https://github.com/cran/aster
Revision 39d4bf9f99bbff5d96f3f4093cdc7a39ca03a29a authored by Charles J. Geyer on 15 March 2017, 08:04:36 UTC, committed by cran-robot on 15 March 2017, 08:04:36 UTC
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Tip revision: 39d4bf9f99bbff5d96f3f4093cdc7a39ca03a29a authored by Charles J. Geyer on 15 March 2017, 08:04:36 UTC
version 0.9.1
Tip revision: 39d4bf9
is.zero.R
### implements test of (35) of the design doc

is.zero <- function(alphabeenu, fixed, random, obj, y, origin, zwz,
    tolerance = sqrt(.Machine$double.eps))
{
    stopifnot(inherits(obj, "aster"))
    if (missing(y)) {
        y <- obj$x
    } else {
        stopifnot(is.matrix(y))
        stopifnot(is.numeric(y))
        stopifnot(is.finite(y))
        stopifnot(dim(y) == dim(obj$x))
    }
    if (missing(origin)) {
        origin <- obj$origin
    } else {
        stopifnot(is.matrix(origin))
        stopifnot(is.numeric(origin))
        stopifnot(is.finite(origin))
        stopifnot(dim(origin) == dim(obj$origin))
    }
    stopifnot(is.matrix(fixed))
    stopifnot(is.numeric(fixed))
    stopifnot(is.finite(fixed))
    nfix <- ncol(fixed)
    stopifnot(is.matrix(random) | is.list(random))
    if (! is.list(random))
        random <- list(random)
    for (i in seq(along = random)) {
        foo <- random[[i]]
        if (! is.matrix(foo))
            stop("random not matrix or list of matrices")
        if (! is.numeric(foo))
            stop("random not numeric matrix or list of such")
        if (! all(is.finite(foo)))
            stop("some random effects model matrix not all finite")
        if (nrow(foo) != nrow(fixed))
            stop("fixed and random effects model matrices with different nrow")
    }
    nrand <- sapply(random, ncol)
    stopifnot(is.matrix(zwz))
    stopifnot(is.numeric(zwz))
    stopifnot(is.finite(zwz))
    if (any(dim(zwz) != sum(nrand)))
        stop("zwz not square matrix with dimension = number of random effects")
    stopifnot(is.vector(alphabeenu))
    stopifnot(is.numeric(alphabeenu))
    stopifnot(is.finite(alphabeenu))
    if (length(alphabeenu) != nfix + sum(nrand) + length(nrand))
        stop("alphabeenu wrong length")

    idx <- seq(along = alphabeenu)
    is.alpha <- idx <= nfix
    is.bee <- nfix < idx & idx <= nfix + sum(nrand)
    is.nu <- nfix + sum(nrand) < idx
    alpha <- alphabeenu[is.alpha]
    bee <- alphabeenu[is.bee]
    nu <- alphabeenu[is.nu]
    dee <- rep(nu, times = nrand)

    if (all(nu > tolerance))
        return(rep(FALSE, length(nu)))
    if (any(nu < (- tolerance)))
        stop("apparently negative components of nu, impossible")
    nu[nu < tolerance] <- 0

    modmat <- cbind(fixed, Reduce(cbind, random))
    ### note: despite documentation of the mlogl function, it actually
    ### works to have modmat a matrix rather than a 3-way array
    mout <- mlogl(c(alpha, bee), obj$pred, obj$fam, y, obj$root, modmat,
        deriv = 2, famlist = obj$famlist, origin = origin)

    idx <- seq(along = mout$gradient)
    is.bee <- nfix < idx
    pb <- mout$gradient[is.bee]

    bigh <- sweep(zwz, 2, dee, "*") + diag(length(dee))
    bigh.inv <- solve(bigh)
    idx <- rep(seq(along = nu), times = nrand)
    pn <- rep(NaN, length(nu))
    for (k in seq(along = nu)) {
        eek <- as.numeric(idx == k)
        fook <- sweep(zwz, 2, eek, "*")
        pn[k] <- sum(t(bigh.inv) * fook) / 2
    }

    result <- rep(FALSE, length(nu))
    for (k in seq(along = nu))
        if (nu[k] == 0)
            result[k] <- pn[k] >= sum(pb[idx == k]^2) / 4
    return(result)
}

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