R/prep-censored-data.R

In geostan: Bayesian Spatial Analysis

#' @description Return index of observed and missing y (elsewhere, these results hould be used to replace NAs with zeros or an indicator integer: Stan cannot accept NA values)
#' Outside of this call, must check that censor_point argument is only used with Poisson likelihood.
#' 
#' @param censor the censor_point argument
#' @param frame from model.frame(formula, tmpdf, na.action = NULL)
#' @noRd
#' 
handle_censored_y <- function(censor, frame) {
    y_raw <- model.response(frame)
    if (inherits(y_raw, "matrix")) {
        y_raw <- y_raw[,1] + y_raw[,2]
    }
    y_mis_idx <- which(is.na(y_raw))
    y_obs_idx <- which(!is.na(y_raw))
    n_mis <- length(y_mis_idx)
    if ( n_mis > 0 ) {
        message( paste0(n_mis, " NA values identified in the outcome variable\nFound in rows: ", paste0(y_mis_idx, collapse = ', ' )) )
    }
    return (list(n_mis = length(y_mis_idx),
                n_obs = length(y_obs_idx),
                y_mis_idx = y_mis_idx,
                y_obs_idx = y_obs_idx,
                censor_point = censor)
           )
}

#' @noRd
handle_missing_x <- function(frame) {
    check_NAs <- apply(as.matrix(frame[,-1]), 2, function(c) any(is.na(c)))
    if (any(check_NAs)) stop("Missing values found in covariates or offset term. Missing values are only permitted in the outcome variable.")
}