log_llh_rcpp: 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
)

Value

The value of the log-likelihood

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