View source: R/joint_surv_VA.R
joint_ms_format | R Documentation |
Formats a parameter vector by putting the model parameters into a list
with elements for each type of parameter.
joint_ms_format(object, par = object$start_val)
object |
a joint_ms object from |
par |
parameter vector to be formatted. |
A list with the following elements:
markers |
list with an element for each marker. The lists contains an
element called |
survival |
list with an element for each survival outcome. The lists
contains an element called |
vcov |
contains three covariance matrices called |
# 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, ders = list(0L, c(0L, -1L)))
# find the starting values
start_vals <- joint_ms_start_val(model_ptr)
# format the starting values
joint_ms_format(model_ptr,start_vals)
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