joint_ms_ptr {VAJointSurv} | R Documentation |
Creates a joint_ms Object to Estimate a Joint Survival and Marker Model
Description
Creates a joint_ms Object to Estimate a Joint Survival and Marker Model
Usage
joint_ms_ptr(
markers = list(),
survival_terms = list(),
max_threads = 1L,
quad_rule = NULL,
cache_expansions = TRUE,
gh_quad_rule = NULL,
ders = NULL
)
Arguments
markers |
either an object from |
survival_terms |
either an object from |
max_threads |
maximum number of threads to use. |
quad_rule |
list with nodes and weights for a quadrature rule for the integral from zero to one. |
cache_expansions |
|
gh_quad_rule |
list with two numeric vectors called node and weight
with Gauss–Hermite quadrature nodes and weights to handle delayed entry.
A low number of quadrature nodes and weights is used when |
ders |
a |
Value
An object of joint_ms
class with the needed C++ and R objects
to estimate the model.
See Also
joint_ms_opt
, joint_ms_lb
,
joint_ms_hess
, and joint_ms_start_val
.
Examples
# load in the data
library(survival)
data(pbc, package = "survival")
# re-scale by year
pbcseq <- transform(pbcseq, day_use = day / 365.25)
pbc <- transform(pbc, time_use = time / 365.25)
# create the marker terms
m1 <- marker_term(
log(bili) ~ 1, id = id, data = pbcseq,
time_fixef = bs_term(day_use, df = 5L),
time_rng = poly_term(day_use, degree = 1L, raw = TRUE, intercept = TRUE))
m2 <- marker_term(
albumin ~ 1, id = id, data = pbcseq,
time_fixef = bs_term(day_use, df = 5L),
time_rng = poly_term(day_use, degree = 1L, raw = TRUE, intercept = TRUE))
# base knots on observed event times
bs_term_knots <-
with(pbc, quantile(time_use[status == 2], probs = seq(0, 1, by = .2)))
boundary <- c(bs_term_knots[ c(1, length(bs_term_knots))])
interior <- c(bs_term_knots[-c(1, length(bs_term_knots))])
# create the survival term
s_term <- surv_term(
Surv(time_use, status == 2) ~ 1, id = id, data = pbc,
time_fixef = bs_term(time_use, Boundary.knots = boundary, knots = interior))
# create the C++ object to do the fitting
model_ptr <- joint_ms_ptr(
markers = list(m1, m2), survival_terms = s_term,
max_threads = 2L)