Nothing
RUVinv <-
function (Y, X, ctl, Z = 1, eta = NULL, include.intercept = TRUE,
fullW0 = NULL, invsvd = NULL, lambda = NULL, randomization = FALSE,
iterN = 1e+05, inputcheck = TRUE)
{
if (is.data.frame(Y))
Y = data.matrix(Y)
m = nrow(Y)
n = ncol(Y)
X = rX = design.matrix(X, include.intercept = FALSE)
p = ncol(X)
if (is.numeric(Z))
if (length(Z) == 1)
Z = matrix(1, m, 1)
if (!is.null(Z)) {
Z = design.matrix(Z, name = "Z", include.intercept = include.intercept)
q = ncol(Z)
}
else q = 0
ctl = tological(ctl, n)
if (inputcheck)
inputcheck1(Y, X, Z, ctl)
Y = RUV1(Y, eta, ctl, include.intercept = include.intercept)
if (q > 0) {
Y = residop(Y, Z)
X = residop(X, Z)
}
Y0 = residop(Y, X)
if (is.null(fullW0)) {
fullW0 = svd(Y0 %*% t(Y0))$u[, 1:(m - p - q), drop = FALSE]
}
if (randomization) {
if (!is.null(lambda))
temp = randinvvar(Y, ctl, XZ = cbind(X, Z), lambda = lambda,
iterN = iterN)
else temp = randinvvar(Y, ctl, XZ = cbind(X, Z), iterN = iterN)
}
else {
if (!is.null(lambda))
temp = invvar(Y, ctl, XZ = cbind(X, Z), lambda = lambda,
invsvd = invsvd)
else temp = invvar(Y, ctl, XZ = cbind(X, Z), invsvd = invsvd)
}
sigma2 = temp[[1]]
df = temp[[2]]
sigma2 = as.vector(sigma2)
k = m - p - q
W0 = fullW0[, 1:k, drop = FALSE]
alpha = solve(t(W0) %*% W0) %*% t(W0) %*% Y0
byx = solve(t(X) %*% X) %*% t(X) %*% Y
bycx = byx[, ctl, drop = FALSE]
alphac = alpha[, ctl, drop = FALSE]
if (!is.null(lambda))
bwx = bycx %*% t(alphac) %*% solve(alphac %*% t(alphac) +
lambda * diag(nrow(alphac)))
else bwx = bycx %*% t(alphac) %*% solve(alphac %*% t(alphac))
W = W0 + X %*% bwx
XZW = cbind(X, Z, W)
A = solve(t(XZW) %*% XZW)
AXZW = A %*% t(XZW)
betagammaalphahat = AXZW %*% Y
betahat = betagammaalphahat[1:p, , drop = FALSE]
multiplier = as.matrix(diag(A)[1:p])
se = sqrt(multiplier %*% t(sigma2))
tvals = betahat/se
pvals = tvals
for (i in 1:nrow(pvals)) pvals[i, ] = 2 * pt(-abs(tvals[i,
]), df)
Fstats = apply(betahat * (solve(AXZW[1:p, , drop = FALSE] %*%
t(AXZW[1:p, , drop = FALSE])) %*% betahat), 2, sum)/p/sigma2
Fpvals = pf(Fstats, p, df, lower.tail = FALSE)
return(list(betahat = betahat, sigma2 = sigma2, t = tvals,
p = pvals, Fstats = Fstats, Fpvals = Fpvals, multiplier = multiplier,
df = df, W = W, alpha = alpha, byx = byx, bwx = bwx,
X = rX, k = k, ctl = ctl, Z = Z, eta = eta, fullW0 = fullW0,
lambda = lambda, invsvd = temp$invsvd, include.intercept = include.intercept,
method = "RUVinv"))
}
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