Nothing
library(mcmc)
set.seed(42)
data(foo)
attach(foo)
out <- glm(y ~ x1 + x2 + x3, family = binomial, x = TRUE)
## IGNORE_RDIFF_BEGIN
summary(out)
## IGNORE_RDIFF_END
modmat <- out$x
models <- cbind(rep(0:1, each = 4), rep(rep(0:1, times = 2), each = 2),
rep(0:1, times = 4))
exes <- paste("x", 1:3, sep = "")
betas <- NULL
for (i in 1:nrow(models)) {
inies <- as.logical(models[i, ])
foo <- exes[inies]
bar <- paste("y ~", paste(foo, collapse = " + "))
if (! any(inies)) bar <- paste(bar, "1")
baz <- glm(as.formula(bar), family = binomial)
beta <- rep(0, 4)
beta[c(TRUE, inies)] <- baz$coef
betas <- rbind(betas, beta)
}
neighbors <- matrix(FALSE, nrow(models), nrow(models))
for (i in 1:nrow(neighbors)) {
for (j in 1:ncol(neighbors)) {
foo <- models[i, ]
bar <- models[j, ]
if (sum(foo != bar) == 1) neighbors[i, j] <- TRUE
}
}
ludfun <- function(state, ...) {
stopifnot(is.numeric(state))
stopifnot(length(state) == ncol(models) + 2)
stopifnot(length(state) == ncol(models) + 2)
icomp <- state[1]
stopifnot(icomp == as.integer(icomp))
stopifnot(1 <= icomp && icomp <= nrow(models))
beta <- state[-1]
inies <- c(TRUE, as.logical(models[icomp, ]))
beta.logl <- beta
beta.logl[! inies] <- 0
eta <- as.numeric(modmat %*% beta.logl)
logp <- ifelse(eta < 0, eta - log1p(exp(eta)), - log1p(exp(- eta)))
logq <- ifelse(eta < 0, - log1p(exp(eta)), - eta - log1p(exp(- eta)))
logl <- sum(logp[y == 1]) + sum(logq[y == 0])
val <- logl - sum(beta^2) / 2
return(val)
}
ludval <- NULL
for (i in 1:nrow(models)) ludval <- c(ludval, ludfun(c(i, betas[i, ])))
all(is.finite(ludval))
out <- temper(ludfun, initial = betas, neighbors = neighbors, nbatch = 20,
blen = 10, nspac = 5, scale = 0.56789, parallel = TRUE, debug = TRUE)
names(out)
### check decision about within-component or jump/swap
identical(out$unif.which < 0.5, out$which)
identical(out$which, out$proposal[ , 1] == out$coproposal[ , 1])
### check proposal and coproposal are actually current state or part thereof
prop <- out$proposal
coprop <- out$coproposal
prop.i <- prop[ , 1]
coprop.i <- coprop[ , 1]
alt.prop <- prop
alt.coprop <- coprop
for (i in 1:nrow(prop)) {
alt.prop[i, ] <- c(prop.i[i], out$state[i, prop.i[i], ])
alt.coprop[i, ] <- c(coprop.i[i], out$state[i, coprop.i[i], ])
}
identical(coprop, alt.coprop)
identical(prop[! out$which, ], alt.prop[! out$which, ])
identical(prop[out$which, 1], alt.prop[out$which, 1])
### check hastings ratio calculated correctly
foo <- apply(prop, 1, ludfun)
fooco <- apply(coprop, 1, ludfun)
prop[ , 1] <- out$coproposal[ , 1]
coprop[ , 1] <- out$proposal[ , 1]
foo.swap <- apply(prop, 1, ludfun)
fooco.swap <- apply(coprop, 1, ludfun)
log.haste <- ifelse(out$which, foo - fooco,
foo.swap + fooco.swap - foo - fooco)
all.equal(log.haste, out$log.hastings)
### check hastings rejection decided correctly
identical(out$log.hastings >= 0, is.na(out$unif.hastings))
all(out$log.hastings < 0 | out$acceptd)
identical(out$acceptd,
out$log.hastings >= 0 | out$unif.hastings < exp(out$log.hastings))
### check acceptance carried out or not (according to decision) correctly
before <- out$state
after <- before
after[- dim(after)[1], , ] <- before[-1, , ]
after[dim(after)[1], , ] <- out$final
my.after <- before
for (i in 1:length(out$acceptd)) {
if (out$acceptd[i]) {
if (out$which[i]) {
j <- out$proposal[i, 1]
my.after[i, j, ] <- out$proposal[i, -1]
} else {
j <- out$proposal[i, 1]
k <- out$coproposal[i, 1]
my.after[i, j, ] <- out$coproposal[i, -1]
my.after[i, k, ] <- out$proposal[i, -1]
}
}
}
identical(after, my.after)
### check within-component proposal
my.coproposal.within <- out$coproposal[out$which, ]
proposal.within <- out$proposal[out$which, ]
my.z <- out$norm[out$which, ]
my.proposal.within <- my.coproposal.within
my.proposal.within[ , -1] <- my.coproposal.within[ , -1] + out$scale * my.z
all.equal(proposal.within, my.proposal.within)
my.unif.choose <- out$unif.choose[out$which, 1]
my.i <- floor(nrow(models) * my.unif.choose) + 1
all(1 <= my.i & my.i <= nrow(models))
identical(my.i, my.coproposal.within[ , 1])
### check swap proposal
coproposal.swap <- out$coproposal[! out$which, ]
proposal.swap <- out$proposal[! out$which, ]
unif.choose.swap <- out$unif.choose[! out$which, ]
my.i <- floor(nrow(models) * unif.choose.swap[ , 1]) + 1
nneighbors <- apply(out$neighbors, 1, sum)
my.nneighbors <- nneighbors[my.i]
my.k <- floor(my.nneighbors * unif.choose.swap[ , 2]) + 1
my.j <- my.k
foo <- seq(1, ncol(out$neighbors))
for (i in seq(along = my.j)) {
my.j[i] <- (foo[out$neighbors[my.i[i], ]])[my.k[i]]
}
identical(coproposal.swap[ , 1], my.i)
identical(proposal.swap[ , 1], my.j)
### check standard normal and uniform random numbers are as purported
save.Random.seed <- .Random.seed
.Random.seed <- out$initial.seed
nx <- ncol(out$initial)
niter <- out$nbatch * out$blen * out$nspac
my.norm <- matrix(NA, nrow = nrow(out$norm), ncol = ncol(out$norm))
my.unif.which <- rep(NA, niter)
my.unif.hastings <- rep(NA, niter)
my.unif.choose <- matrix(NA, niter, 2)
for (iiter in 1:niter) {
my.unif.which[iiter] <- runif(1)
if (out$which[iiter]) {
my.unif.choose[iiter, 1] <- runif(1)
my.norm[iiter, ] <- rnorm(nx)
if (out$log.hastings[iiter] < 0) my.unif.hastings[iiter] <- runif(1)
} else {
my.unif.choose[iiter, ] <- runif(2)
if (out$log.hastings[iiter] < 0) my.unif.hastings[iiter] <- runif(1)
}
}
identical(my.norm, out$norm)
identical(my.unif.which, out$unif.which)
identical(my.unif.hastings, out$unif.hastings)
identical(my.unif.choose, out$unif.choose)
.Random.seed <- save.Random.seed
### check batch means
foo <- after[seq(1, niter) %% out$nspac == 0, , ]
foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2:3]))
foo <- apply(foo, c(2, 3, 4), mean)
all.equal(foo, out$batch)
### check acceptance rates
accept.within <- out$acceptd[out$which]
my.i.within <- out$coproposal[out$which, 1]
my.acceptx <- as.vector(sapply(split(accept.within, my.i.within), mean))
identical(my.acceptx, out$acceptx)
accept.swap <- out$acceptd[! out$which]
my.i.swap <- out$coproposal[! out$which, 1]
my.j.swap <- out$proposal[! out$which, 1]
nmodel <- nrow(out$neighbors)
my.accepti <- matrix(NA, nmodel, nmodel)
for (i in 1:nmodel) {
for (j in 1:nmodel) {
if (out$neighbors[i, j]) {
my.accepti[i, j] <-
mean(accept.swap[my.i.swap == i & my.j.swap == j])
}
}
}
identical(my.accepti, out$accepti)
### check scale vector
nx <- ncol(models) + 1
newscale <- rnorm(nx, 0.5, 0.1)
out <- temper(out, scale = newscale)
my.coproposal.within <- out$coproposal[out$which, ]
proposal.within <- out$proposal[out$which, ]
my.z <- out$norm[out$which, ]
my.proposal.within <- my.coproposal.within
my.proposal.within[ , -1] <- my.coproposal.within[ , -1] +
sweep(my.z, 2, out$scale, "*")
all.equal(proposal.within, my.proposal.within)
### check scale matrix
matscale <- matrix(rnorm(nx * nx, 0.0, 0.1), nx, nx)
diag(matscale) <- 0.56789
out <- temper(out, scale = matscale)
my.coproposal.within <- out$coproposal[out$which, ]
proposal.within <- out$proposal[out$which, ]
my.z <- out$norm[out$which, ]
my.proposal.within <- my.coproposal.within
my.proposal.within[ , -1] <- my.coproposal.within[ , -1] +
my.z %*% t(out$scale)
all.equal(proposal.within, my.proposal.within)
### check scale list
lisztscale <- list(0.56789, newscale, matscale, matscale, newscale,
0.98765, 0.98765, newscale)
out <- temper(out, scale = lisztscale)
my.coproposal.within <- out$coproposal[out$which, ]
proposal.within <- out$proposal[out$which, ]
my.z <- out$norm[out$which, ]
my.proposal.within <- my.coproposal.within
for (iiter in 1:nrow(my.z)) {
my.i <- my.coproposal.within[iiter, 1]
my.scale <- out$scale[[my.i]]
if (is.matrix(my.scale)) {
my.proposal.within[iiter, -1] <- my.coproposal.within[iiter, -1] +
my.z[iiter, , drop = FALSE] %*% t(my.scale)
} else {
my.proposal.within[iiter, -1] <- my.coproposal.within[iiter, -1] +
my.z[iiter, ] * my.scale
}
}
all.equal(proposal.within, my.proposal.within)
### check outfun
outfun <- function(state, icomp, ...) {
stopifnot(is.matrix(state))
stopifnot(is.numeric(state))
nx <- ncol(betas)
ncomp <- nrow(betas)
stopifnot(ncol(state) == nx)
stopifnot(nrow(state) == ncomp)
stopifnot(1 <= icomp && icomp <= ncomp)
foo <- state[icomp, ]
bar <- foo^2
return(c(foo, bar))
}
out <- temper(out, outfun = outfun, icomp = 4)
before <- out$state
after <- before
after[- dim(after)[1], , ] <- before[-1, , ]
after[dim(after)[1], , ] <- out$final
outies <- apply(after, 1, outfun, icomp = 4)
outies <- t(outies)
foo <- outies[seq(1, niter) %% out$nspac == 0, ]
foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2]))
foo <- apply(foo, c(2, 3), mean)
all.equal(foo, out$batch)
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