log_llh_rcpp {FlexVarJM}

Log-likelihood computation in RCPP

Description

Log-likelihood computation in RCPP

Usage

log_llh_rcpp(
  param,
  nb.e.a,
  nb.priorMean.beta,
  nb.alpha,
  competing_risk,
  nb.alpha.CR,
  variability_hetero,
  S,
  Zq,
  sharedtype,
  sharedtype_CR,
  hazard_baseline,
  hazard_baseline_CR,
  ord.splines,
  Xtime,
  Utime,
  nb_pointsGK,
  Xs,
  Us,
  Xslope,
  Uslope,
  Xs.slope,
  Us.slope,
  indices_beta_slope,
  Time,
  st_calc,
  B,
  Bs,
  wk,
  Z,
  P,
  left_trunc,
  Z_CR,
  X_base,
  offset,
  U,
  y.new.prog,
  event1,
  event2,
  Ind,
  Xs.0,
  Us.0,
  Xs.slope.0,
  Us.slope.0,
  P.0,
  st.0,
  Bs.0,
  B.CR,
  Bs.CR,
  Bs.0.CR,
  nb.e.a.sigma = nb.e.a.sigma,
  nb.omega = nb.omega,
  Otime = Otime,
  Wtime = Wtime,
  Os = Os,
  Ws = Ws,
  O_base = O_base,
  W_base = W_base,
  correlated_re = correlated_re,
  Os.0 = Os.0,
  Ws.0 = Ws.0
)

Arguments

param

a vector : paramaters to be estimated

nb.e.a

integer : number of RE

nb.priorMean.beta

integer : number of fixed effects

nb.alpha

integer : number of covariates in survival model

competing_risk

boolean : allow competing risk or not, FALSE by default

nb.alpha.CR

integer : number of covariates in survival model for competing risks

variability_hetero

boolean : allow the heterogeneous variability or not

S

integer : the number of QMC points

Zq

vector : sobol points

sharedtype

vector : dependence structure for survival model : "RE" (random effects) or "CV" (current value) or "CVS" (current value and slope) or "S" (slope)

sharedtype_CR

vector : dependence structure for competing risk survival model : "RE" (random effects) or "CV" (current value) or "CVS" (current value and slope) or "S" (slope)

hazard_baseline

char : baseline hazard function : "Exponential" or "Weibull" or "Splines"

hazard_baseline_CR

char : baseline hazard function, competing risk : "Exponential" or "Weibull" or "Splines"

ord.splines

integer : the order of splines function for baseline hazard function

Xtime

matrix : fixed effects at event time

Utime

matrix : RE at event time

nb_pointsGK

integer : number of points for Gauss-Kronrod approximation, 7 or 15 (default)

Xs

matrix : fixed effects at Gauss-Kronrod times

Us

matrix : RE at Gauss-Kronrod times

Xslope

matrix : fixed effects of slope at event times

Uslope

matrix : RE of slope at event times

Xs.slope

matrix : fixed effects of slope at Gauss-Kronrod times

Us.slope

matrix : RE of slope at Gauss-Kronrod times

indices_beta_slope

vector : position of beta which will be used in the slope computation

Time

vector : observed event times

st_calc

matrix : Gauss-Kronrod times

B

matrix : splines for baseline hazard function of event 1

Bs

matrix : splines for baseline survival function of event 1

wk

vector : Gauss-Kronrod weights

Z

matrix : covariates for survival function of event 1

P

vector : Time/2

left_trunc

boolean : left truncation indicator

Z_CR

matrix : covariates for survival function of event 2

X_base

matrix : fixed effects for longitudinal submodel

offset

vector : number of lines per subjects

U

matrix : RE for longitudinal submodel

y.new.prog

vector : y measures for longitudinal submodel

event1

vector : event 1 indicator

event2

vector : event 2 indicator

Ind

integer : number of subjects

Xs.0

same for left truncation

Us.0

same for left truncation

Xs.slope.0

same for left truncation

Us.slope.0

same for left truncation

P.0

same for left truncation

st.0

same for left truncation

Bs.0

same for left truncation

B.CR

same for left truncation

Bs.CR

same for left truncation

Bs.0.CR

same for left truncation

nb.e.a.sigma

integer : number of RE for variability

nb.omega

integer : number of fixed effects for variability

Otime

matrix : fixed effects of variability at event time

Wtime

matrix : RE of variability at event time

Os

matrix : fixed effects of variability at Gauss-Kronrod times

Ws

matrix : random effects of variability at Gauss-Kronrod times

O_base

matrix : fixed effects for variability

W_base

matrix : fixed effects for variability

correlated_re

boolean : indicator to allow all the random effects to be correlated

Os.0

matrix : same for left truncation

Ws.0

matrix : same for left truncation

Value

The value of the log-likelihood