R/Tabu_refit.R

In ShortForm: Automatic Short Form Creation

#' Given a fitted lavaan model and a search table, refits the model using the search
#' table as specifying what changes should be done (parmeters fixed/freed).
#'
#' This is not meant to be called explicity as \link{tabu.sem} uses this
#' internally for model refitting.
#'
#' @param fitted.model fitted model of class lavaan
#' @param ptab search table
#'
#' @return An object of class \code{lavaan} if the new model fits, or an object of class \code{try-error} if the model update fails.
#' @family Tabu Search
#' @import lavaan
#' @export
#'
#' @author Carl F. Falk
#' @references \doi{10.1080/10705511.2017.1409074}

refit.model <- function(fitted.model, ptab) {

  # Extract parameter table
  tab <- lavaan::parTable(fitted.model)

  # Expand to get full table
  fulltab <- lav_partable_full(tab)
  mergetab <- lavaan::lav_partable_merge(tab, fulltab, remove.duplicated = TRUE, warn = FALSE)

  # Modify parameter table based on new input matrix

  # Obtain indices for matching
  mergetab$labels <- paste(mergetab$lhs, mergetab$op, mergetab$rhs, sep = "")
  ptab$labels <- paste(ptab$lhs, ptab$op, ptab$rhs, sep = "")
  midx <- vector("numeric")
  nidx <- vector("numeric")
  for (j in 1:nrow(ptab)) {
    idx <- which(ptab$labels[j] == mergetab$labels & ptab$block[j] == mergetab$block)
    if (length(idx) > 0) {
      midx <- c(midx, idx)
      nidx <- c(nidx, j)
    }
  }

  # Replace free parameters
  mergetab$free[midx] <- ptab$free[nidx]

  # If some parameters are now fixed; what are they fixed to?<-function
  mergetab$ustart[mergetab$free != 0] <- NA
  mergetab[midx, ]$ustart[mergetab[midx, ]$free == 0] <- ptab[nidx, ]$nullval[ptab[nidx, ]$free == 0]

  # Get rid of old parameter estimates and starting values
  mergetab$est <- NULL
  mergetab$se <- NULL
  mergetab$start <- NULL
  mergetab$labels <- NULL

  # Re-order values in mergetab
  lvnames <- lavaan::lavNames(mergetab, "lv")
  ovnames <- lavaan::lavNames(mergetab, "ov")
  mergetab <- mergetab[order(
    mergetab$block, # by group (or block)
    is.na(match(mergetab$lhs, c(lvnames))), # put latent vars first
    mergetab$op, # by op w/in lv and ov sections
    match(mergetab$lhs, c(lvnames, ovnames)), # then by lv and ov names on lhs
    match(mergetab$rhs, c(lvnames, ovnames))
  ), ] # then by same on rhs

  # Refit model
  prevmodel <- as.list(fitted.model@call)
  prevmodel$model <- mergetab
  newmod <- try(do.call(eval(parse(text = "lavaan::lavaan")), prevmodel[-1]), silent = TRUE)

  return(newmod)
}