8, persp.ntick=2)
# test ndiscrete
par(mfrow=c(3,5))
par(mar = c(2, 2, 3, 0.5), cex=.6)
plotmo(a2, do.par=F, type2="persp", degree1=2, ndiscrete=0, main="ndiscrete=0",
persp.theta=NA, persp.ticktype="d", persp.ntick=2,
col.response=col.response, pt.cex=.3)
plotmo(a2, do.par=F, type2="im", degree1=NA, ndiscrete=0)
plotmo(a2, do.par=F, type2="con", degree1=NA, ndiscrete=0)
plotmo(a2, do.par=F, type2="persp", degree1=2, degree2=NA, ndiscrete=0, main="center", center=TRUE,
col.response=col.response, pt.cex=.3)
plotmo(a2, do.par=F, type2="persp", degree1=2, ndiscrete=3, main="ndiscrete=3",
persp.theta=NA, persp.ticktype="d", persp.ntick=2,
col.response=col.response, pt.cex=.3)
plotmo(a2, do.par=F, type2="im", degree1=NA, ndiscrete=3)
plotmo(a2, do.par=F, type2="con", degree1=NA, ndiscrete=3)
plotmo(a2, do.par=F, type2="persp", degree1=2, degree2=NA, ndiscrete=3, main="center", center=TRUE,
col.response=col.response, pt.cex=.3)
plotmo(a2, do.par=F, type2="persp", degree1=2, ndiscrete=10, main="ndiscrete=10",
persp.theta=NA, persp.ticktype="d", persp.ntick=2,
col.response=col.response, pt.cex=.3)
plotmo(a2, do.par=F, type2="im", degree1=NA, ndiscrete=10)
plotmo(a2, do.par=F, type2="con", degree1=NA, ndiscrete=10)
plotmo(a2, do.par=F, type2="persp", degree1=2, degree2=NA, ndiscrete=10, main="center", center=TRUE,
col.response=col.response, pt.cex=.3)
}
test.fac.with.rpart()
cat("==test plotmo swapxy with factors==\n")
test.swapxy.with.rpart <- function(ngrid2=20)
{
et <- etitanic[c(1:50,300:350,600:650),]
col.response <- as.numeric(et$sex)+2
et$pclass.fac <- et$pclass
et$parch.int <- et$parch
parch.fac <- et$parch
parch.fac[parch.fac > 2] <- 2
# use non alphabetically sorted factor levels
et$parch.fac <- factor(parch.fac, labels=c("lev.zero", "lev.one", "lev.two.or.more"))
print(et$parch.fac)
et$pclass.num <- as.numeric(et$pclass)
et$pclass <- et$sex <- et$age <- et$sibsp <- et$parch <- NULL
cat("names(et):", names(et), "\n") # survived pclass.fac parch.int parch.fac pclass.num
old.par <- par(no.readonly=TRUE)
on.exit(par(old.par))
par(mfrow=c(4,4))
par(mar = c(2, 3, 5, 0.5), cex=.6)
# factor x factor
a5 <- rpart(survived ~ pclass.fac+parch.fac, data=et)
for(swapxy in c(F,T)) {
for(xflip in c(F,T))
for(yflip in c(F,T)) {
set.seed(145)
plotmo(a5, do.par=F, type2="im", degree1=NA,
swapxy=swapxy, xflip=xflip, yflip=yflip,
main=paste("swapxy=", swapxy, "\nxflip=", xflip, "\nyflip=", yflip),
col.response=col.response, pt.cex=3,
pt.pch=".")
set.seed(145)
plotmo(a5, do.par=F, type2="con", degree1=NA,
swapxy=swapxy, xflip=xflip, yflip=yflip,
main=paste("swapxy=", swapxy, "\nxflip=", xflip, "\nyflip=", yflip),
col.response=col.response, pt.cex=.3)
}
}
par(mfrow=c(2,2))
set.seed(146)
plotmo(a5, do.par=F, type2="persp", degree1=NA,
swapxy=FALSE, main=paste("swapxy=", FALSE),
ngrid2=40, persp.theta=145, persp.ticktype="d", cex.lab=.8, persp.ntick=5)
set.seed(146)
plotmo(a5, do.par=F, type2="persp", degree1=NA,
swapxy=TRUE, main=paste("swapxy=", TRUE),
ngrid2=40, persp.theta=145, persp.ticktype="d", cex.lab=.8, persp.ntick=5)
set.seed(146)
plotmo(a5, do.par=F, type2="im", degree1=2,
swapxy=FALSE, main=paste("swapxy=", FALSE))
}
test.swapxy.with.rpart()
aflip <- earth(O3~vh + wind + humidity + temp, data=ozone1, degree=2)
col.response<- ifelse(ozone1$O3 == 38, "red", "pink")
# test xflip arg, degree1 plots
par(mfrow=c(2,2))
set.seed(102)
plotmo(aflip, degree1=1:2, degree2=0, do.par=F, col.response=col.response, nrug=-1, ylab="O3", smooth.col="gray")
plotmo(aflip, degree1=1:2, degree2=F, do.par=F, col.response=col.response, nrug=-1, ylab="O3", xflip=T, main="xflip=TRUE, degree1 plots", , smooth.col="gray")
col.response<- ifelse(ozone1$O3 == 1, "green", "pink")
# test flip args, type2=persp
par(mfrow=c(2,2))
plotmo(aflip, degree1=0, degree2=2, do.par=F, persp.ticktype="d")
plotmo(aflip, degree1=0, degree2=2, do.par=F, persp.tickt="d", swapxy=T, main="swapxy=TRUE")
plot(0, 0, type="n", axes=FALSE, xlab="", ylab="")
plot(0, 0, type="n", axes=FALSE, xlab="", ylab="")
# test swapxy args, type2=image
par(mfrow=c(3,3))
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, main="test swapxy on image plots\nreference plot")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, swapxy=T, main="swapxy=T")
plot(0, 0, type="n", axes=FALSE, xlab="", ylab="")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, xflip=T, main="xflip=T")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, yflip=T, main="yflip=T")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, xflip=T, yflip=T, main="xflip=T, yflip=T")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, swapxy=T, xflip=T, main="swapxy=T, xflip=T")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, swapxy=T, yflip=T, main="swapxy=T, yflip=T")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="im", col.response=col.response, swapxy=T, xflip=T, yflip=T, main="swapxy=T, xflip=T, yflip=T")
# test flip args, type2=contour
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, main="test flip on contour plots\nreference plot")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, swapxy=T)
plot(0, 0, type="n", axes=FALSE, xlab="", ylab="")
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, xflip=T)
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, yflip=T)
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, xflip=T, yflip=T)
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, swapxy=T, xflip=T)
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, swapxy=T, yflip=T)
plotmo(aflip, degree1=0, degree2=2, do.par=F, type2="con", col.response=col.response, swapxy=T, xflip=T, yflip=T)
# ordered factor
cat("==test plotmo with ordered factor==\n")
par(mfcol=c(2,2))
par(mar=c(3, 3, 3, 1))
par(mgp=c(1.5, .5, 0))
a <- lm(height~., data=Loblolly)
termplot(a, partial.resid=T, rug=T, terms=2, main="Seed is an ordered factor") # compare to termplot
plotmo(a, do.par=F, col.resp="gray", nrug=T, all2=T)
#---------------------------------------------------------------------------
# test ndiscrete with integer and non integer predictors, with missing values
par(mfcol=c(2,4))
par(mar=c(3, 3, 3, 1))
par(mgp=c(1.5, .5, 0))
et <- etitanic
et$var <- et$parch
et$var[et$var==1] <- 0 # want a "hole" in var's value, for testing
et$var[1:3] <- 6
cat("table(et$var):")
print(table(et$var))
cat("\n")
a <- earth(survived~var+age, data=et, degree=2, pm="none")
plotmo(a, trace=FALSE, ndiscrete=0,
main="integral var\n(var levels are 0 2 3 4 5 6)\nndiscrete=0", cex.lab=.8,
do.par=F, smooth.col="indianred", persp.ticktype="d", clip=F, degree1=0, persp.theta=40)
plotmo(a, ndiscrete=0,
do.par=F, smooth.col="indianred", ylim=c(-.5,1), degree2=0, degree1=1)
#------------
plotmo(a, ndiscrete=10, main="integral var\nndiscrete=10", cex.lab=.8,
do.par=F, smooth.col="indianred", persp.ticktype="d", clip=F, degree1=0, persp.theta=40)
plotmo(a, trace=0, ndiscrete=10,
do.par=F, smooth.col="indianred", ylim=c(-.5,1), degree2=0, degree1=1)
#------------
et$var <- et$var / 2
cat("table(et$var):")
print(table(et$var))
cat("\n")
a <- earth(survived~var+age, data=et, degree=2, pm="none")
plotmo(a, ndiscrete=0,
main="integral var\n(var levels are 0 1 1.5 2 2.5 3)\nndiscrete=0", cex.lab=.8,
do.par=F, smooth.col="indianred", persp.ticktype="d", clip=F, degree1=0, persp.theta=40)
plotmo(a, ndiscrete=0,
do.par=F, smooth.col="indianred", ylim=c(-.5,1), degree2=0, degree1=1)
#------------
plotmo(a, ndiscrete=10, main="non integral var\nndiscrete=10", cex.lab=.8,
do.par=F, smooth.col="indianred", persp.ticktype="d", clip=F, degree1=0, persp.theta=40)
plotmo(a, ndiscrete=10,
do.par=F, smooth.col="indianred", ylim=c(-.5,1), degree2=0, degree1=1)
source("test.epilog.R")
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