dynLong: Dynamic predictions for the longitudinal data sub-model

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/dynLong.R

Description

Calculates the conditional expected longitudinal values for a new subject from the last observation time given their longitudinal history data and a fitted mjoint object.

Usage

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dynLong(
  object,
  newdata,
  newSurvData = NULL,
  u = NULL,
  type = "first-order",
  M = 200,
  scale = 1.6,
  ci,
  progress = TRUE,
  ntimes = 100,
  level = 1
)

Arguments

object

an object inheriting from class mjoint for a joint model of time-to-event and multivariate longitudinal data.

newdata

a list of data.frame objects for each longitudinal outcome for a single new patient in which to interpret the variables named in the formLongFixed and formLongRandom formulae of object. As per mjoint, the list structure enables one to include multiple longitudinal outcomes with different measurement protocols. If the multiple longitudinal outcomes are measured at the same time points for each patient, then a data.frame object can be given instead of a list. It is assumed that each data frame is in long format.

newSurvData

a data.frame in which to interpret the variables named in the formSurv formulae from the mjoint object. This is optional, and if omitted, the data will be searched for in newdata. Note that no event time or censoring indicator data are required for dynamic prediction. Defaults to newSurvData=NULL.

u

an optional time that must be greater than the last observed measurement time. If omitted (default is u=NULL), then conditional failure probabilities are reported for all observed failure times in the mjoint object data from the last known follow-up time of the subject.

type

a character string for whether a first-order (type="first-order") or Monte Carlo simulation approach (type="simulated") should be used for the dynamic prediction. Defaults to the computationally faster first-order prediction method.

M

for type="simulated", the number of simulations to performs. Default is M=200.

scale

a numeric scalar that scales the variance parameter of the proposal distribution for the Metropolis-Hastings algorithm, which therefore controls the acceptance rate of the sampling algorithm.

ci

a numeric value with value in the interval (0, 1) specifying the confidence interval level for predictions of type='simulated'. If missing, defaults to ci=0.95 for a 95% confidence interval. If type='first-order' is used, then this argument is ignored.

progress

logical: should a progress bar be shown on the console to indicate the percentage of simulations completed? Default is progress=TRUE.

ntimes

an integer controlling the number of points to discretize the extrapolated time region into. Default is ntimes=100.

level

an optional integer giving the level of grouping to be used in extracting the residuals from object. Level values increase from outermost to innermost grouping, with level 0 corresponding to the population model fit and level 1 corresponding to subject-specific model fit. Defaults to level=1.

Details

Dynamic predictions for the longitudinal data sub-model based on an observed measurement history for the longitudinal outcomes of a new subject are based on either a first-order approximation or Monte Carlo simulation approach, both of which are described in Rizopoulos (2011). Namely, given that the subject was last observed at time t, we calculate the conditional expectation of each longitudinal outcome at time u as

E[y_k(u) | T ≥ t, y, θ] \approx x^T(u)β_k + z^T(u)\hat{b}_k,

where T is the failure time for the new subject, and y is the stacked-vector of longitudinal measurements up to time t.

First order predictions

For type="first-order", \hat{b} is the mode of the posterior distribution of the random effects given by

\hat{b} = {\arg \max}_b f(b | y, T ≥ t; θ).

The predictions are based on plugging in θ = \hat{θ}, which is extracted from the mjoint object.

Monte Carlo simulation predictions

For type="simulated", θ is drawn from a multivariate normal distribution with means \hat{θ} and variance-covariance matrix both extracted from the fitted mjoint object via the coef() and vcov() functions. \hat{b} is drawn from the the posterior distribution of the random effects

f(b | y, T ≥ t; θ)

by means of a Metropolis-Hasting algorithm with independent multivariate non-central t-distribution proposal distributions with non-centrality parameter \hat{b} from the first-order prediction and variance-covariance matrix equal to scale \times the inverse of the negative Hessian of the posterior distribution. The choice os scale can be used to tune the acceptance rate of the Metropolis-Hastings sampler. This simulation algorithm is iterated M times, at each time calculating the conditional survival probability.

Value

A list object inheriting from class dynLong. The list returns the arguments of the function and a list containing K data.frames of 2 columns, with first column (named timeVar[k]; see mjoint) denoting times and the second column (named y.pred) denoting the expected outcome at each time point.

Author(s)

Graeme L. Hickey (graemeleehickey@gmail.com)

References

Rizopoulos D. Dynamic predictions and prospective accuracy in joint models for longitudinal and time-to-event data. Biometrics. 2011; 67: 819–829.

See Also

mjoint, dynSurv.

Examples

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## Not run: 
# Fit a joint model with bivariate longitudinal outcomes

data(heart.valve)
hvd <- heart.valve[!is.na(heart.valve$log.grad) & !is.na(heart.valve$log.lvmi), ]

fit2 <- mjoint(
    formLongFixed = list("grad" = log.grad ~ time + sex + hs,
                         "lvmi" = log.lvmi ~ time + sex),
    formLongRandom = list("grad" = ~ 1 | num,
                          "lvmi" = ~ time | num),
    formSurv = Surv(fuyrs, status) ~ age,
    data = list(hvd, hvd),
    inits = list("gamma" = c(0.11, 1.51, 0.80)),
    timeVar = "time",
    verbose = TRUE)

hvd2 <- droplevels(hvd[hvd$num == 1, ])
dynLong(fit2, hvd2)
dynLong(fit2, hvd2, u = 7) # outcomes at 7-years only

out <- dynLong(fit2, hvd2, type = "simulated")
out

## End(Not run)

joineRML documentation built on Jan. 5, 2021, 5:07 p.m.