Development/Dev_Local_GP/MS_CR/sim_ms_basic.R
In drizopoulos/JMbayes2: Extended Joint Models for Longitudinal and Time-to-Event Data
sim_mstate <- function(seed, nsubj = 500) {
require(splines)
require(JMbayes)
require(mstate)
require(MASS)
require(Matrix)
set.seed(seed)
N <- nsubj
n <- 20
id <- rep(1:N, each = n)
min.t <- 0.01
max.t <- 12
time <- replicate(N, c(0, sort(runif(n - 1, min = min.t, max = max.t))), simplify = FALSE)
time <- do.call(c, time)
Xcov.s <- rnorm(N, mean = 4.763, sd = 2.8)
Xcov <- rep(Xcov.s, each = n)
Xcov2.s <- sample(c(0, 1), N, replace = T)
Xcov2 <- rep(Xcov.s, each = n)
simDF <- data.frame("id" = id, "time" = time, "X" = Xcov, "X2" = Xcov2)
X <- model.matrix(~ 1 + time + X, data = simDF)
Z <- model.matrix(~ 1 + time, data = simDF)
D <- matrix(c(1.35, 4, 4, 2), ncol = 2, nrow = 2)
D <- as.matrix(Matrix:::nearPD(D)$mat)
b <- MASS:::mvrnorm(n = N, mu = rep(0, ncol(D)), D)
true.betas <- c(-0.482, 0.243, 1.52)
eta.y <- as.vector(X %*% true.betas + rowSums(Z * b[id, ]))
sigma.e <- 1.242
alpha <- c("alpha.01" = 0.8, "alpha.02" = 0.55, "alpha.12" = 1.45,
"alpha.sl.01" = 0, "alpha.sl.02" = 0, "alpha.sl.12" = 0,
"alpha.ar.01" = 0, "alpha.ar.02" = 0, "alpha.ar.12" = 0)
phi <- c("phi.01" = 12.325, "phi.02" = 12.216, "phi.12" = 10.657)
gammas <- c("(Intercept)1" = -22.25, "X.01" = 1.2,
"(Intercept)2" = -18.25, "X.02" = 0.75,
"(Intercept)3" = -17.25, "X.12" = 0.5)
W <- cbind("(Intercept)1"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)2"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)3"= rep(1, N), Xcov[seq(1, by = n, N*n)])
eta.t1 <- as.vector(W[, c(1, 2), drop = FALSE] %*% gammas[1:2])
## transition: 0 -> 2
eta.t2 <- as.vector(W[, c(3, 4), drop = FALSE] %*% gammas[3:4])
## transition: 1 -> 2
eta.t3 <- as.vector(W[, c(5, 6), drop = FALSE] %*% gammas[5:6])
invS01 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
XXslope <- cbind(0, rep(1, length(s)))
ZZslope <- cbind(0, rep(1, length(s)))
XXarea <- cbind(s, (s^2)/2, s*Xcov[i])
ZZarea <- cbind(s, (s^2)/2)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
#f1.sl <- as.vector(XXslope %*% true.betas[1:2] + rowSums(ZZslope * b[rep(i, nrow(ZZ)), ]))
#f1.ar <- as.vector(XXarea %*% true.betas + rowSums(ZZarea * b[rep(i, nrow(ZZ)), ]))
#exp(log(phi["phi.01"]) + (phi["phi.01"])*log(s) + eta.t1[i] + f1*alpha["alpha.01"] +
# f1.sl*alpha["alpha.sl.01"] + f1.ar*alpha["alpha.ar.01"])
exp(log(phi["phi.01"]) + (phi["phi.01"])*log(s) + eta.t1[i] + f1*alpha["alpha.01"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS02 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
#XXslope <- cbind(0, rep(1, length(s)))
#ZZslope <- cbind(0, rep(1, length(s)))
#XXarea <- cbind(s, (s^2)/2, s*Xcov[i])
#ZZarea <- cbind(s, (s^2)/2)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
#f1.sl <- as.vector(XXslope %*% true.betas[1:2] + rowSums(ZZslope * b[rep(i, nrow(ZZ)), ]))
#f1.ar <- as.vector(XXarea %*% true.betas + rowSums(ZZarea * b[rep(i, nrow(ZZ)), ]))
#exp(log(phi["phi.02"]) + (phi["phi.02"])*log(s) + eta.t2[i] + f1*alpha["alpha.02"] +
# f1.sl*alpha["alpha.sl.02"] + f1.ar*alpha["alpha.ar.02"])
exp(log(phi["phi.02"]) + (phi["phi.02"])*log(s) + eta.t2[i] + f1*alpha["alpha.02"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS12 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
#XXslope <- cbind(0, rep(1, length(s)))
#ZZslope <- cbind(0, rep(1, length(s)))
#XXarea <- cbind(s, (s^2)/2, s*Xcov[i])
#ZZarea <- cbind(s, (s^2)/2)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
#f1.sl <- as.vector(XXslope %*% true.betas[1:2] + rowSums(ZZslope * b[rep(i, nrow(ZZ)), ]))
#f1.ar <- as.vector(XXarea %*% true.betas + rowSums(ZZarea * b[rep(i, nrow(ZZ)), ]))
#exp(log(phi["phi.12"]) + (phi["phi.12"])*log(s) + eta.t3[i] + f1*alpha["alpha.12"] +
# f1.sl*alpha["alpha.sl.12"] + f1.ar*alpha["alpha.ar.12"])
exp(log(phi["phi.12"]) + (phi["phi.12"])*log(s) + eta.t3[i] + f1*alpha["alpha.12"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
# Probability for each transition
u01 <- runif(N, 0, 1)
u02 <- runif(N, 0, 1)
u12 <- runif(N, 0, 1)
trueT01 <- numeric(N)
trueT02 <- numeric(N)
trueT12 <- numeric(N)
mean.Cens <- 9
C <- runif(N, 0, 2 * mean.Cens)
for (i in 1:N) {
Root01 <- NULL
Root02 <- NULL
Root12 <- NULL
Up <- 50
tries <- 5
# Transition 0->1
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
while(inherits(Root01, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
}
trueT01[i] <- if (!inherits(Root01, "try-error")) Root01 else 500
# Transition 0->2
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
while(inherits(Root02, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
}
trueT02[i] <- if (!inherits(Root02, "try-error")) Root02 else 500
# Transition 1->2
if(as.numeric(trueT01[i]) < as.numeric(trueT02[i]) && as.numeric(trueT01[i]) < C[i]) {
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
while(inherits(Root12, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
}
} else {Root12 <- 500}
trueT12[i] <- if (!inherits(Root12, "try-error")) Root12 else 500
#cat(paste("Subject:", i), "\n")
}
matsurv <- NULL
datasurv <- NULL
for(k in 1:N){
if (C[k] < min(trueT01[k], trueT02[k])) { # if 0 -> C
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], C[k], 0, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else {
if (trueT02[k] < trueT01[k]) { # if 0 -> 2
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], trueT02[k], 0, trueT02[k], 1)
matsurv <- rbind(matsurv, aux1)
} else {
if (C[k] < trueT12[k]) { # if 0 -> 1 -> C
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], trueT01[k], 1, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else { # if 0 -> 1 -> 2
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], trueT01[k], 1, trueT12[k], 1)
matsurv <- rbind(matsurv, aux1)
}
}
}
}
y <- rnorm(N*n, eta.y, sigma.e)
matlongit <- NULL
aux2 <- NULL
datalongit <- NULL
for(k in 1:N){
n_final <- NULL
n_final <- if (matsurv[k,4] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT12[k])
} else if (matsurv[k,6] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT02[k])
} else{
sum(time[(n*(k-1)+1) : (k*n)] < C[k])
}
aux2 <- matrix(nrow = n_final, ncol = 4,
c(rep(k, n_final),
y[(n*(k-1)+1) : (n*(k-1) + n_final)],
time[(n*(k-1)+1) : (n*(k-1) + n_final)],
Xcov[(n*(k-1)+1) : (n*(k-1) + n_final)]))
matlongit <- rbind(matlongit, aux2)
}
datasurv <- data.frame(matsurv, row.names = NULL)
names(datasurv) <- c("id", "X", "X2", "t_State1", "State1", "t_State2", "State2")
row.names(datasurv) <- as.integer(1:nrow(datasurv))
datalongit <- data.frame(matlongit, row.names = NULL)
names(datalongit) <- c("id", "Y", "times", "X")
row.names(datalongit) <- as.integer(1:nrow(datalongit))
simDF$y <- y
tmat <- matrix(NA, 3, 3)
tmat[1, 2:3] <- 1:2
tmat[2, 3] <- 3
dimnames(tmat) <- list(from = c("State0", "State1", "State2"),
to = c("State0", "State1", "State2"))
covs <- c("X", "X2")
data_mstate <- msprep(time = c(NA, "t_State1", "t_State2"),
status = c(NA, "State1", "State2"),
data = datasurv,
keep = covs,
id = "id",
trans = tmat)
data_mstate <- expand.covs(data_mstate, covs,
append = TRUE, longnames = FALSE)
trans1.evnts <- table(data_mstate[data_mstate$trans == 1, "status"])
trans2.evnts <- table(data_mstate[data_mstate$trans == 2, "status"])
trans3.evnts <- table(data_mstate[data_mstate$trans == 3, "status"])
range(datalongit$times)
median(tapply(datalongit$times, datalongit$id, length))
out <- list("params" = list(N = N, n = n, knots = knots, D = D, alpha = alpha, phi = phi,
sigma = sigma.e, gammas = gammas, eta.y = eta.y),
"event_summary" = list("trans01" = trans1.evnts, "trans02" = trans3.evnts,
"trans12" = trans3.evnts),
"datasets" = list("datasurv" = datasurv, "datalongit" = datalongit,
"data_mstate" = data_mstate))
out
}
############################
set.seed(1234)
# number of subjects
N <- 500
# number of measurements per subject
n <- 20
# vector of ids
id <- rep(1:N, each = n)
# minimum and maximum follow-up times
min.t <- 0.01
max.t <- 16
# sample time-points
time <- replicate(N, c(0, sort(runif(n - 1, min = min.t, max = max.t))), simplify = FALSE)
time <- do.call(c, time)
# sample continuous covariate values
Xcov.s <- rnorm(N, mean = 4.763, sd = 2.8) # wide version
Xcov <- rep(Xcov.s, each = n) # long
# initiate data frame to store results
DF <- data.frame("id" = id, "time" = time, "X" = Xcov)
# design matrices for fixed and random effects
X <- model.matrix(~ 1 + time + X, data = DF)
Z <- model.matrix(~ 1 + time, data = DF)
D11 <- 1.0 # variance of random intercepts
D22 <- 0.5 # variance of random slopes
# we simulate random effects
b <- cbind(rnorm(N, sd = sqrt(D11)), rnorm(n, sd = sqrt(D22)))
# fixed effects coefficients
true.betas <- c(-0.482, 0.243, 1.52)
# linear predictor
eta.y <- as.vector(X %*% true.betas + rowSums(Z * b[id, ]))
# residual standard error
sigma.e <- 1.242
# sample longitudinal outcome values
y <- rnorm(N*n, eta.y, sigma.e)
# values for the association parameter per transition
alpha <- c("alpha.01" = 0.8, "alpha.02" = 0.55, "alpha.12" = 1.25)
# shape of Weibull for each transition
phi <- c("phi.01" = 12.325, "phi.02" = 8.216, "phi.12" = 3.243)
# regression coefficients for transition intensities
gammas <- c("(Intercept)1" = -22.25, "X" = 1.2,
"(Intercept)2" = -18.25, "X" = 1.2,
"(Intercept)3" = -19.25, "X" = 1.2)
# design matrix transition intensities
W <- cbind("(Intercept)1"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)2"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)3"= rep(1, N), Xcov[seq(1, by = n, N*n)])
## linear predictor for transition: 0 -> 1
eta.t1 <- as.vector(W[, c(1, 2), drop = FALSE] %*% gammas[1:2])
## linear predictor for transition: 0 -> 2
eta.t2 <- as.vector(W[, c(3, 4), drop = FALSE] %*% gammas[3:4])
## linear predictor for transition: 1 -> 2
eta.t3 <- as.vector(W[, c(5, 6), drop = FALSE] %*% gammas[5:6])
# we simulate event times using inverse transform sampling
invS01 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
exp(log(phi["phi.01"]) + (phi["phi.01"] - 1)*log(s) + eta.t1[i] + f1*alpha["alpha.01"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS02 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
exp(log(phi["phi.02"]) + (phi["phi.02"] - 1)*log(s) + eta.t2[i] + f1*alpha["alpha.02"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS12 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
exp(log(phi["phi.12"]) + (phi["phi.12"] - 1)*log(s) + eta.t3[i] + f1*alpha["alpha.12"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
# Probability for each transition
u01 <- runif(N, 0, 1)
u02 <- runif(N, 0, 1)
u12 <- runif(N, 0, 1)
trueT01 <- numeric(N)
trueT02 <- numeric(N)
trueT12 <- numeric(N)
mean.Cens <- 9
C <- runif(N, 0, 2 * mean.Cens)
for (i in 1:N) {
Root01 <- NULL
Root02 <- NULL
Root12 <- NULL
Up <- 50
tries <- 5
# Transition 0->1
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
while(inherits(Root01, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
}
trueT01[i] <- if (!inherits(Root01, "try-error")) Root01 else 500
# Transition 0->2
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
while(inherits(Root02, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
}
trueT02[i] <- if (!inherits(Root02, "try-error")) Root02 else 500
# Transition 1->2
if(as.numeric(trueT01[i]) < as.numeric(trueT02[i]) && as.numeric(trueT01[i]) < C[i]) {
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
while(inherits(Root12, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
}
} else {Root12 <- 500}
trueT12[i] <- if (!inherits(Root12, "try-error")) Root12 else 500
}
matsurv <- NULL
datasurv <- NULL
for(k in 1:N){
if (C[k] < min(trueT01[k], trueT02[k])) { # if 0 -> C
aux1 <- c(k, Xcov.s[k], C[k], 0, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else {
if (trueT02[k] < trueT01[k]) { # if 0 -> 2
aux1 <- c(k, Xcov.s[k], trueT02[k], 0, trueT02[k], 1)
matsurv <- rbind(matsurv, aux1)
} else {
if (C[k] < trueT12[k]) { # if 0 -> 1 -> C
aux1 <- c(k, Xcov.s[k], trueT01[k], 1, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else { # if 0 -> 1 -> 2
aux1 <- c(k, Xcov.s[k], trueT01[k], 1, trueT12[k], 1)
matsurv <- rbind(matsurv, aux1)
}
}
}
}
matlongit <- NULL
aux2 <- NULL
datalongit <- NULL
for(k in 1:N){
n_final <- NULL
n_final <- if (matsurv[k, 4] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT12[k])
} else if (matsurv[k, 6] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT02[k])
} else{
sum(time[(n*(k-1)+1) : (k*n)] < C[k])
}
aux2 <- matrix(nrow = n_final, ncol = 4,
c(rep(k, n_final),
y[(n*(k-1)+1) : (n*(k-1) + n_final)],
time[(n*(k-1)+1) : (n*(k-1) + n_final)],
Xcov[(n*(k-1)+1) : (n*(k-1) + n_final)]))
matlongit <- rbind(matlongit, aux2)
}
datasurv <- data.frame(matsurv, row.names = NULL)
names(datasurv) <- c("id", "X", "t_illness", "illness", "t_death", "death")
row.names(datasurv) <- as.integer(1:nrow(datasurv))
datalongit <- data.frame(matlongit, row.names = NULL)
names(datalongit) <- c("id", "Y", "times", "X")
row.names(datalongit) <- as.integer(1:nrow(datalongit))
tmat <- matrix(NA, 3, 3)
tmat[1, 2:3] <- 1:2
tmat[2, 3] <- 3
dimnames(tmat) <- list(from = c("healthy", "illness", "death"),
to = c("healthy", "illness", "death"))
covs <- c("X")
data_mstate <- msprep(time = c(NA, "t_State1", "t_State2"),
status = c(NA, "State1", "State2"),
data = datasurv,
keep = covs,
id = "id",
trans = tmat)
data_mstate <- ms_setup(data = datasurv,
timevars = c(NA, 't_illness', 't_death'),
statusvars = c(NA, 'illness', 'death'),
transitionmat = tmat,
id = 'id',
covs = covs)
out <- list("datasets" = list("long_data" = datalongit,
"data_mstate" = data_mstate))
drizopoulos/JMbayes2 documentation built on July 15, 2024, 11:13 p.m.
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sim_mstate <- function(seed, nsubj = 500) {
require(splines)
require(JMbayes)
require(mstate)
require(MASS)
require(Matrix)
set.seed(seed)
N <- nsubj
n <- 20
id <- rep(1:N, each = n)
min.t <- 0.01
max.t <- 12
time <- replicate(N, c(0, sort(runif(n - 1, min = min.t, max = max.t))), simplify = FALSE)
time <- do.call(c, time)
Xcov.s <- rnorm(N, mean = 4.763, sd = 2.8)
Xcov <- rep(Xcov.s, each = n)
Xcov2.s <- sample(c(0, 1), N, replace = T)
Xcov2 <- rep(Xcov.s, each = n)
simDF <- data.frame("id" = id, "time" = time, "X" = Xcov, "X2" = Xcov2)
X <- model.matrix(~ 1 + time + X, data = simDF)
Z <- model.matrix(~ 1 + time, data = simDF)
D <- matrix(c(1.35, 4, 4, 2), ncol = 2, nrow = 2)
D <- as.matrix(Matrix:::nearPD(D)$mat)
b <- MASS:::mvrnorm(n = N, mu = rep(0, ncol(D)), D)
true.betas <- c(-0.482, 0.243, 1.52)
eta.y <- as.vector(X %*% true.betas + rowSums(Z * b[id, ]))
sigma.e <- 1.242
alpha <- c("alpha.01" = 0.8, "alpha.02" = 0.55, "alpha.12" = 1.45,
"alpha.sl.01" = 0, "alpha.sl.02" = 0, "alpha.sl.12" = 0,
"alpha.ar.01" = 0, "alpha.ar.02" = 0, "alpha.ar.12" = 0)
phi <- c("phi.01" = 12.325, "phi.02" = 12.216, "phi.12" = 10.657)
gammas <- c("(Intercept)1" = -22.25, "X.01" = 1.2,
"(Intercept)2" = -18.25, "X.02" = 0.75,
"(Intercept)3" = -17.25, "X.12" = 0.5)
W <- cbind("(Intercept)1"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)2"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)3"= rep(1, N), Xcov[seq(1, by = n, N*n)])
eta.t1 <- as.vector(W[, c(1, 2), drop = FALSE] %*% gammas[1:2])
## transition: 0 -> 2
eta.t2 <- as.vector(W[, c(3, 4), drop = FALSE] %*% gammas[3:4])
## transition: 1 -> 2
eta.t3 <- as.vector(W[, c(5, 6), drop = FALSE] %*% gammas[5:6])
invS01 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
XXslope <- cbind(0, rep(1, length(s)))
ZZslope <- cbind(0, rep(1, length(s)))
XXarea <- cbind(s, (s^2)/2, s*Xcov[i])
ZZarea <- cbind(s, (s^2)/2)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
#f1.sl <- as.vector(XXslope %*% true.betas[1:2] + rowSums(ZZslope * b[rep(i, nrow(ZZ)), ]))
#f1.ar <- as.vector(XXarea %*% true.betas + rowSums(ZZarea * b[rep(i, nrow(ZZ)), ]))
#exp(log(phi["phi.01"]) + (phi["phi.01"])*log(s) + eta.t1[i] + f1*alpha["alpha.01"] +
# f1.sl*alpha["alpha.sl.01"] + f1.ar*alpha["alpha.ar.01"])
exp(log(phi["phi.01"]) + (phi["phi.01"])*log(s) + eta.t1[i] + f1*alpha["alpha.01"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS02 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
#XXslope <- cbind(0, rep(1, length(s)))
#ZZslope <- cbind(0, rep(1, length(s)))
#XXarea <- cbind(s, (s^2)/2, s*Xcov[i])
#ZZarea <- cbind(s, (s^2)/2)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
#f1.sl <- as.vector(XXslope %*% true.betas[1:2] + rowSums(ZZslope * b[rep(i, nrow(ZZ)), ]))
#f1.ar <- as.vector(XXarea %*% true.betas + rowSums(ZZarea * b[rep(i, nrow(ZZ)), ]))
#exp(log(phi["phi.02"]) + (phi["phi.02"])*log(s) + eta.t2[i] + f1*alpha["alpha.02"] +
# f1.sl*alpha["alpha.sl.02"] + f1.ar*alpha["alpha.ar.02"])
exp(log(phi["phi.02"]) + (phi["phi.02"])*log(s) + eta.t2[i] + f1*alpha["alpha.02"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS12 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
#XXslope <- cbind(0, rep(1, length(s)))
#ZZslope <- cbind(0, rep(1, length(s)))
#XXarea <- cbind(s, (s^2)/2, s*Xcov[i])
#ZZarea <- cbind(s, (s^2)/2)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
#f1.sl <- as.vector(XXslope %*% true.betas[1:2] + rowSums(ZZslope * b[rep(i, nrow(ZZ)), ]))
#f1.ar <- as.vector(XXarea %*% true.betas + rowSums(ZZarea * b[rep(i, nrow(ZZ)), ]))
#exp(log(phi["phi.12"]) + (phi["phi.12"])*log(s) + eta.t3[i] + f1*alpha["alpha.12"] +
# f1.sl*alpha["alpha.sl.12"] + f1.ar*alpha["alpha.ar.12"])
exp(log(phi["phi.12"]) + (phi["phi.12"])*log(s) + eta.t3[i] + f1*alpha["alpha.12"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
# Probability for each transition
u01 <- runif(N, 0, 1)
u02 <- runif(N, 0, 1)
u12 <- runif(N, 0, 1)
trueT01 <- numeric(N)
trueT02 <- numeric(N)
trueT12 <- numeric(N)
mean.Cens <- 9
C <- runif(N, 0, 2 * mean.Cens)
for (i in 1:N) {
Root01 <- NULL
Root02 <- NULL
Root12 <- NULL
Up <- 50
tries <- 5
# Transition 0->1
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
while(inherits(Root01, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
}
trueT01[i] <- if (!inherits(Root01, "try-error")) Root01 else 500
# Transition 0->2
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
while(inherits(Root02, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
}
trueT02[i] <- if (!inherits(Root02, "try-error")) Root02 else 500
# Transition 1->2
if(as.numeric(trueT01[i]) < as.numeric(trueT02[i]) && as.numeric(trueT01[i]) < C[i]) {
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
while(inherits(Root12, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
}
} else {Root12 <- 500}
trueT12[i] <- if (!inherits(Root12, "try-error")) Root12 else 500
#cat(paste("Subject:", i), "\n")
}
matsurv <- NULL
datasurv <- NULL
for(k in 1:N){
if (C[k] < min(trueT01[k], trueT02[k])) { # if 0 -> C
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], C[k], 0, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else {
if (trueT02[k] < trueT01[k]) { # if 0 -> 2
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], trueT02[k], 0, trueT02[k], 1)
matsurv <- rbind(matsurv, aux1)
} else {
if (C[k] < trueT12[k]) { # if 0 -> 1 -> C
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], trueT01[k], 1, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else { # if 0 -> 1 -> 2
aux1 <- c(k, Xcov.s[k], Xcov2.s[k], trueT01[k], 1, trueT12[k], 1)
matsurv <- rbind(matsurv, aux1)
}
}
}
}
y <- rnorm(N*n, eta.y, sigma.e)
matlongit <- NULL
aux2 <- NULL
datalongit <- NULL
for(k in 1:N){
n_final <- NULL
n_final <- if (matsurv[k,4] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT12[k])
} else if (matsurv[k,6] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT02[k])
} else{
sum(time[(n*(k-1)+1) : (k*n)] < C[k])
}
aux2 <- matrix(nrow = n_final, ncol = 4,
c(rep(k, n_final),
y[(n*(k-1)+1) : (n*(k-1) + n_final)],
time[(n*(k-1)+1) : (n*(k-1) + n_final)],
Xcov[(n*(k-1)+1) : (n*(k-1) + n_final)]))
matlongit <- rbind(matlongit, aux2)
}
datasurv <- data.frame(matsurv, row.names = NULL)
names(datasurv) <- c("id", "X", "X2", "t_State1", "State1", "t_State2", "State2")
row.names(datasurv) <- as.integer(1:nrow(datasurv))
datalongit <- data.frame(matlongit, row.names = NULL)
names(datalongit) <- c("id", "Y", "times", "X")
row.names(datalongit) <- as.integer(1:nrow(datalongit))
simDF$y <- y
tmat <- matrix(NA, 3, 3)
tmat[1, 2:3] <- 1:2
tmat[2, 3] <- 3
dimnames(tmat) <- list(from = c("State0", "State1", "State2"),
to = c("State0", "State1", "State2"))
covs <- c("X", "X2")
data_mstate <- msprep(time = c(NA, "t_State1", "t_State2"),
status = c(NA, "State1", "State2"),
data = datasurv,
keep = covs,
id = "id",
trans = tmat)
data_mstate <- expand.covs(data_mstate, covs,
append = TRUE, longnames = FALSE)
trans1.evnts <- table(data_mstate[data_mstate$trans == 1, "status"])
trans2.evnts <- table(data_mstate[data_mstate$trans == 2, "status"])
trans3.evnts <- table(data_mstate[data_mstate$trans == 3, "status"])
range(datalongit$times)
median(tapply(datalongit$times, datalongit$id, length))
out <- list("params" = list(N = N, n = n, knots = knots, D = D, alpha = alpha, phi = phi,
sigma = sigma.e, gammas = gammas, eta.y = eta.y),
"event_summary" = list("trans01" = trans1.evnts, "trans02" = trans3.evnts,
"trans12" = trans3.evnts),
"datasets" = list("datasurv" = datasurv, "datalongit" = datalongit,
"data_mstate" = data_mstate))
out
}
############################
set.seed(1234)
# number of subjects
N <- 500
# number of measurements per subject
n <- 20
# vector of ids
id <- rep(1:N, each = n)
# minimum and maximum follow-up times
min.t <- 0.01
max.t <- 16
# sample time-points
time <- replicate(N, c(0, sort(runif(n - 1, min = min.t, max = max.t))), simplify = FALSE)
time <- do.call(c, time)
# sample continuous covariate values
Xcov.s <- rnorm(N, mean = 4.763, sd = 2.8) # wide version
Xcov <- rep(Xcov.s, each = n) # long
# initiate data frame to store results
DF <- data.frame("id" = id, "time" = time, "X" = Xcov)
# design matrices for fixed and random effects
X <- model.matrix(~ 1 + time + X, data = DF)
Z <- model.matrix(~ 1 + time, data = DF)
D11 <- 1.0 # variance of random intercepts
D22 <- 0.5 # variance of random slopes
# we simulate random effects
b <- cbind(rnorm(N, sd = sqrt(D11)), rnorm(n, sd = sqrt(D22)))
# fixed effects coefficients
true.betas <- c(-0.482, 0.243, 1.52)
# linear predictor
eta.y <- as.vector(X %*% true.betas + rowSums(Z * b[id, ]))
# residual standard error
sigma.e <- 1.242
# sample longitudinal outcome values
y <- rnorm(N*n, eta.y, sigma.e)
# values for the association parameter per transition
alpha <- c("alpha.01" = 0.8, "alpha.02" = 0.55, "alpha.12" = 1.25)
# shape of Weibull for each transition
phi <- c("phi.01" = 12.325, "phi.02" = 8.216, "phi.12" = 3.243)
# regression coefficients for transition intensities
gammas <- c("(Intercept)1" = -22.25, "X" = 1.2,
"(Intercept)2" = -18.25, "X" = 1.2,
"(Intercept)3" = -19.25, "X" = 1.2)
# design matrix transition intensities
W <- cbind("(Intercept)1"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)2"= rep(1, N), Xcov[seq(1, by = n, N*n)],
"(Intercept)3"= rep(1, N), Xcov[seq(1, by = n, N*n)])
## linear predictor for transition: 0 -> 1
eta.t1 <- as.vector(W[, c(1, 2), drop = FALSE] %*% gammas[1:2])
## linear predictor for transition: 0 -> 2
eta.t2 <- as.vector(W[, c(3, 4), drop = FALSE] %*% gammas[3:4])
## linear predictor for transition: 1 -> 2
eta.t3 <- as.vector(W[, c(5, 6), drop = FALSE] %*% gammas[5:6])
# we simulate event times using inverse transform sampling
invS01 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
exp(log(phi["phi.01"]) + (phi["phi.01"] - 1)*log(s) + eta.t1[i] + f1*alpha["alpha.01"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS02 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
exp(log(phi["phi.02"]) + (phi["phi.02"] - 1)*log(s) + eta.t2[i] + f1*alpha["alpha.02"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
invS12 <- function(t, u, i) {
h <- function(s) {
XX <- cbind(1, s, Xcov[i])
ZZ <- cbind(1, s)
f1 <- as.vector(XX %*% true.betas + rowSums(ZZ * b[rep(i, nrow(ZZ)), ]))
exp(log(phi["phi.12"]) + (phi["phi.12"] - 1)*log(s) + eta.t3[i] + f1*alpha["alpha.12"])
}
integrate(h, lower = 0, upper = t, subdivisions = 10000)$value + log(u)
}
# Probability for each transition
u01 <- runif(N, 0, 1)
u02 <- runif(N, 0, 1)
u12 <- runif(N, 0, 1)
trueT01 <- numeric(N)
trueT02 <- numeric(N)
trueT12 <- numeric(N)
mean.Cens <- 9
C <- runif(N, 0, 2 * mean.Cens)
for (i in 1:N) {
Root01 <- NULL
Root02 <- NULL
Root12 <- NULL
Up <- 50
tries <- 5
# Transition 0->1
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
while(inherits(Root01, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root01 <- try(uniroot(invS01, interval = c(1e-05, Up), u = u01[i], i = i)$root, TRUE)
}
trueT01[i] <- if (!inherits(Root01, "try-error")) Root01 else 500
# Transition 0->2
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
while(inherits(Root02, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root02 <- try(uniroot(invS02, interval = c(1e-05, Up), u = u02[i], i = i)$root, TRUE)
}
trueT02[i] <- if (!inherits(Root02, "try-error")) Root02 else 500
# Transition 1->2
if(as.numeric(trueT01[i]) < as.numeric(trueT02[i]) && as.numeric(trueT01[i]) < C[i]) {
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
while(inherits(Root12, "try-error") && tries > 0) {
tries <- tries - 1
Up <- Up + 200
Root12 <- try(uniroot(invS12, interval = c(as.numeric(trueT01[i]), Up), u = u12[i], i = i)$root, TRUE)
}
} else {Root12 <- 500}
trueT12[i] <- if (!inherits(Root12, "try-error")) Root12 else 500
}
matsurv <- NULL
datasurv <- NULL
for(k in 1:N){
if (C[k] < min(trueT01[k], trueT02[k])) { # if 0 -> C
aux1 <- c(k, Xcov.s[k], C[k], 0, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else {
if (trueT02[k] < trueT01[k]) { # if 0 -> 2
aux1 <- c(k, Xcov.s[k], trueT02[k], 0, trueT02[k], 1)
matsurv <- rbind(matsurv, aux1)
} else {
if (C[k] < trueT12[k]) { # if 0 -> 1 -> C
aux1 <- c(k, Xcov.s[k], trueT01[k], 1, C[k], 0)
matsurv <- rbind(matsurv, aux1)
} else { # if 0 -> 1 -> 2
aux1 <- c(k, Xcov.s[k], trueT01[k], 1, trueT12[k], 1)
matsurv <- rbind(matsurv, aux1)
}
}
}
}
matlongit <- NULL
aux2 <- NULL
datalongit <- NULL
for(k in 1:N){
n_final <- NULL
n_final <- if (matsurv[k, 4] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT12[k])
} else if (matsurv[k, 6] == 1){
sum(time[(n*(k-1)+1) : (k*n)] < trueT02[k])
} else{
sum(time[(n*(k-1)+1) : (k*n)] < C[k])
}
aux2 <- matrix(nrow = n_final, ncol = 4,
c(rep(k, n_final),
y[(n*(k-1)+1) : (n*(k-1) + n_final)],
time[(n*(k-1)+1) : (n*(k-1) + n_final)],
Xcov[(n*(k-1)+1) : (n*(k-1) + n_final)]))
matlongit <- rbind(matlongit, aux2)
}
datasurv <- data.frame(matsurv, row.names = NULL)
names(datasurv) <- c("id", "X", "t_illness", "illness", "t_death", "death")
row.names(datasurv) <- as.integer(1:nrow(datasurv))
datalongit <- data.frame(matlongit, row.names = NULL)
names(datalongit) <- c("id", "Y", "times", "X")
row.names(datalongit) <- as.integer(1:nrow(datalongit))
tmat <- matrix(NA, 3, 3)
tmat[1, 2:3] <- 1:2
tmat[2, 3] <- 3
dimnames(tmat) <- list(from = c("healthy", "illness", "death"),
to = c("healthy", "illness", "death"))
covs <- c("X")
data_mstate <- msprep(time = c(NA, "t_State1", "t_State2"),
status = c(NA, "State1", "State2"),
data = datasurv,
keep = covs,
id = "id",
trans = tmat)
data_mstate <- ms_setup(data = datasurv,
timevars = c(NA, 't_illness', 't_death'),
statusvars = c(NA, 'illness', 'death'),
transitionmat = tmat,
id = 'id',
covs = covs)
out <- list("datasets" = list("long_data" = datalongit,
"data_mstate" = data_mstate))
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