In drizopoulos/JMbayes2: Extended Joint Models for Longitudinal and Time-to-Event Data
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library("JMbayes2")
Multi-state Processes
Introduction
It is very often the case that a subject may transition between multiple states and we are interested to assess the association of longitudinal marker(s) with each of these transitions. In this vignette we will illustrate how to do so using JMbayes2.
We will consider a simple case with one longitudinal outcome and a three-state (illness-death) model, but this application can be extended for the cases of multiple longitudinal markers and more than three states.
Data
First we will simulate data from a joint model with a single linear mixed effects model and a multi-state process with three possible states. The multi-state process can be visualized as:
library("ggplot2")
d <- data.frame("xmin" = c(0, 45, 22.5), "xmax" = c(15, 60, 37.5),
"ymin" = c(50, 50, 0), "ymax" = c(60, 60, 15))
dline <- data.frame("x1" = c(15), "y1" = c(55), "xend" = c(45), "yend" = c(55))
dcurve <- data.frame("x1" = c(7.5, 52.5), "y1" = c(50, 50),
"xend" = c(22.4, 37.4), "yend" = c(7.5, 7.5),
"curvature" = c(1, -1))
ggplot() + geom_rect(data = d, aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax),
fill = "#ffffff", color = 'black',
size = 1) +
geom_text(aes(x = 7.5, y = 55, label = "Healthy"), size = 6.5) +
geom_text(aes(x = 52.5, y = 55, label = "Illness"), size = 6.5) +
geom_text(aes(x = 30, y = 7, label = "Death"), size = 6.5) +
geom_text(aes(x = 30, y = 52.5, label = 'h[1][2](t)'), size = 4, parse = TRUE) +
geom_text(aes(x = 12.5, y = 30, label = "h[1][3](t)"), size = 4, parse = TRUE) +
geom_text(aes(x = 47.5, y = 30, label = "h[2][3](t)"), size = 4, parse = TRUE) +
geom_segment(data = dline, aes(x = x1, y = y1, xend = xend, yend = yend), size = 1,
arrow = arrow(length = unit(0.02, "npc"))) +
geom_curve(data = dcurve[1, ], aes(x = x1, y = y1, xend = xend, yend = yend),
size = 1, curvature = 0.3,
arrow = arrow(length = unit(0.02, "npc"))) +
geom_curve(data = dcurve[2, ], aes(x = x1, y = y1, xend = xend, yend = yend),
size = 1, curvature = -0.3,
arrow = arrow(length = unit(0.02, "npc"))) +
ylim(0, 60) + xlim(0, 60) +
theme_void()
where all subjects start from state "Healthy" and then can transition to either state "Illness" and then state "Death" or directly to state "Death". In this case, states "Healthy" and "Illness" are transient states as the subject, when occupying these states, can still transition to other states whereas "Death" is an absorbing state as when a subject reaches this state then no further transitions can occur. This means that three transitions are possible: $1 \rightarrow 2$, $1 \rightarrow 3$ and $2 \rightarrow 3$ with transition intensities $h_{12}\left(t\right)$, $h_{13}\left(t\right)$ and $h_{23}\left(t\right)$ respectively.
For our example the default functional form is assumed, i.e., that the linear predictor $\eta(t)$ of the mixed model is associated with the each transition intensity at time $t$. The following piece of code simulates the data:
# function ms_setup needs to be sourced to be used in the simulation
ms_setup <- function (data, timevars, statusvars, transitionmat, id, covs = NULL) {
# setup times matrix with NAs
# First row is NA as this is starting state
timesmat <- matrix(NA, nrow(data), length(timevars))
timecols_data <- which(colnames(data) %in% timevars[!is.na(timevars)])
timesmat[, -which(is.na(timevars))] <- as.matrix(data[, timecols_data])
# setup status matrix with NAs
# First row is NA as this is starting state
statusmat <- matrix(NA, nrow(data), length(statusvars))
statuscols_data <- which(colnames(data) %in% statusvars[!is.na(statusvars)])
statusmat[, -which(is.na(statusvars))] <- as.matrix(data[, statuscols_data])
# ensure convert to matrices
timesmat <- as.matrix(timesmat)
statusmat <- as.matrix(statusmat)
# check dimesnions are the same
if (any(dim(timesmat) != dim(statusmat)))
stop("Dimensions of \"time\" and \"status\" data should be equal")
# components
# number of unique subjects
n_subj <- nrow(timesmat)
# number of states
n_states <- dim(transitionmat)[1]
# set start state to 1 and start time to 0 for all subjects
# ATTENTION: this needs to be adjusted to more flexible to allow subjects starting at different states
# this could be achieved by a requesting a separate argument (vector with starting state)
starting_state <- rep(1, n_subj)
starting_time <- rep(0, n_subj)
idnam <- id
id <- data[[id]]
order_id <- order(id)
out <- ms_prepdat(timesmat = timesmat, statusmat = statusmat, id = id,
starting_time = starting_time, starting_state = starting_state,
transitionmat = transitionmat,
original_states = (1:nrow(transitionmat)), longmat = NULL)
out <- as.data.frame(out)
names(out) <- c(idnam, "from_state", "to_state", "transition",
"Tstart", "Tstop", "status")
out$time <- out$Tstop - out$Tstart
out <- out[, c(1:6, 8, 7)]
ord <- order(out[, 1], out[, 5], out[, 2], out[, 3])
out <- out[ord, ]
row.names(out) <- 1:nrow(out)
# Covariates
if (!is.null(covs)) {
n_covs <- length(covs)
cov_cols <- match(covs, names(data))
cov_names <- covs
covs <- data[, cov_cols]
if (!is.factor(out[, 1]))
out[, 1] <- factor(out[, 1])
n_per_subject <- tapply(out[, 1], out[, 1], length)
if (n_covs > 1)
covs <- covs[order_id, , drop = FALSE]
if (n_covs == 1) {
longcovs <- rep(covs, n_per_subject)
longcovs <- longcovs[ord]
longcovs <- as.data.frame(longcovs)
names(longcovs) <- cov_names
} else {
longcovs <- lapply(1:n_covs, function(i) rep(covs[, i], n_per_subject))
longcovs <- as.data.frame(longcovs)
names(longcovs) <- cov_names
}
out <- cbind(out, longcovs)
}
# add attributes maybe
# add specific class maybe
# need to add functionality for covariates (e.g. like keep in mstate)
return(out)
}
# used internally by ms_setup and needs also to be sourced
ms_prepdat <- function (timesmat, statusmat, id, starting_time, starting_state, transitionmat,
original_states, longmat) {
if (is.null(nrow(timesmat)))
return(longmat)
if (nrow(timesmat) == 0)
return(longmat)
from_states <- apply(!is.na(transitionmat), 2, sum)
to_states <- apply(!is.na(transitionmat), 1, sum)
absorbing_states <- which(to_states == 0)
starts <- which(from_states == 0)
new_states <- starting_state
new_times <- starting_time
rmv <- NULL
for (i in 1:starts) {
subjects <- which(starting_state == starts)
n_start <- length(subjects)
to_states_2 <- which(!is.na(transitionmat[starts, ]))
trans_states <- transitionmat[starts, to_states_2]
n_trans_states <- length(to_states_2)
if (all(n_start > 0, n_trans_states > 0)) {
Tstart <- starting_time[subjects]
Tstop <- timesmat[subjects, to_states_2, drop = FALSE]
Tstop[Tstop <= Tstart] <- Inf
state_status <- statusmat[subjects, to_states_2, drop = FALSE]
mintime <- apply(Tstop, 1, min)
hlp <- Tstop * 1 / state_status
hlp[Tstop == 0 & state_status == 0] <- Inf
next_time <- apply(hlp, 1, min)
censored <- which(is.infinite(apply(hlp, 1, min)))
wh <- which(mintime < next_time)
whminc <- setdiff(wh, censored)
if (length(whminc) > 0) {
whsubjs <- id[subjects[whminc]]
whsubjs <- paste(whsubjs, collapse = " ")
warning("Subjects ", whsubjs, " Have smaller transition time with status = 0, larger transition time with status = 1,
from starting state ", original_states[starts])
}
next_time[censored] <- mintime[censored]
if (ncol(hlp) > 1) {
hlpsrt <- t(apply(hlp, 1, sort))
warn1 <- which(hlpsrt[, 1] - hlpsrt[, 2] == 0)
if (length(warn1) > 0) {
isw <- id[subjects[warn1]]
isw <- paste(isw, collapse = " ")
hsw <- hlpsrt[warn1, 1]
hsw <- paste(hsw, collapse = " ")
warning("simultaneous transitions possible for subjects ", isw, " at times ", hsw,
" -> Smallest receiving state will be used")
}
}
if (length(censored) > 0) {
next_state <- apply(hlp[-censored, , drop = FALSE],
1, which.min)
absorbed <- (1:n_start)[-censored][which(to_states_2[next_state] %in% absorbing_states)]
} else {
next_state <- apply(hlp, 1, which.min)
absorbed <- (1:n_start)[which(to_states_2[next_state] %in% absorbing_states)]
}
states_matrix <- matrix(0, n_start, n_trans_states)
if (length(censored) > 0) {
states_matrix_min <- states_matrix[-censored, , drop = FALSE]
} else {
states_matrix_min <- states_matrix
}
if (nrow(states_matrix_min) > 0)
states_matrix_min <- t(sapply(1:nrow(states_matrix_min), function(i) {
x <- states_matrix_min[i, ]
x[next_state[i]] <- 1
return(x)
}))
if (length(censored) > 0) {
states_matrix[-censored, ] <- states_matrix_min
} else {
states_matrix <- states_matrix_min
}
mm <- matrix(c(rep(id[subjects], rep(n_trans_states, n_start)),
rep(original_states[starts], n_trans_states * n_start),
rep(original_states[to_states_2], n_start),
rep(trans_states, n_start), rep(Tstart, rep(n_trans_states, n_start)),
rep(next_time, rep(n_trans_states, n_start)), as.vector(t(states_matrix))),
n_trans_states * n_start, 7)
longmat <- rbind(longmat, mm)
rmv <- c(rmv, subjects[c(censored, absorbed)])
if (length(censored) > 0) {
new_states[subjects[-censored]] <- to_states_2[next_state]
} else {
new_states[subjects] <- to_states_2[next_state]
}
if (length(censored) > 0) {
new_times[subjects[-censored]] <- next_time[-censored]
} else {
new_times[subjects] <- next_time
}
}
}
if (length(rmv) > 0) {
timesmat <- timesmat[-rmv, ]
statusmat <- statusmat[-rmv, ]
new_times <- new_times[-rmv]
new_states <- new_states[-rmv]
id <- id[-rmv]
}
n_states <- nrow(transitionmat)
idx <- rep(1, n_states)
idx[starts] <- 0
idx <- cumsum(idx)
new_states <- idx[new_states]
Recall(timesmat = timesmat[, -starts], statusmat = statusmat[, -starts],
id = id, starting_time = new_times, starting_state = new_states,
transitionmat = transitionmat[-starts, -starts], original_states = original_states[-starts],
longmat = longmat)
}
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 = 10000L)$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)
# initiate vectors to save true event times
trueT01 <- numeric(N)
trueT02 <- numeric(N)
trueT12 <- numeric(N)
# sample censoring times
mean.Cens <- 9
C <- runif(N, 0, 2 * mean.Cens)
# simulate time-to-event data
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
}
# arrange data in appropriate format
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 <- JMbayes2:::ms_setup(data = datasurv,
timevars = c(NA, 't_illness', 't_death'),
statusvars = c(NA, 'illness', 'death'),
transitionmat = tmat,
id = 'id',
covs = covs)
data_mstate$transition <- factor(data_mstate$transition)
out <- list("datasets" = list("long_data" = datalongit,
"data_mstate" = data_mstate))
The data for the muti state process need to be in the appropriate long format:
head(out$datasets$data_mstate, n = 5L)
for example subject 1 experienced the following transition: $1 \rightarrow 2$ and therefore is represented in 3 rows, one for each transition, because all of these transitions were plausible. On the other hand subject 2 is only represented by two rows, only for transitions $1 \rightarrow 2$ and $1 \rightarrow 3$ since these are the only transitions that are possible from state 1. That is, since subject 2 never actually transitioned to state 2, transition $2 \rightarrow 3$ was never possible and therefore no row for this transition is in the dataset. It is also importnt to note that the time in the dataset follows the counting process formulation with intervals specified by Tstart and Tstop and that there is a variable (in this case transition) which indicates to which transition the row correspond to.
Fitting the model
As soon data in the appropriate format are available, fitting the model is very straightforward. First we fit a linear mixed model using the lme() function from package nlme:
mixedmodel <- lme(Y ~ times + X, random = ~ times | id, data = out$datasets$long_data)
then we fit a multi-state model using function coxph() from package survival making sure we use the counting process specification and that we add strata(transition) to stratify by the transition indicator variable in the dataset:
msmodel <- coxph(Surv(Tstart, Tstop, status) ~ X + strata(transition), data = out$datasets$data_mstate)
Finally, to fit the joint model we simply run:
jm_ms_model <- jm(msmodel, mixedmodel, time_var = "times",
functional_forms = ~ value(Y):transition,
n_iter = 10000L, GK_k = 7L)
summary(jm_ms_model)
which differs from a default call to jm() by the addition of the functional_forms argument by which we specify that we want an "interaction" between the value of the marker and each transition which translates into a separate association parameter for the longitudinal marker and each transition.
drizopoulos/JMbayes2 documentation built on July 15, 2024, 11:13 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library("JMbayes2")
Multi-state Processes
Introduction
It is very often the case that a subject may transition between multiple states and we are interested to assess the association of longitudinal marker(s) with each of these transitions. In this vignette we will illustrate how to do so using JMbayes2.
We will consider a simple case with one longitudinal outcome and a three-state (illness-death) model, but this application can be extended for the cases of multiple longitudinal markers and more than three states.
Data
First we will simulate data from a joint model with a single linear mixed effects model and a multi-state process with three possible states. The multi-state process can be visualized as:
library("ggplot2") d <- data.frame("xmin" = c(0, 45, 22.5), "xmax" = c(15, 60, 37.5), "ymin" = c(50, 50, 0), "ymax" = c(60, 60, 15)) dline <- data.frame("x1" = c(15), "y1" = c(55), "xend" = c(45), "yend" = c(55)) dcurve <- data.frame("x1" = c(7.5, 52.5), "y1" = c(50, 50), "xend" = c(22.4, 37.4), "yend" = c(7.5, 7.5), "curvature" = c(1, -1)) ggplot() + geom_rect(data = d, aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax), fill = "#ffffff", color = 'black', size = 1) + geom_text(aes(x = 7.5, y = 55, label = "Healthy"), size = 6.5) + geom_text(aes(x = 52.5, y = 55, label = "Illness"), size = 6.5) + geom_text(aes(x = 30, y = 7, label = "Death"), size = 6.5) + geom_text(aes(x = 30, y = 52.5, label = 'h[1][2](t)'), size = 4, parse = TRUE) + geom_text(aes(x = 12.5, y = 30, label = "h[1][3](t)"), size = 4, parse = TRUE) + geom_text(aes(x = 47.5, y = 30, label = "h[2][3](t)"), size = 4, parse = TRUE) + geom_segment(data = dline, aes(x = x1, y = y1, xend = xend, yend = yend), size = 1, arrow = arrow(length = unit(0.02, "npc"))) + geom_curve(data = dcurve[1, ], aes(x = x1, y = y1, xend = xend, yend = yend), size = 1, curvature = 0.3, arrow = arrow(length = unit(0.02, "npc"))) + geom_curve(data = dcurve[2, ], aes(x = x1, y = y1, xend = xend, yend = yend), size = 1, curvature = -0.3, arrow = arrow(length = unit(0.02, "npc"))) + ylim(0, 60) + xlim(0, 60) + theme_void()
where all subjects start from state "Healthy" and then can transition to either state "Illness" and then state "Death" or directly to state "Death". In this case, states "Healthy" and "Illness" are transient states as the subject, when occupying these states, can still transition to other states whereas "Death" is an absorbing state as when a subject reaches this state then no further transitions can occur. This means that three transitions are possible: $1 \rightarrow 2$, $1 \rightarrow 3$ and $2 \rightarrow 3$ with transition intensities $h_{12}\left(t\right)$, $h_{13}\left(t\right)$ and $h_{23}\left(t\right)$ respectively.
For our example the default functional form is assumed, i.e., that the linear predictor $\eta(t)$ of the mixed model is associated with the each transition intensity at time $t$. The following piece of code simulates the data:
# function ms_setup needs to be sourced to be used in the simulation ms_setup <- function (data, timevars, statusvars, transitionmat, id, covs = NULL) { # setup times matrix with NAs # First row is NA as this is starting state timesmat <- matrix(NA, nrow(data), length(timevars)) timecols_data <- which(colnames(data) %in% timevars[!is.na(timevars)]) timesmat[, -which(is.na(timevars))] <- as.matrix(data[, timecols_data]) # setup status matrix with NAs # First row is NA as this is starting state statusmat <- matrix(NA, nrow(data), length(statusvars)) statuscols_data <- which(colnames(data) %in% statusvars[!is.na(statusvars)]) statusmat[, -which(is.na(statusvars))] <- as.matrix(data[, statuscols_data]) # ensure convert to matrices timesmat <- as.matrix(timesmat) statusmat <- as.matrix(statusmat) # check dimesnions are the same if (any(dim(timesmat) != dim(statusmat))) stop("Dimensions of \"time\" and \"status\" data should be equal") # components # number of unique subjects n_subj <- nrow(timesmat) # number of states n_states <- dim(transitionmat)[1] # set start state to 1 and start time to 0 for all subjects # ATTENTION: this needs to be adjusted to more flexible to allow subjects starting at different states # this could be achieved by a requesting a separate argument (vector with starting state) starting_state <- rep(1, n_subj) starting_time <- rep(0, n_subj) idnam <- id id <- data[[id]] order_id <- order(id) out <- ms_prepdat(timesmat = timesmat, statusmat = statusmat, id = id, starting_time = starting_time, starting_state = starting_state, transitionmat = transitionmat, original_states = (1:nrow(transitionmat)), longmat = NULL) out <- as.data.frame(out) names(out) <- c(idnam, "from_state", "to_state", "transition", "Tstart", "Tstop", "status") out$time <- out$Tstop - out$Tstart out <- out[, c(1:6, 8, 7)] ord <- order(out[, 1], out[, 5], out[, 2], out[, 3]) out <- out[ord, ] row.names(out) <- 1:nrow(out) # Covariates if (!is.null(covs)) { n_covs <- length(covs) cov_cols <- match(covs, names(data)) cov_names <- covs covs <- data[, cov_cols] if (!is.factor(out[, 1])) out[, 1] <- factor(out[, 1]) n_per_subject <- tapply(out[, 1], out[, 1], length) if (n_covs > 1) covs <- covs[order_id, , drop = FALSE] if (n_covs == 1) { longcovs <- rep(covs, n_per_subject) longcovs <- longcovs[ord] longcovs <- as.data.frame(longcovs) names(longcovs) <- cov_names } else { longcovs <- lapply(1:n_covs, function(i) rep(covs[, i], n_per_subject)) longcovs <- as.data.frame(longcovs) names(longcovs) <- cov_names } out <- cbind(out, longcovs) } # add attributes maybe # add specific class maybe # need to add functionality for covariates (e.g. like keep in mstate) return(out) } # used internally by ms_setup and needs also to be sourced ms_prepdat <- function (timesmat, statusmat, id, starting_time, starting_state, transitionmat, original_states, longmat) { if (is.null(nrow(timesmat))) return(longmat) if (nrow(timesmat) == 0) return(longmat) from_states <- apply(!is.na(transitionmat), 2, sum) to_states <- apply(!is.na(transitionmat), 1, sum) absorbing_states <- which(to_states == 0) starts <- which(from_states == 0) new_states <- starting_state new_times <- starting_time rmv <- NULL for (i in 1:starts) { subjects <- which(starting_state == starts) n_start <- length(subjects) to_states_2 <- which(!is.na(transitionmat[starts, ])) trans_states <- transitionmat[starts, to_states_2] n_trans_states <- length(to_states_2) if (all(n_start > 0, n_trans_states > 0)) { Tstart <- starting_time[subjects] Tstop <- timesmat[subjects, to_states_2, drop = FALSE] Tstop[Tstop <= Tstart] <- Inf state_status <- statusmat[subjects, to_states_2, drop = FALSE] mintime <- apply(Tstop, 1, min) hlp <- Tstop * 1 / state_status hlp[Tstop == 0 & state_status == 0] <- Inf next_time <- apply(hlp, 1, min) censored <- which(is.infinite(apply(hlp, 1, min))) wh <- which(mintime < next_time) whminc <- setdiff(wh, censored) if (length(whminc) > 0) { whsubjs <- id[subjects[whminc]] whsubjs <- paste(whsubjs, collapse = " ") warning("Subjects ", whsubjs, " Have smaller transition time with status = 0, larger transition time with status = 1, from starting state ", original_states[starts]) } next_time[censored] <- mintime[censored] if (ncol(hlp) > 1) { hlpsrt <- t(apply(hlp, 1, sort)) warn1 <- which(hlpsrt[, 1] - hlpsrt[, 2] == 0) if (length(warn1) > 0) { isw <- id[subjects[warn1]] isw <- paste(isw, collapse = " ") hsw <- hlpsrt[warn1, 1] hsw <- paste(hsw, collapse = " ") warning("simultaneous transitions possible for subjects ", isw, " at times ", hsw, " -> Smallest receiving state will be used") } } if (length(censored) > 0) { next_state <- apply(hlp[-censored, , drop = FALSE], 1, which.min) absorbed <- (1:n_start)[-censored][which(to_states_2[next_state] %in% absorbing_states)] } else { next_state <- apply(hlp, 1, which.min) absorbed <- (1:n_start)[which(to_states_2[next_state] %in% absorbing_states)] } states_matrix <- matrix(0, n_start, n_trans_states) if (length(censored) > 0) { states_matrix_min <- states_matrix[-censored, , drop = FALSE] } else { states_matrix_min <- states_matrix } if (nrow(states_matrix_min) > 0) states_matrix_min <- t(sapply(1:nrow(states_matrix_min), function(i) { x <- states_matrix_min[i, ] x[next_state[i]] <- 1 return(x) })) if (length(censored) > 0) { states_matrix[-censored, ] <- states_matrix_min } else { states_matrix <- states_matrix_min } mm <- matrix(c(rep(id[subjects], rep(n_trans_states, n_start)), rep(original_states[starts], n_trans_states * n_start), rep(original_states[to_states_2], n_start), rep(trans_states, n_start), rep(Tstart, rep(n_trans_states, n_start)), rep(next_time, rep(n_trans_states, n_start)), as.vector(t(states_matrix))), n_trans_states * n_start, 7) longmat <- rbind(longmat, mm) rmv <- c(rmv, subjects[c(censored, absorbed)]) if (length(censored) > 0) { new_states[subjects[-censored]] <- to_states_2[next_state] } else { new_states[subjects] <- to_states_2[next_state] } if (length(censored) > 0) { new_times[subjects[-censored]] <- next_time[-censored] } else { new_times[subjects] <- next_time } } } if (length(rmv) > 0) { timesmat <- timesmat[-rmv, ] statusmat <- statusmat[-rmv, ] new_times <- new_times[-rmv] new_states <- new_states[-rmv] id <- id[-rmv] } n_states <- nrow(transitionmat) idx <- rep(1, n_states) idx[starts] <- 0 idx <- cumsum(idx) new_states <- idx[new_states] Recall(timesmat = timesmat[, -starts], statusmat = statusmat[, -starts], id = id, starting_time = new_times, starting_state = new_states, transitionmat = transitionmat[-starts, -starts], original_states = original_states[-starts], longmat = longmat) }
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 = 10000L)$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) # initiate vectors to save true event times trueT01 <- numeric(N) trueT02 <- numeric(N) trueT12 <- numeric(N) # sample censoring times mean.Cens <- 9 C <- runif(N, 0, 2 * mean.Cens) # simulate time-to-event data 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 } # arrange data in appropriate format 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 <- JMbayes2:::ms_setup(data = datasurv, timevars = c(NA, 't_illness', 't_death'), statusvars = c(NA, 'illness', 'death'), transitionmat = tmat, id = 'id', covs = covs) data_mstate$transition <- factor(data_mstate$transition) out <- list("datasets" = list("long_data" = datalongit, "data_mstate" = data_mstate))
The data for the muti state process need to be in the appropriate long format:
head(out$datasets$data_mstate, n = 5L)
for example subject 1 experienced the following transition: $1 \rightarrow 2$ and therefore is represented in 3 rows, one for each transition, because all of these transitions were plausible. On the other hand subject 2 is only represented by two rows, only for transitions $1 \rightarrow 2$ and $1 \rightarrow 3$ since these are the only transitions that are possible from state 1. That is, since subject 2 never actually transitioned to state 2, transition $2 \rightarrow 3$ was never possible and therefore no row for this transition is in the dataset. It is also importnt to note that the time in the dataset follows the counting process formulation with intervals specified by Tstart and Tstop and that there is a variable (in this case transition) which indicates to which transition the row correspond to.
Fitting the model
As soon data in the appropriate format are available, fitting the model is very straightforward. First we fit a linear mixed model using the lme() function from package nlme:
mixedmodel <- lme(Y ~ times + X, random = ~ times | id, data = out$datasets$long_data)
then we fit a multi-state model using function coxph() from package survival making sure we use the counting process specification and that we add strata(transition) to stratify by the transition indicator variable in the dataset:
msmodel <- coxph(Surv(Tstart, Tstop, status) ~ X + strata(transition), data = out$datasets$data_mstate)
Finally, to fit the joint model we simply run:
jm_ms_model <- jm(msmodel, mixedmodel, time_var = "times", functional_forms = ~ value(Y):transition, n_iter = 10000L, GK_k = 7L) summary(jm_ms_model)
which differs from a default call to jm() by the addition of the functional_forms argument by which we specify that we want an "interaction" between the value of the marker and each transition which translates into a separate association parameter for the longitudinal marker and each transition.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.