Expected Values of the Posterior Predictive Distribution

Source: R/posterior_epred.R

This method is an alias of posterior_epred.brmsfit with additional arguments for obtaining summaries of the computed draws.

# S3 method for brmsfit
fitted(
  object,
  newdata = NULL,
  re_formula = NULL,
  scale = c("response", "linear"),
  resp = NULL,
  dpar = NULL,
  nlpar = NULL,
  ndraws = NULL,
  draw_ids = NULL,
  sort = FALSE,
  summary = TRUE,
  robust = FALSE,
  probs = c(0.025, 0.975),
  ...
)

Arguments

object

An object of class brmsfit.

newdata

An optional data.frame for which to evaluate predictions. If NULL (default), the original data of the model is used. NA values within factors are interpreted as if all dummy variables of this factor are zero. This allows, for instance, to make predictions of the grand mean when using sum coding.

re_formula

formula containing group-level effects to be considered in the prediction. If NULL (default), include all group-level effects; if NA, include no group-level effects.

scale

Either "response" or "linear". If "response", results are returned on the scale of the response variable. If "linear", results are returned on the scale of the linear predictor term, that is without applying the inverse link function or other transformations.

resp

Optional names of response variables. If specified, predictions are performed only for the specified response variables.

dpar

Optional name of a predicted distributional parameter. If specified, expected predictions of this parameters are returned.

nlpar

Optional name of a predicted non-linear parameter. If specified, expected predictions of this parameters are returned.

ndraws

Positive integer indicating how many posterior draws should be used. If NULL (the default) all draws are used. Ignored if draw_ids is not NULL.

draw_ids

An integer vector specifying the posterior draws to be used. If NULL (the default), all draws are used.

sort

Logical. Only relevant for time series models. Indicating whether to return predicted values in the original order (FALSE; default) or in the order of the time series (TRUE).

summary

Should summary statistics be returned instead of the raw values? Default is TRUE..

robust

If FALSE (the default) the mean is used as the measure of central tendency and the standard deviation as the measure of variability. If TRUE, the median and the median absolute deviation (MAD) are applied instead. Only used if summary is TRUE.

probs

The percentiles to be computed by the quantile function. Only used if summary is TRUE.

...

Further arguments passed to prepare_predictions that control several aspects of data validation and prediction.

Value

An array of predicted mean response values. If summary = FALSE the output resembles those of

posterior_epred.brmsfit.

If summary = TRUE the output depends on the family: For categorical and ordinal families, the output is an N x E x C array, where N is the number of observations, E is the number of summary statistics, and C is the number of categories. For all other families, the output is an N x E matrix. The number of summary statistics E is equal to 2 + length(probs): The Estimate column contains point estimates (either mean or median depending on argument robust), while the

Est.Error column contains uncertainty estimates (either standard deviation or median absolute deviation depending on argument

robust). The remaining columns starting with Q contain quantile estimates as specified via argument probs.

In multivariate models, an additional dimension is added to the output which indexes along the different response variables.

Examples

if (FALSE) {
## fit a model
fit <- brm(rating ~ treat + period + carry + (1|subject),
           data = inhaler)

## compute expected predictions
fitted_values <- fitted(fit)
head(fitted_values)

## plot expected predictions against actual response
dat <- as.data.frame(cbind(Y = standata(fit)$Y, fitted_values))
ggplot(dat) + geom_point(aes(x = Estimate, y = Y))
}