R/get_predictions_lrm.R

In javifar/ggeffects: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs

get_predictions_lrm <- function(model, fitfram, ci.lvl, linv, ...) {
  # does user want standard errors?
  se <- !is.null(ci.lvl) && !is.na(ci.lvl)

  # compute ci, two-ways
  if (!is.null(ci.lvl) && !is.na(ci.lvl))
    ci <- (1 + ci.lvl) / 2
  else
    ci <- .975

  prdat <-
    stats::predict(
      model,
      newdata = fitfram,
      type = "lp",
      se.fit = se,
      ...
    )

  # copy predictions
  fitfram$predicted <- stats::plogis(prdat$linear.predictors)

  # did user request standard errors? if yes, compute CI
  if (se) {

    # calculate CI
    fitfram$conf.low <- stats::plogis(prdat$linear.predictors - stats::qnorm(ci) * prdat$se.fit)
    fitfram$conf.high <- stats::plogis(prdat$linear.predictors + stats::qnorm(ci) * prdat$se.fit)

    # copy standard errors
    attr(fitfram, "std.error") <- prdat$se.fit

  } else {
    # No CI
    fitfram$conf.low <- NA
    fitfram$conf.high <- NA
  }

  fitfram
}