R/est-param-beta.R

In TidyDensity: Functions for Tidy Analysis and Generation of Random Data

#' Estimate Beta Parameters
#'
#' @family Parameter Estimation
#' @family Beta
#'
#' @author Steven P. Sanderson II, MPH
#'
#' @details This function will attempt to estimate the beta shape1 and shape2
#' parameters given some vector of values.
#'
#' @description This function will automatically scale the data from 0 to 1 if
#' it is not already. This means you can pass a vector like `mtcars$mpg` and not
#' worry about it.
#'
#' The function will return a list output by default, and  if the parameter
#' `.auto_gen_empirical` is set to `TRUE` then the empirical data given to the
#' parameter `.x` will be run through the `tidy_empirical()` function and combined
#' with the estimated beta data.
#'
#' Three different methods of shape parameters are supplied:
#' -  Bayes
#' -  NIST mme
#' -  EnvStats mme, see [EnvStats::ebeta()]
#'
#' @param .x The vector of data to be passed to the function. Must be numeric, and
#' all values must be 0 <= x <= 1
#' @param .auto_gen_empirical This is a boolean value of TRUE/FALSE with default
#' set to TRUE. This will automatically create the `tidy_empirical()` output
#' for the `.x` parameter and use the `tidy_combine_distributions()`. The user
#' can then plot out the data using `$combined_data_tbl` from the function output.
#'
#' @examples
#' library(dplyr)
#' library(ggplot2)
#'
#' x <- mtcars$mpg
#' output <- util_beta_param_estimate(x)
#'
#' output$parameter_tbl
#'
#' output$combined_data_tbl %>%
#'   tidy_combined_autoplot()
#'
#' tb <- rbeta(50, 2.5, 1.4)
#' util_beta_param_estimate(tb)$parameter_tbl
#'
#' @return
#' A tibble/list
#'
#' @export
#'

util_beta_param_estimate <- function(.x, .auto_gen_empirical = TRUE) {

  # Tidyeval ----
  x_term <- as.numeric(.x)
  minx <- min(x_term)
  maxx <- max(x_term)
  n <- length(x_term)
  unique_terms <- length(unique(x_term))

  # Checks ----
  if (n < 2 || unique_terms < 2) {
    rlang::abort(
      message = "The data must have at least two (2) unique data points.",
      use_cli_format = TRUE
    )
  }

  if (!is.numeric(x_term)) {
    rlang::abort(
      "The '.x' parameter must be numeric."
    )
  }

  if (minx < 0 | maxx > 1) {
    rlang::inform(
      message = "For the beta distribution, its mean 'mu' should be 0 < mu < 1.
      The data will therefore be scaled to enforce this.",
      use_cli_format = TRUE
    )
    x_term <- tidy_scale_zero_one_vec(x_term)
    scaled <- TRUE
  } else {
    rlang::inform(
      message = "There was no need to scale the data.",
      use_cli_format = TRUE
    )
    x_term <- x_term
    scaled <- FALSE
  }

  # Get params ----
  m <- mean(x_term, na.rm = TRUE)
  s2 <- var(x_term, na.rm = TRUE)

  # wikipedia generic
  alpha <- m * n
  beta <- sqrt(((1 - m) * n)^2)

  # https://itl.nist.gov/div898/handbook/eda/section3/eda366h.htm
  p <- m * (((m * (1 - m)) / s2) - 1)
  q <- (1 - m) * (((m * (1 - m)) / s2) - 1)

  if (p < 0) {
    p <- sqrt((p)^2)
  }

  if (q < 0) {
    q <- sqrt((q)^2)
  }

  # EnvStats
  term <- ((m * (1 - m)) / (((n - 1) / n) * s2)) - 1
  esshape1 <- m * term
  esshape2 <- (1 - m) * term

  # Return Tibble ----
  if (.auto_gen_empirical) {
    te <- tidy_empirical(.x = x_term)
    td <- tidy_beta(.n = n, .shape1 = round(p, 3), .shape2 = round(q, 3))
    combined_tbl <- tidy_combine_distributions(te, td)
  }

  ret <- dplyr::tibble(
    dist_type = rep("Beta", 3),
    samp_size = rep(n, 3),
    min = rep(minx, 3),
    max = rep(maxx, 3),
    mean = rep(m, 3),
    variance = rep(s2, 3),
    method = c("Bayes", "NIST_MME", "EnvStats_MME"),
    shape1 = c(alpha, p, esshape1),
    shape2 = c(beta, q, esshape2),
    shape_ratio = c(alpha / beta, p / q, esshape1 / esshape2)
  )

  # Return ----
  attr(ret, "tibble_type") <- "parameter_estimation"
  attr(ret, "family") <- "beta"
  attr(ret, "x_term") <- .x
  attr(ret, "scaled") <- scaled
  attr(ret, "n") <- n

  if (.auto_gen_empirical) {
    output <- list(
      combined_data_tbl = combined_tbl,
      parameter_tbl     = ret
    )
  } else {
    output <- list(
      parameter_tbl = ret
    )
  }

  return(output)
}