R/lccBuilder.R

In lcc: Longitudinal Concordance Correlation

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# Package: lcc                                                        #
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# File: lccBuilder.R                                                  #
# Contains: lccBuilder function                                       #
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# Written by Thiago de Paula Oliveira                                 #
# copyright (c) 2017-18, Thiago P. Oliveira                           #
#                                                                     #
# First version: 11/10/2017                                           #
# Last update: 29/07/2019                                             #
# License: GNU General Public License version 2 (June, 1991) or later #
#                                                                     #
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##' @title Internal Function to Estimate the Longitudinal Concordance
##'   Correlation.
##'
##' @description This is an internally called function used to estimate
##'   the longitudinal concordance correlation (LCC).
##'
##' @usage NULL
##'
##' @return returns a vector or list containing the longitudinal
##'   concordance correlation estimates.
##' @author Thiago de Paula Oliveira, \email{thiago.paula.oliveira@@alumni.usp.br}
##'
##' @keywords internal
lccBuilder <- function(G, diffbeta, tk, q_r, q_f, g, sig2_epsilon, delta,
                       deltal, model) {
  Tk_r <- sapply(0:q_r, function(x) tk^x)
  Tk_f <- sapply(0:q_f, function(x) tk^x)
  S2 <- try((as.matrix(Tk_f[,c(1:(length(diffbeta)))]) %*% (diffbeta))^2,
            silent = TRUE)
  if (!inherits(S2, "try-error")) {
    tGt <- diag(Tk_r %*% G %*% t(Tk_r))
    varcomp <- summary(model)
    var.f <- class(varcomp$modelStruct$varStruct)[1]
    rho <- list()
    if(var.f == "varIdent") {
      gd <- g(delta)
      gdl <- g(deltal)
      ldb2 <- length(gdl)
      for(i in 1:ldb2){
        rho[[i]] <- as.numeric(
          tGt / (tGt + 0.5 * (sig2_epsilon * (gd + gdl[i]) + S2))
        )
      }
    }
    if(var.f == "varExp") {
      if(attr(varcomp$modelStruct$varStruct, "formula")==~time){
        gd <- g(delta,tk)
        gdl <- g(deltal,tk)
        rho <-list(tGt / (tGt + 0.5 * (sig2_epsilon * (gd + gdl) + S2)),NA)
      } else {if(attr(varcomp$modelStruct$varStruct, "formula")==~time | method){
        gd <- g(delta,tk)
        ldb2 <- length(deltal)
        gdl<-list()
        for(i in 1:ldb2){
          gdl[[i]] <- g(deltal[i],tk)
          rho[[i]] <-
            as.numeric(
              unlist(
                tGt / (tGt + 0.5 * (sig2_epsilon * (gd + gdl[[i]]) + S2))
              )
            )
        }
      }else{print("method not implemented yet")}
      }
    }
    if(var.f == "NULL"){
      rho <- list(tGt / (tGt + sig2_epsilon + 0.5*S2),NA)
    }
    return(rho)
  }else{
    stop(print("Please, change the name of factor levels associated with
               method argument. Example:  levels M1, M2, M3, ..., Mn, with
               n=0, 1, 2, ..., N."), call. = FALSE)
  }
}