View source: R/joint_surv_VA.R
joint_ms_ptr | R Documentation |
Creates a joint_ms Object to Estimate a Joint Survival and Marker Model
joint_ms_ptr( markers = list(), survival_terms = list(), max_threads = 1L, quad_rule = NULL, cache_expansions = TRUE, gh_quad_rule = NULL, ders = NULL )
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 |
An object of joint_ms
class with the needed C++ and R objects
to estimate the model.
joint_ms_opt
, joint_ms_lb
,
joint_ms_hess
, and joint_ms_start_val
.
# 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)
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