R/est-param-lognormal.R

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

#' Estimate Lognormal Parameters
#'
#' @family Parameter Estimation
#' @family Lognormal
#'
#' @author Steven P. Sanderson II, MPH
#'
#' @details This function will attempt to estimate the lognormal meanlog and log sd
#' parameters given some vector of values.
#'
#' @description 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 lognormal data.
#'
#' Three different methods of shape parameters are supplied:
#' -  mme, see [EnvStats::elnorm()]
#' -  mle, see [EnvStats::elnorm()]
#'
#' @param .x The vector of data to be passed to the function.
#' @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_lognormal_param_estimate(x)
#'
#' output$parameter_tbl
#'
#' output$combined_data_tbl |>
#'   tidy_combined_autoplot()
#'
#' tb <- tidy_lognormal(.meanlog = 2, .sdlog = 1) |> pull(y)
#' util_lognormal_param_estimate(tb)$parameter_tbl
#'
#' @return
#' A tibble/list
#'
#' @export
#'

util_lognormal_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 (!is.vector(x_term, mode = "numeric")) {
    rlang::abort(
      message = "'.x' must be a numeric vector.",
      use_cli_format = TRUE
    )
  }

  if (n < 2 || unique_terms < 2 || any(x_term <= 0)) {
    rlang::abort(
      message = paste0("'.x' must contain at least two non-missing distict values.
                             All non-missing values must be positive."),
      use_cli_format = TRUE
    )
  }

  log_x <- log(x_term)
  muhat <- mean(log_x)
  es_mvue_sd <- sd(log_x)
  es_mme_sd <- sqrt((n - 1) / n) * sd(log_x)

  # Return Tibble ----
  if (.auto_gen_empirical) {
    te <- tidy_empirical(.x = x_term)
    td <- tidy_lognormal(.n = n, .meanlog = round(muhat, 3), .sdlog = round(es_mme_sd, 3))
    combined_tbl <- tidy_combine_distributions(te, td)
  }

  ret <- dplyr::tibble(
    dist_type = rep("Lognormal", 2),
    samp_size = rep(n, 2),
    min = rep(minx, 2),
    max = rep(maxx, 2),
    method = c("EnvStats_MVUE", "EnvStats_MME"),
    mean_log = c(muhat, muhat),
    sd_log = c(es_mvue_sd, es_mme_sd),
    shape_ratio = c(muhat / es_mvue_sd, muhat / es_mme_sd)
  )

  # Return ----
  attr(ret, "tibble_type") <- "parameter_estimation"
  attr(ret, "family") <- "lognormal"
  attr(ret, "x_term") <- .x
  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)
}