関数plot.CAvariantには、knitrがうまく処理できないdev.new（）への呼び出しがいくつかあります。できることは、次のように手動で機能を編集してこれらの通話を削除することです：
---
title: "Test"
ouptut: html_document
---
```{r fig.keep='all'}
library(CAvariants)
data(asbestos)
head(asbestos)
str(asbestos)
plot.CAvariants <-
function (x, firstaxis = 1, lastaxis = 2, cex = 0.8, cex.lab = 0.8,
prop = 1, plottype = "biplot", biptype = "row", scaleplot = 1,
posleg = "topleft", pos = 2, ell = FALSE, Mell = x$Mell,
alpha = 0.05, ...)
{
if ((firstaxis < 1) | (firstaxis > x$r))
stop(paste("incorrect first axis =", firstaxis, "\n\n"))
if (lastaxis > x$r)
stop(paste("incorrect last axis =", lastaxis, "\n\n"))
if (firstaxis >= lastaxis)
stop(paste("last axis must be greater than first axis\n\n"))
n <- sum(x$Xtable)
I <- nrow(x$Xtable)
rowgroup <- list(1:x$rows, rep(1, x$rows))
rowgrlab <- list(1, "", "*", "red", "T")
colgroup <- list(1:x$cols, rep(1, x$cols))
colgrlab <- list(1, "", "+", "blue", "T")
if ((plottype == "Classical") | (plottype == "classical") |
(plottype == "classic") | (plottype == "c")) {
nthings <- x$cols
nvars <- x$rows
cord1 <- x$Cprinccoord
cord2 <- x$Rprinccoord
dmu = diag(x$inertias[, 1])
inertiapc = x$inertias[, 2]
dimnames(cord1)[1] <- dimnames(x$Xtable)[2]
dimnames(cord2)[1] <- dimnames(x$Xtable)[1]
thinggroup <- colgroup
thinggrlab <- colgrlab
vargroup <- rowgroup
vargrlab <- rowgrlab
thinglabels <- x$collabels
varlabels <- x$rowlabels
main = "Classical plot"
if ((x$catype == "DONSCA") | (x$catype == "DOCA") | (x$catype ==
"SOCA") | (x$catype == "SONSCA")) {
cat("\n ERROR: NO CLASSICAL PLOT for ordered analysis. ONLY A BIPLOT can be constructed (Please change 'plottype' and specify 'biptype')\n")
stop()
}
}
if ((plottype == "Biplot") | (plottype == "biplot") | (plottype ==
"bip") | (plottype == "b")) {
if ((biptype == "rows") | (biptype == "Rows") | (biptype ==
"row") | (biptype == "r")) {
plottype <- "biplot"
cord1 <- x$Rprinccoord * scaleplot
cord2 <- x$Cstdcoord/scaleplot
nthings <- x$rows
nvars <- x$cols
thinglabels <- x$rowlabels
varlabels <- x$collabels
thinggroup <- rowgroup
thinggrlab <- rowgrlab
vargroup <- colgroup
vargrlab <- colgrlab
main <- "Row Isometric Biplot"
inertiapc = x$inertias[, 2]
dmu = diag(x$inertias[, 1])
dimnames(cord2)[1] <- dimnames(x$Xtable)[2]
dimnames(cord1)[1] <- dimnames(x$Xtable)[1]
if ((x$catype == "DONSCA") | (x$catype == "DOCA") |
(x$catype == "SOCA") | (x$catype == "SONSCA")) {
cord2 <- x$Rprinccoord * scaleplot
cord1 <- x$Cstdcoord/scaleplot
nthings <- x$cols
nvars <- x$rows
thinglabels <- x$collabels
varlabels <- x$rowlabels
thinggroup <- colgroup
thinggrlab <- colgrlab
vargroup <- rowgroup
vargrlab <- rowgrlab
inertiapc = x$inertias2[, 2]
dmu = diag(x$inertias2[, 1])
dimnames(cord2)[1] <- dimnames(x$Xtable)[1]
dimnames(cord1)[1] <- dimnames(x$Xtable)[2]
}
}
else {
plottype <- "biplot"
if (ell == TRUE) {
scaleplot <- 1
}
if ((x$catype == "CA") | (x$catype == "NSCA")) {
cord1 <- x$Cprinccoord * scaleplot
cord2 <- x$Rstdcoord/scaleplot
nthings <- x$cols
nvars <- x$rows
thinggroup <- colgroup
thinggrlab <- colgrlab
vargroup <- rowgroup
vargrlab <- rowgrlab
thinglabels <- x$collabels
varlabels <- x$rowlabels
main <- "Column Isometric Biplot"
inertiapc = x$inertias[, 2]
dmu = diag(x$inertias[, 1])
dimnames(cord1)[1] <- dimnames(x$Xtable)[2]
dimnames(cord2)[1] <- dimnames(x$Xtable)[1]
}
if ((x$catype == "DONSCA") | (x$catype == "DOCA") |
(x$catype == "SOCA") | (x$catype == "SONSCA")) {
if (ell == TRUE) {
scaleplot <- 1
}
cord2 <- x$Cprinccoord * scaleplot
cord1 <- x$Rstdcoord/scaleplot
nthings <- x$rows
nvars <- x$cols
thinggroup <- rowgroup
thinggrlab <- rowgrlab
vargroup <- colgroup
vargrlab <- colgrlab
thinglabels <- x$rowlabels
varlabels <- x$collabels
inertiapc = x$inertias[, 2]
dmu = diag(x$inertias[, 1])
dimnames(cord1)[1] <- dimnames(x$Xtable)[1]
dimnames(cord2)[1] <- dimnames(x$Xtable)[2]
}
}
}
if ((x$catype == "DOCA") | (x$catype == "SOCA") | (x$catype ==
"SONSCA") | (x$catype == "DONSCA")) {
cat("\n Looking at the Trends of rows and columns\n")
trendplot(x$mj, (x$Trend), posleg = posleg, main = "Reconstructed rows of the centred column profile",
xlab = "ordered scores", prop = prop)
trendplot(x$mi, t(x$Trend), posleg = posleg, main = "Reconstructed columns of the centred column profile",
xlab = "ordered scores", prop = prop)
}
picsize1 <- c(range(cord1[, c(firstaxis, lastaxis)], cord2[,
c(firstaxis, lastaxis)])/prop)
if (picsize1[1] >= picsize1[2])
stop(paste("incorrect axis scale picsize =", picsize1[1],
picsize1[2], "\n\n"))
if ((x$catype == "DONSCA") || (x$catype == "DOCA")) {
plotone(firstaxis, lastaxis, plottype = plottype, things = x$catype,
nthings, nvars, cord1, cord2, inertiapc = round(inertiapc,
digits = 1), thinggroup, thinggrlab, vargroup,
vargrlab, thinglabels, varlabels, picsize = picsize1,
cex = cex, cex.lab = cex.lab, type = "b", catype = x$catype,
pos = pos)
}
if ((x$catype == "SOCA") || (x$catype == "SONSCA")) {
if (biptype == "row") {
type = "b"
}
else {
type = "p"
}
plotone(firstaxis, lastaxis, plottype = plottype, things = x$catype,
nthings, nvars, cord1, cord2, inertiapc = round(inertiapc,
digits = 1), thinggroup, thinggrlab, vargroup,
vargrlab, thinglabels, varlabels, picsize = picsize1,
cex = cex, cex.lab = cex.lab, catype = x$catype,
type = type, pos = pos)
}
if ((x$catype == "CA") || (x$catype == "NSCA")) {
plotone(firstaxis, lastaxis, plottype = plottype, things = x$catype,
nthings, nvars, cord1, cord2, inertiapc = round(inertiapc,
digits = 1), thinggroup, thinggrlab, vargroup,
vargrlab, thinglabels, varlabels, picsize = picsize1,
cex = cex, cex.lab = cex.lab, type = "p", catype = x$catype,
pos = pos)
}
if (ell == TRUE) {
if (((x$catype == "NSCA") | (x$catype == "CA") | (x$catype ==
"DOCA") | (x$catype == "SOCA") | (x$catype == "SONSCA") |
(x$catype == "DONSCA")) & (plottype == "biplot") &
(biptype == "row") | (biptype == "r") | (biptype ==
"rows")) {
cordr <- cord2
cordc <- cord1
cord1 <- cordr
cord2 <- cordc
}
switch(x$catype, CA = caellipse(Xtable = x$Xtable, a1 = firstaxis,
a2 = lastaxis, alpha = alpha, M = Mell, cex = cex,
cex.lab = cex.lab, prop = prop, Imass = x$Imass,
Jmass = x$Jmass, a = x$Rstdcoord, b = x$Cstdcoord,
g = cord1, fr = cord2, dmu = dmu, inertiapc = round(inertiapc,
digits = 1), plottype = plottype, biptype = biptype,
pos = pos, arrow = TRUE, length = 0, graphy = TRUE,
ell = TRUE), SOCA = caellipse(Xtable = x$Xtable,
a1 = firstaxis, a2 = lastaxis, alpha = alpha, M = Mell,
cex = cex, cex.lab = cex.lab, prop = prop, Imass = x$Imass,
Jmass = x$Jmass, a = solve(x$Imass^0.5) %*% x$Rstdcoord,
b = solve(x$Jmass^0.5) %*% x$Cstdcoord, g = cord2,
fr = cord1, dmu = dmu, inertiapc = round(inertiapc,
digits = 1), plottype = plottype, biptype = biptype,
pos = pos, arrow = FALSE, length = 0, graphy = T,
ell = TRUE), DOCA = caellipse(Xtable = x$Xtable,
a1 = firstaxis, a2 = lastaxis, alpha = alpha, M = Mell,
cex = cex, cex.lab = cex.lab, prop = prop, Imass = x$Imass,
Jmass = x$Jmass, a = solve(x$Imass^0.5) %*% x$Rstdcoord,
b = solve(x$Jmass^0.5) %*% x$Cstdcoord, g = cord2,
fr = cord1, dmu = dmu, inertiapc = round(inertiapc,
digits = 1), plottype = plottype, biptype = biptype,
pos = pos, arrow = FALSE, length = 0, graphy = T,
ell = TRUE), NSCA = nscaellipse(Xtable = x$Xtable,
a1 = firstaxis, a2 = lastaxis, alpha = alpha, M = Mell,
cex = cex, cex.lab = cex.lab, prop = prop, Imass = x$Imass,
Jmass = x$Jmass, a = x$Rstdcoord, b = x$Cstdcoord,
g = cord1, fr = cord2, dmu = dmu, tauden = x$tauden,
inertiapc = round(inertiapc, digits = 1), plottype = plottype,
biptype = biptype, pos = pos, arrow = T, length = 0,
graphy = T, ell = TRUE), SONSCA = nscaellipse(Xtable = x$Xtable,
a1 = firstaxis, a2 = lastaxis, alpha = alpha, M = Mell,
cex = cex, cex.lab = cex.lab, prop = prop, Imass = x$Imass,
Jmass = x$Jmass, a = x$Rstdcoord, b = x$Cstdcoord,
g = cord2, fr = cord1, dmu = dmu, tauden = x$tauden,
inertiapc = round(inertiapc, digits = 1), plottype = plottype,
biptype = biptype, pos = pos, arrow = FALSE, length = 0,
graphy = T, ell = TRUE), DONSCA = nscaellipse(Xtable = x$Xtable,
a1 = firstaxis, a2 = lastaxis, alpha = alpha, M = Mell,
cex = cex, cex.lab = cex.lab, prop = prop, Imass = x$Imass,
Jmass = x$Jmass, a = x$Rstdcoord, b = x$Cstdcoord,
g = cord2, fr = cord1, dmu = dmu, tauden = x$tauden,
inertiapc = round(inertiapc, digits = 1), plottype = plottype,
biptype = biptype, pos = pos, arrow = FALSE, length = 0,
graphy = T, ell = TRUE))
}
}
plot(CAvariants(asbestos, catype = "CA", firstaxis = 1, lastaxis = 2))
plot(CAvariants(asbestos, catype = "DOCA", firstaxis = 1,lastaxis = 2))
plot(CAvariants(asbestos, catype = "DONSCA",firstaxis=1, lastaxis = 2, ellcomp = FALSE))
risasbestos<-CAvariants(asbestos, catype = "DOCA", firstaxis=1, lastaxis=2)
plot(risasbestos, plotype = "biplot", biptype = "row")
```