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prevalence <- function (obs = NULL, model = NULL, event = 1, na.rm = TRUE) {
# version 1.4 (2 May 2022)
#model_classes_implemented <- c("glm", "gam", "gbm", "randomForest", "bart")
#if (any(class(obs) %in% model_classes_implemented)) model <- obs # (in case the user provides unnamed model argument)
if (!is.null(obs)) {
obs <- unlist(obs)
if (!is(obs, "vector") && !is(obs, "factor")) stop("'obs' must be of class 'vector' or 'factor'.")
if (!(event %in% obs)) warning("'event' is not among of the values of 'obs'.")
}
if (!is.null(model)) {
if (!is.null(obs)) warning("Argument 'obs' ignored in favour of 'model'.")
obs <- mod2obspred(model, obs.only = TRUE)[ , "obs"]
} # end if model
if(na.rm) obs <- obs[!is.na(obs)]
sum(obs == event) / length(obs)
}
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