R/longst.R

In joineR: Joint Modelling of Repeated Measurements and Time-to-Event Data

#' @keywords internal
#' @import nlme
longst <- function(longdat, long.formula, model, longdat2) {
  
  if (model == "int") {
    rf <- as.formula(
      paste("~1", colnames(longdat)[1], sep = "|"))
  } else if (model == "intslope") {
    rf <- as.formula(
      paste(paste0("~", colnames(longdat)[3]), colnames(longdat)[1], sep = "|"))
  } else {
    tsq <- paste0(paste0("I(", paste(colnames(longdat)[3], "^2", sep = "")), ")")
    rf <- as.formula(
      paste(paste0("~", paste(colnames(longdat)[3], tsq, sep = "+")),
            colnames(longdat)[1], sep = "|"))
  }
  
  long.start <- nlme::lme(long.formula,
                          random = rf,
                          method = "ML", 
                          data = data.frame(longdat2),
                          na.action = na.omit,
                          control = lmeControl(maxIter = 1000, 
                                               msMaxIter = 1000,
                                               opt = "optim",
                                               tolerance = 1e-05,
                                               msTol = 1e-06))
  
  q <- dim(nlme::VarCorr(long.start))[1] - 1
  sigma.u <- as.matrix(nlme::getVarCov(long.start))
  rownames(sigma.u) <- paste("U_", 0:(q - 1), sep = "")
  colnames(sigma.u) <- paste("U_", 0:(q - 1), sep = "")
  if (model == "intslope") {
    corr <- as.numeric(nlme::VarCorr(long.start)[2, 3])
  } else if (model == "int") {
    corr <- NA
  } else if (model == "quad") {
    corr <- as.numeric(nlme::VarCorr(long.start)[2:3, 3])
  }
  sigma.z <- long.start$sigma^2
  ll <- long.start$logLik
  b1 <- nlme::fixef(long.start)
  
  list("b1" = data.frame(b1),
       "sigma.z" = sigma.z, # variance, not SD
       "sigma.u" = sigma.u,
       "corr" = corr,
       "log.like" = ll)
  
}