R/get_predictions_geeglm.R

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

get_predictions_geeglm <- function(model,
                                   fitfram,
                                   ci_level,
                                   linv,
                                   type,
                                   model_class,
                                   value_adjustment,
                                   terms,
                                   condition,
                                   ...) {
  se <- (!is.null(ci_level) && !is.na(ci_level))

  # compute ci, two-ways
  if (!is.null(ci_level) && !is.na(ci_level)) {
    ci <- (1 + ci_level) / 2
  } else {
    ci <- 0.975
  }

  # degrees of freedom
  dof <- .get_df(model)
  tcrit <- stats::qt(ci, df = dof)

  # get predictions
  prdat <- stats::predict(
    model,
    newdata = fitfram,
    ...
  )


  fitfram$predicted <- as.vector(prdat)


  # get standard errors from variance-covariance matrix
  se.pred <- .standard_error_predictions(
    model = model,
    prediction_data = fitfram,
    value_adjustment = value_adjustment,
    type = type,
    terms = terms,
    model_class = model_class,
    vcov = NULL,
    vcov_args = NULL,
    condition = condition,
    interval = NULL
  )


  if (.check_returned_se(se.pred) && isTRUE(se)) {
    se.fit <- se.pred$se.fit
    fitfram <- se.pred$prediction_data

    # CI
    fitfram$conf.low <- linv(fitfram$predicted - tcrit * se.fit)
    fitfram$conf.high <- linv(fitfram$predicted + tcrit * se.fit)

    # copy standard errors
    attr(fitfram, "std.error") <- se.fit
    attr(fitfram, "prediction.interval") <- attr(se.pred, "prediction_interval")
  } else {
    # CI
    fitfram$conf.low <- NA
    fitfram$conf.high <- NA
  }

  fitfram$predicted <- linv(fitfram$predicted)

  fitfram
}