example/iv/ivsim.R
In XingruiWang/iv2sr: An R package implementing of Regularization Methods for High-Dimensional Instrumental Variables Regression With an Application to Genetical Genomics
gen.data <- function(n, p, q, s=5, s0=10, r=5, r0=50, weak=FALSE, mixed=FALSE) {
require(MASS)
gam <- matrix(0, q, p)
for (j in 1:p)
if (mixed) {
ind <- sample(1:q, r)
gam[ind, j] <- (2*rbinom(r, 1, 0.5) - 1)*runif(r, 0.5, 1)
gam[sample(setdiff(1:q, ind), r0 - r), j] <- (2*rbinom(r0 - r, 1, 0.5) - 1)*runif(r0 - r, 0.05, 0.1)
} else if (weak)
gam[sample(1:q, r), j] <- (2*rbinom(r, 1, 0.5) - 1)*runif(r, 0.5, 0.75)
else
gam[sample(1:q, r), j] <- (2*rbinom(r, 1, 0.5) - 1)*runif(r, 0.75, 1)
bet <- rep(0, p)
ind <- sample(1:p, s)
bet[ind] <- (2*rbinom(s, 1, 0.5) - 1)*runif(s, 0.5, 1)
sig <- matrix(, p + 1, p + 1)
sig <- 0.2^abs(row(sig) - col(sig))
sig[1:p, p + 1] <- 0
sig[c(ind, sample(setdiff(1:p, ind), s0 - s)), p + 1] <- 0.3
sig[p + 1, 1:p] <- sig[1:p, p + 1]
e <- mvrnorm(n, rep(0, p + 1), sig)
if (mixed)
z <- matrix(rbinom(n*q, 1, runif(n*q, 0, 0.5)), n, q)
else
z <- matrix(rbinom(n*q, 1, 0.5), n, q)
x <- z %*% gam + e[, 1:p]
y <- drop(x %*% bet) + e[, p + 1]
list(x=x, y=y, z=z, bet=bet, gam=gam)
}
ivgen <- function(n, p, q, nsim=50, seed=19, weak=FALSE, mixed=FALSE) {
set.seed(seed)
data <- vector("list", nsim)
for (i in 1:nsim) {
data[[i]] <- gen.data(n, p, q, weak=weak, mixed=mixed)
cat("Sim.", i, "generated.\n")
}
fn <- paste(ifelse(weak, "w", ifelse(mixed, "m", "s")), paste(n, p, q, sep="_"), ".rda", sep="")
save(data, file=paste("data/", fn, sep=""))
}
ivsim <- function(n, p, q, nsim=50, nfold=10, seed=42, weak=FALSE, mixed=FALSE, batch) {
set.seed(seed)
fn <- paste(ifelse(weak, "w", ifelse(mixed, "m", "s")), paste(n, p, q, sep="_"), sep="")
load(paste("data/", fn, ".rda", sep=""))
if (missing(batch)) result <- vector("list", nsim)
for (i in 1:nsim) {
ind <- split(1:n, sample(rep(1:nfold, length=n)))
if (!missing(batch) && batch != i) next
x <- data[[i]]$x; y <- data[[i]]$y; z <- data[[i]]$z
bet <- data[[i]]$bet; gam <- data[[i]]$gam
x <- scale(x, scale=FALSE)
y <- scale(y, scale=FALSE)
z <- scale(z, scale=FALSE)
# PLS-oracle
supp <- bet != 0
y1 <- scale(y, scale=FALSE); x1 <- x[, supp]
bet.pls.oracle <- rep(0, p)
bet.pls.oracle[supp] <- solve(crossprod(x1), crossprod(x1, y1))
# PLS-Lasso
ans <- cd(y, x, "Lasso")
sol.pls.lasso <- ans$sol; lam <- ans$lam
i.lam <- cv(y, x, "Lasso", lam, ind)$i
bet.pls.lasso <- sol.pls.lasso[, i.lam]
# PLS-SCAD
ans <- cd(y, x, "SCAD")
sol.pls.scad <- ans$sol; lam <- ans$lam
i.lam <- cv(y, x, "SCAD", lam, ind)$i
bet.pls.scad <- sol.pls.scad[, i.lam]
# PLS-MCP
ans <- cd(y, x, "MCP")
sol.pls.mcp <- ans$sol; lam <- ans$lam
i.lam <- cv(y, x, "MCP", lam, ind)$i
bet.pls.mcp <- sol.pls.mcp[, i.lam]
# 2SR-oracle
x1 <- scale(x, scale=FALSE)
gam.2sr.oracle <- matrix(0, q, p)
for (j in 1:p) {
supp <- gam[, j] != 0
z1 <- z[, supp]
gam.2sr.oracle[supp, j] <- solve(crossprod(z1), crossprod(z1, x1[, j]))
}
x.hat <- z %*% gam.2sr.oracle
supp <- bet != 0
x1.hat <- x.hat[, supp]
y1 <- scale(y, scale=FALSE)
bet.2sr.oracle <- rep(0, p)
bet.2sr.oracle[supp] <- solve(crossprod(x1.hat), crossprod(x1.hat, y1))
# 2SR-Lasso
cat("2SR-Lasso\n")
gam.2sr.lasso <- matrix(, q, p)
for (j in 1:p) {
ans <- cd(x[, j], z, "Lasso", upto=0.25*n)
sol <- ans$sol; lam <- ans$lam
i.lam <- cv(x[, j], z, "Lasso", lam, ind)$i
gam.2sr.lasso[, j] <- sol[, i.lam]
}
x.hat <- z %*% gam.2sr.lasso
ind.x <- colSums(gam.2sr.lasso != 0) != 0
ans <- cd(y, x.hat[, ind.x], "Lasso", upto=0.25*n)
lam <- ans$lam; sol.2sr.lasso <- matrix(0, p, length(lam))
sol.2sr.lasso[ind.x, ] <- ans$sol
i.lam <- cv(y, x.hat[, ind.x], "Lasso", lam, ind)$i
bet.2sr.lasso <- sol.2sr.lasso[, i.lam]
# 2SR-SCAD
cat("2SR-SCAD\n")
gam.2sr.scad <- matrix(, q, p)
for (j in 1:p) {
ans <- cd(x[, j], z, "SCAD", upto=0.2*n)
sol <- ans$sol; lam <- ans$lam
i.lam <- cv(x[, j], z, "SCAD", lam, ind)$i
gam.2sr.scad[, j] <- sol[, i.lam]
}
x.hat <- z %*% gam.2sr.scad
ind.x <- colSums(gam.2sr.scad != 0) != 0
ans <- cd(y, x.hat[, ind.x], "SCAD", upto=0.2*n)
lam <- ans$lam; sol.2sr.scad <- matrix(0, p, length(lam))
sol.2sr.scad[ind.x, ] <- ans$sol
i.lam <- cv(y, x.hat[, ind.x], "SCAD", lam, ind)$i
bet.2sr.scad <- sol.2sr.scad[, i.lam]
# 2SR-MCP
cat("2SR-MCP\n")
gam.2sr.mcp <- matrix(, q, p)
for (j in 1:p) {
ans <- cd(x[, j], z, "MCP", upto=0.15*n)
sol <- ans$sol; lam <- ans$lam
i.lam <- cv(x[, j], z, "MCP", lam, ind)$i
gam.2sr.mcp[, j] <- sol[, i.lam]
}
x.hat <- z %*% gam.2sr.mcp
ind.x <- colSums(gam.2sr.mcp != 0) != 0
ans <- cd(y, x.hat[, ind.x], "MCP", upto=0.15*n)
lam <- ans$lam; sol.2sr.mcp <- matrix(0, p, length(lam))
sol.2sr.mcp[ind.x, ] <- ans$sol
i.lam <- cv(y, x.hat[, ind.x], "MCP", lam, ind)$i
bet.2sr.mcp <- sol.2sr.mcp[, i.lam]
if (missing(batch))
result[[i]] <- list(bet.pls.oracle=bet.pls.oracle, bet.pls.lasso=bet.pls.lasso,
bet.pls.scad=bet.pls.scad, bet.pls.mcp=bet.pls.mcp,
bet.2sr.oracle=bet.2sr.oracle, bet.2sr.lasso=bet.2sr.lasso,
bet.2sr.scad=bet.2sr.scad, bet.2sr.mcp=bet.2sr.mcp,
gam.2sr.oracle=gam.2sr.oracle, gam.2sr.lasso=gam.2sr.lasso,
gam.2sr.scad=gam.2sr.scad, gam.2sr.mcp=gam.2sr.mcp,
sol.pls.lasso=sol.pls.lasso, sol.pls.scad=sol.pls.scad,
sol.pls.mcp=sol.pls.mcp, sol.2sr.lasso=sol.2sr.lasso,
sol.2sr.scad=sol.2sr.scad, sol.2sr.mcp=sol.2sr.mcp)
else
result1 <- list(bet.pls.oracle=bet.pls.oracle, bet.pls.lasso=bet.pls.lasso,
bet.pls.scad=bet.pls.scad, bet.pls.mcp=bet.pls.mcp,
bet.2sr.oracle=bet.2sr.oracle, bet.2sr.lasso=bet.2sr.lasso,
bet.2sr.scad=bet.2sr.scad, bet.2sr.mcp=bet.2sr.mcp,
gam.2sr.oracle=gam.2sr.oracle, gam.2sr.lasso=gam.2sr.lasso,
gam.2sr.scad=gam.2sr.scad, gam.2sr.mcp=gam.2sr.mcp,
sol.pls.lasso=sol.pls.lasso, sol.pls.scad=sol.pls.scad,
sol.pls.mcp=sol.pls.mcp, sol.2sr.lasso=sol.2sr.lasso,
sol.2sr.scad=sol.2sr.scad, sol.2sr.mcp=sol.2sr.mcp)
cat("Sim.", i, "done.\n")
}
if (missing(batch))
save(result, file=paste("result/", fn, ".rda", sep=""))
else
save(result1, file=paste("result/", fn, "b", batch, ".rda", sep=""))
}
XingruiWang/iv2sr documentation built on Dec. 31, 2020, 6:33 p.m.
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gen.data <- function(n, p, q, s=5, s0=10, r=5, r0=50, weak=FALSE, mixed=FALSE) {
require(MASS)
gam <- matrix(0, q, p)
for (j in 1:p)
if (mixed) {
ind <- sample(1:q, r)
gam[ind, j] <- (2*rbinom(r, 1, 0.5) - 1)*runif(r, 0.5, 1)
gam[sample(setdiff(1:q, ind), r0 - r), j] <- (2*rbinom(r0 - r, 1, 0.5) - 1)*runif(r0 - r, 0.05, 0.1)
} else if (weak)
gam[sample(1:q, r), j] <- (2*rbinom(r, 1, 0.5) - 1)*runif(r, 0.5, 0.75)
else
gam[sample(1:q, r), j] <- (2*rbinom(r, 1, 0.5) - 1)*runif(r, 0.75, 1)
bet <- rep(0, p)
ind <- sample(1:p, s)
bet[ind] <- (2*rbinom(s, 1, 0.5) - 1)*runif(s, 0.5, 1)
sig <- matrix(, p + 1, p + 1)
sig <- 0.2^abs(row(sig) - col(sig))
sig[1:p, p + 1] <- 0
sig[c(ind, sample(setdiff(1:p, ind), s0 - s)), p + 1] <- 0.3
sig[p + 1, 1:p] <- sig[1:p, p + 1]
e <- mvrnorm(n, rep(0, p + 1), sig)
if (mixed)
z <- matrix(rbinom(n*q, 1, runif(n*q, 0, 0.5)), n, q)
else
z <- matrix(rbinom(n*q, 1, 0.5), n, q)
x <- z %*% gam + e[, 1:p]
y <- drop(x %*% bet) + e[, p + 1]
list(x=x, y=y, z=z, bet=bet, gam=gam)
}
ivgen <- function(n, p, q, nsim=50, seed=19, weak=FALSE, mixed=FALSE) {
set.seed(seed)
data <- vector("list", nsim)
for (i in 1:nsim) {
data[[i]] <- gen.data(n, p, q, weak=weak, mixed=mixed)
cat("Sim.", i, "generated.\n")
}
fn <- paste(ifelse(weak, "w", ifelse(mixed, "m", "s")), paste(n, p, q, sep="_"), ".rda", sep="")
save(data, file=paste("data/", fn, sep=""))
}
ivsim <- function(n, p, q, nsim=50, nfold=10, seed=42, weak=FALSE, mixed=FALSE, batch) {
set.seed(seed)
fn <- paste(ifelse(weak, "w", ifelse(mixed, "m", "s")), paste(n, p, q, sep="_"), sep="")
load(paste("data/", fn, ".rda", sep=""))
if (missing(batch)) result <- vector("list", nsim)
for (i in 1:nsim) {
ind <- split(1:n, sample(rep(1:nfold, length=n)))
if (!missing(batch) && batch != i) next
x <- data[[i]]$x; y <- data[[i]]$y; z <- data[[i]]$z
bet <- data[[i]]$bet; gam <- data[[i]]$gam
x <- scale(x, scale=FALSE)
y <- scale(y, scale=FALSE)
z <- scale(z, scale=FALSE)
# PLS-oracle
supp <- bet != 0
y1 <- scale(y, scale=FALSE); x1 <- x[, supp]
bet.pls.oracle <- rep(0, p)
bet.pls.oracle[supp] <- solve(crossprod(x1), crossprod(x1, y1))
# PLS-Lasso
ans <- cd(y, x, "Lasso")
sol.pls.lasso <- ans$sol; lam <- ans$lam
i.lam <- cv(y, x, "Lasso", lam, ind)$i
bet.pls.lasso <- sol.pls.lasso[, i.lam]
# PLS-SCAD
ans <- cd(y, x, "SCAD")
sol.pls.scad <- ans$sol; lam <- ans$lam
i.lam <- cv(y, x, "SCAD", lam, ind)$i
bet.pls.scad <- sol.pls.scad[, i.lam]
# PLS-MCP
ans <- cd(y, x, "MCP")
sol.pls.mcp <- ans$sol; lam <- ans$lam
i.lam <- cv(y, x, "MCP", lam, ind)$i
bet.pls.mcp <- sol.pls.mcp[, i.lam]
# 2SR-oracle
x1 <- scale(x, scale=FALSE)
gam.2sr.oracle <- matrix(0, q, p)
for (j in 1:p) {
supp <- gam[, j] != 0
z1 <- z[, supp]
gam.2sr.oracle[supp, j] <- solve(crossprod(z1), crossprod(z1, x1[, j]))
}
x.hat <- z %*% gam.2sr.oracle
supp <- bet != 0
x1.hat <- x.hat[, supp]
y1 <- scale(y, scale=FALSE)
bet.2sr.oracle <- rep(0, p)
bet.2sr.oracle[supp] <- solve(crossprod(x1.hat), crossprod(x1.hat, y1))
# 2SR-Lasso
cat("2SR-Lasso\n")
gam.2sr.lasso <- matrix(, q, p)
for (j in 1:p) {
ans <- cd(x[, j], z, "Lasso", upto=0.25*n)
sol <- ans$sol; lam <- ans$lam
i.lam <- cv(x[, j], z, "Lasso", lam, ind)$i
gam.2sr.lasso[, j] <- sol[, i.lam]
}
x.hat <- z %*% gam.2sr.lasso
ind.x <- colSums(gam.2sr.lasso != 0) != 0
ans <- cd(y, x.hat[, ind.x], "Lasso", upto=0.25*n)
lam <- ans$lam; sol.2sr.lasso <- matrix(0, p, length(lam))
sol.2sr.lasso[ind.x, ] <- ans$sol
i.lam <- cv(y, x.hat[, ind.x], "Lasso", lam, ind)$i
bet.2sr.lasso <- sol.2sr.lasso[, i.lam]
# 2SR-SCAD
cat("2SR-SCAD\n")
gam.2sr.scad <- matrix(, q, p)
for (j in 1:p) {
ans <- cd(x[, j], z, "SCAD", upto=0.2*n)
sol <- ans$sol; lam <- ans$lam
i.lam <- cv(x[, j], z, "SCAD", lam, ind)$i
gam.2sr.scad[, j] <- sol[, i.lam]
}
x.hat <- z %*% gam.2sr.scad
ind.x <- colSums(gam.2sr.scad != 0) != 0
ans <- cd(y, x.hat[, ind.x], "SCAD", upto=0.2*n)
lam <- ans$lam; sol.2sr.scad <- matrix(0, p, length(lam))
sol.2sr.scad[ind.x, ] <- ans$sol
i.lam <- cv(y, x.hat[, ind.x], "SCAD", lam, ind)$i
bet.2sr.scad <- sol.2sr.scad[, i.lam]
# 2SR-MCP
cat("2SR-MCP\n")
gam.2sr.mcp <- matrix(, q, p)
for (j in 1:p) {
ans <- cd(x[, j], z, "MCP", upto=0.15*n)
sol <- ans$sol; lam <- ans$lam
i.lam <- cv(x[, j], z, "MCP", lam, ind)$i
gam.2sr.mcp[, j] <- sol[, i.lam]
}
x.hat <- z %*% gam.2sr.mcp
ind.x <- colSums(gam.2sr.mcp != 0) != 0
ans <- cd(y, x.hat[, ind.x], "MCP", upto=0.15*n)
lam <- ans$lam; sol.2sr.mcp <- matrix(0, p, length(lam))
sol.2sr.mcp[ind.x, ] <- ans$sol
i.lam <- cv(y, x.hat[, ind.x], "MCP", lam, ind)$i
bet.2sr.mcp <- sol.2sr.mcp[, i.lam]
if (missing(batch))
result[[i]] <- list(bet.pls.oracle=bet.pls.oracle, bet.pls.lasso=bet.pls.lasso,
bet.pls.scad=bet.pls.scad, bet.pls.mcp=bet.pls.mcp,
bet.2sr.oracle=bet.2sr.oracle, bet.2sr.lasso=bet.2sr.lasso,
bet.2sr.scad=bet.2sr.scad, bet.2sr.mcp=bet.2sr.mcp,
gam.2sr.oracle=gam.2sr.oracle, gam.2sr.lasso=gam.2sr.lasso,
gam.2sr.scad=gam.2sr.scad, gam.2sr.mcp=gam.2sr.mcp,
sol.pls.lasso=sol.pls.lasso, sol.pls.scad=sol.pls.scad,
sol.pls.mcp=sol.pls.mcp, sol.2sr.lasso=sol.2sr.lasso,
sol.2sr.scad=sol.2sr.scad, sol.2sr.mcp=sol.2sr.mcp)
else
result1 <- list(bet.pls.oracle=bet.pls.oracle, bet.pls.lasso=bet.pls.lasso,
bet.pls.scad=bet.pls.scad, bet.pls.mcp=bet.pls.mcp,
bet.2sr.oracle=bet.2sr.oracle, bet.2sr.lasso=bet.2sr.lasso,
bet.2sr.scad=bet.2sr.scad, bet.2sr.mcp=bet.2sr.mcp,
gam.2sr.oracle=gam.2sr.oracle, gam.2sr.lasso=gam.2sr.lasso,
gam.2sr.scad=gam.2sr.scad, gam.2sr.mcp=gam.2sr.mcp,
sol.pls.lasso=sol.pls.lasso, sol.pls.scad=sol.pls.scad,
sol.pls.mcp=sol.pls.mcp, sol.2sr.lasso=sol.2sr.lasso,
sol.2sr.scad=sol.2sr.scad, sol.2sr.mcp=sol.2sr.mcp)
cat("Sim.", i, "done.\n")
}
if (missing(batch))
save(result, file=paste("result/", fn, ".rda", sep=""))
else
save(result1, file=paste("result/", fn, "b", batch, ".rda", sep=""))
}
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