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`varpart3` <-
function (Y, X1, X2, X3, chisquare, permat)
{
collinwarn <- function(case, mm, m)
warning(gettextf("collinearity detected in %s: mm = %d, m = %d",
case, mm, m), call. = FALSE)
if (inherits(Y, "dist")) {
Y <- GowerDblcen(as.matrix(Y^2), na.rm = FALSE)
Y <- -Y/2
SS.Y <- sum(diag(Y))
simpleRDA2 <- match.fun(simpleDBRDA)
} else {
Y <- as.matrix(Y)
if (chisquare) {
SS.Y <- sum(initCA(Y)^2)
simpleRDA2 <- match.fun(simpleCCA)
} else {
Y <- scale(Y, center = TRUE, scale = FALSE)
SS.Y <- sum(Y * Y)
}
}
X1 <- as.matrix(X1)
X2 <- as.matrix(X2)
X3 <- as.matrix(X3)
n <- nrow(Y)
n1 <- nrow(X1)
n2 <- nrow(X2)
n3 <- nrow(X3)
p <- ncol(Y)
mm1 <- ncol(X1)
mm2 <- ncol(X2)
mm3 <- ncol(X3)
if (n1 != n)
stop("Y and X1 do not have the same number of rows")
if (n2 != n)
stop("Y and X2 do not have the same number of rows")
if (n3 != n)
stop("Y and X3 do not have the same number of rows")
X1 <- scale(X1, center = TRUE, scale = FALSE)
X2 <- scale(X2, center = TRUE, scale = FALSE)
X3 <- scale(X3, center = TRUE, scale = FALSE)
dummy <- simpleRDA2(Y, X1, SS.Y, permat)
adfg.ua <- dummy$Rsquare
adfg <- dummy$RsquareAdj
m1 <- dummy$m
if (m1 != mm1)
collinwarn("X1", mm1, m1)
dummy <- simpleRDA2(Y, X2, SS.Y, permat)
bdeg.ua <- dummy$Rsquare
bdeg <- dummy$RsquareAdj
m2 <- dummy$m
if (m2 != mm2)
collinwarn("X2", mm2, m2)
dummy <- simpleRDA2(Y, X3, SS.Y, permat)
cefg.ua <- dummy$Rsquare
cefg <- dummy$RsquareAdj
m3 <- dummy$m
if (m3 != mm3)
collinwarn("X3", mm3, m3)
mm4 = mm1 + mm2
dummy <- simpleRDA2(Y, cbind(X1, X2), SS.Y, permat)
abdefg.ua <- dummy$Rsquare
abdefg <- dummy$RsquareAdj
m4 <- dummy$m
if (m4 != mm4)
collinwarn("cbind(X1,X2)", mm4, m4)
mm5 = mm1 + mm3
dummy <- simpleRDA2(Y, cbind(X1, X3), SS.Y, permat)
acdefg.ua <- dummy$Rsquare
acdefg <- dummy$RsquareAdj
m5 <- dummy$m
if (m5 != mm5)
collinwarn("cbind(X1,X3)", mm5, m5)
mm6 = mm2 + mm3
dummy <- simpleRDA2(Y, cbind(X2, X3), SS.Y, permat)
bcdefg.ua <- dummy$Rsquare
bcdefg <- dummy$RsquareAdj
m6 <- dummy$m
if (m6 != mm6)
collinwarn("cbind(X2,X3)", mm6, m6)
mm7 = mm1 + mm2 + mm3
dummy <- simpleRDA2(Y, cbind(X1, X2, X3), SS.Y, permat)
abcdefg.ua <- dummy$Rsquare
abcdefg <- dummy$RsquareAdj
m7 <- dummy$m
if (m7 != mm7)
collinwarn("cbind(X1,X2,X3)", mm7, m7)
bigwarning <- NULL
if ((m1 + m2) > m4)
bigwarning <- c(bigwarning, c("X1, X2"))
if ((m1 + m3) > m5)
bigwarning <- c(bigwarning, c("X1, X3"))
if ((m2 + m3) > m6)
bigwarning <- c(bigwarning, c("X2, X3"))
if ((m1 + m2 + m3) > m7)
bigwarning <- c(bigwarning, c("X1, X2, X3"))
Df <- c(m1, m2, m3, m4, m5, m6, m7)
fract <- data.frame(Df = Df,
R.square = c(adfg.ua, bdeg.ua, cefg.ua, abdefg.ua, acdefg.ua,
bcdefg.ua, abcdefg.ua),
Adj.R.square = c(adfg, bdeg, cefg, abdefg, acdefg, bcdefg,
abcdefg), Testable = rep(TRUE, 7) & Df)
rownames(fract) <- c("[a+d+f+g] = X1", "[b+d+e+g] = X2",
"[c+e+f+g] = X3", "[a+b+d+e+f+g] = X1+X2", "[a+c+d+e+f+g] = X1+X3",
"[b+c+d+e+f+g] = X2+X3", "[a+b+c+d+e+f+g] = All")
a <- abcdefg - bcdefg
b <- abcdefg - acdefg
c <- abcdefg - abdefg
d <- acdefg - cefg - a
e <- abdefg - adfg - b
f <- bcdefg - bdeg - c
g <- adfg - a - d - f
ma <- m7 - m6
mb <- m7 - m5
mc <- m7 - m4
mad <- m5 - m3
maf <- m4 - m2
mbd <- m6 - m3
mbe <- m4 - m1
mce <- m5 - m1
mcf <- m6 - m2
Df <- c(ma, mb, mc, rep(0, 4), NA)
indfract <- data.frame(Df = Df,
R.square = rep(NA, 8),
Adj.R.square = c(a, b, c, d, e, f, g, 1 - abcdefg),
Testable = c(rep(TRUE, 3), rep(FALSE, 5)) & Df)
rownames(indfract) <- c("[a] = X1 | X2+X3", "[b] = X2 | X1+X3",
"[c] = X3 | X1+X2", "[d]", "[e]", "[f]", "[g]", "[h] = Residuals")
Df <- c(mad, maf, mbd, mbe, mce, mcf)
contr1 <- data.frame(Df = Df,
R.square = rep(NA, 6),
Adj.R.square = c(a + d, a + f, b + d, b + e, c + e, c + f),
Testable = rep(TRUE, 6) & Df)
rownames(contr1) <- c("[a+d] = X1 | X3", "[a+f] = X1 | X2",
"[b+d] = X2 | X3", "[b+e] = X2 | X1", "[c+e] = X3 | X1",
"[c+f] = X3 | X2")
out <- list(fract = fract, indfract = indfract, contr1 = contr1,
SS.Y = SS.Y, nsets = 3, bigwarning = bigwarning, n = n1)
class(out) <- "varpart234"
out
}
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