R/logbin.smooth.allref.r

In mdonoghoe/logbin: Relative Risk Regression Using the Log-Binomial Model

logbin.smooth.allref <- function(object, data = environment(object), type = c("cem","em"), mono,
                                    logbin.smooth.spec, num.knots)
{
  type <- match.arg(type)
  t <- if (missing(data)) terms(object)
       else terms(object, data = data)
    
  int <- attr(t, "response")
    
  nobs <- nrow(data)
  termlist <- attr(t, "term.labels")
  nvar <- length(termlist)
  smoothlist <- sapply(logbin.smooth.spec$smooth.spec, "[[", "term")
  smoothtype <- sapply(logbin.smooth.spec$smooth.spec, class)
  names(smoothtype) <- smoothlist
  nsmvar <- length(smoothlist)
    
  if (length(num.knots) != nsmvar)
      stop(gettextf("num.knots has length %d should equal %d (number of smooth terms)",
                    length(num.knots), nsmvar), domain = NA)
  num.knots <- as.vector(num.knots, mode = "integer")
  names(num.knots) <- smoothlist
  
  if (missing(mono) || is.null(mono)) mono <- rep(FALSE, nvar)
  monotonic <- rep(FALSE, nvar)
  names(monotonic) <- termlist
  monotonic[mono] <- TRUE
  names(monotonic) <- termlist
  
  allref <- list()
  for (smth in smoothlist) {
    allref[[smth]] <- list()
    if (smoothtype[smth] == "Iso.smooth")
      allref[[smth]][[1]] <- 1
    else if (smoothtype[smth] == "B.smooth") {
      if (monotonic[smth]) allref[[smth]][[1]] <- 1:(num.knots[smth] + 3)
      else if(type == "em") allref[[smth]][[1]] <- num.knots[smth] + 3
      else allref[[smth]] <- as.list(rev(1:(num.knots[smth] + 3)))
    } else
      stop("smooth type not recognized. Only B() and Iso() are supported by logbin.smooth")
  }
  
  list(allref = allref, terms = t, data = data, monotonic = monotonic)
}