Defines functions fixed_effects

Documented in fixed_effects

#' Effects of covariates on outcome in baggr models
#' @param bg a [baggr] model
#' @param summary logical; if `TRUE` returns summary statistic instead of all MCMC samples
#' @param transform a transformation (R function) to apply to the result;
#'                  (this is commonly used when calling from other
#'                  plotting or printing functions)
#' @param interval uncertainty interval width (numeric between 0 and 1), if `summary=TRUE`
#' @return A list with 2 vectors (corresponding to MCMC samples)
#'         `tau` (mean effect) and `sigma_tau` (SD). If `summary=TRUE`,
#'         both vectors are summarised as mean and lower/upper bounds according to
#'         `interval`
#' @seealso [treatment_effect] for overall treatment effect across groups,
#'          [group_effects] for effects within each group,
#'          [effect_draw] and [effect_plot] for predicted treatment effect in new group
#' @export
#' @importFrom rstan extract

fixed_effects <- function(bg, summary = FALSE,
                             transform = NULL, interval = .95) {
  if(length(bg$covariates) == 0)
    return(array(0, dim = c(0,0,1)))

  beta <- rstan::extract(bg$fit, pars="beta")[[1]]
  # colnames(beta) <- bg$covariates
  colnames(beta) <- attr(bg$inputs, "covariate_coding")

    beta <- do.call(transform, list(beta))

    beta <- t(apply(beta, 2, mint, int=interval, median=TRUE, sd = TRUE))
    colnames(beta) <- c("lci", "mean", "uci", "median", "sd")
    beta <- replicate(1, beta) #by the convention where 3rd dimension is effect

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baggr documentation built on Sept. 5, 2021, 5:46 p.m.