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# Main function -----------------------------------------------------------
#' Fitted theoretical density
#'
#' @description Estimates the parameters of a given distribution and evaluates
#' the probability density function with these parameters. This can be useful
#' for comparing histograms or kernel density estimates against a theoretical
#' distribution.
#'
#' @inheritParams ggplot2::geom_density
#' @param distri A `character` of length 1 naming a distribution without
#' prefix. See details.
#' @param n An `integer` of length 1 with the number of equally spaced
#' points at which the density function is evaluated. Ignored if distribution
#' is discrete.
#' @param fix.arg An optional named list giving values of fixed parameters of
#' the named distribution. Parameters with fixed value are not estimated by
#' maximum likelihood procedures.
#' @param start.arg A named list giving initial values of parameters for the
#' named distribution. This argument may be omitted (default) for some
#' distributions for which reasonable starting values are computed.
#' @param geom Use to override the default geom for `stat_theodensity`.
#'
#' @details Valid `distri` arguments are the names of distributions for
#' which there exists a density function. The names should be given without a
#' prefix (typically 'd', 'r', 'q' and 'r'). For example: `"norm"` for
#' the normal distribution and `"nbinom"` for the negative binomial
#' distribution. Take a look at [`distributions()`][stats::Distributions] in the
#' \pkg{stats} package for an overview.
#'
#' There are a couple of distribution for which there exist no reasonable
#' starting values, such as the Student t-distribution and the F-distribution.
#' In these cases, it would probably be wise to provide reasonable starting
#' values as a named list to the `start.arg` argument. When estimating a
#' binomial distribution, it would be best to supply the `size` to the
#' `fix.arg` argument.
#'
#' By default, the y values are such that the integral of the distribution is
#' 1, which scales well with the defaults of kernel density estimates. When
#' comparing distributions with absolute count histograms, a sensible choice
#' for aesthetic mapping would be `aes(y = stat(count) * binwidth)`,
#' wherein `binwidth` is matched with the bin width of the histogram.
#'
#' For discrete distributions, the input data are expected to be integers, or
#' doubles that can be divided by 1 without remainders.
#'
#' Parameters are estimated using the
#' [fitdistrplus::fitdist()]`()` function in the
#' \pkg{fitdistrplus} package using maximum likelihood estimation.
#' Hypergeometric and multinomial distributions from the \pkg{stats} package
#' are not supported.
#'
#' @section Computed variables: \describe{ \item{density}{probability density}
#' \item{count}{density * number of observations - useful for comparing to
#' histograms} \item{scaled}{density scaled to a maximum of 1} }
#'
#' @seealso [stats::Distributions()]
#' [fitdistrplus::fitdist()] [ggplot2::geom_density()]
#' [ggplot2::geom_histogram()]
#'
#' @export
#'
#' @return A *Layer* ggproto object.
#'
#' @examples
#' # A mixture of normal distributions where the standard deviation is
#' # inverse gamma distributed resembles a cauchy distribution.
#' x <- rnorm(2000, 10, 1/rgamma(2000, 2, 0.5))
#' df <- data.frame(x = x)
#'
#' ggplot(df, aes(x)) +
#' geom_histogram(binwidth = 0.1,
#' alpha = 0.3, position = "identity") +
#' stat_theodensity(aes(y = stat(count) * 0.1, colour = "Normal"),
#' distri = "norm", geom = "line") +
#' stat_theodensity(aes(y = stat(count) * 0.1, colour = "Cauchy"),
#' distri = "cauchy", geom = "line") +
#' coord_cartesian(xlim = c(5, 15))
#'
#' # A negative binomial can be understood as a Poisson-gamma mixture
#' df <- data.frame(x = c(rpois(500, 25),
#' rpois(500, rgamma(500, 5, 0.2))),
#' cat = rep(c("Poisson", "Poisson-gamma"), each = 500))
#'
#' ggplot(df, aes(x)) +
#' geom_histogram(binwidth = 1, aes(fill = cat),
#' alpha = 0.3, position = "identity") +
#' stat_theodensity(aes(y = stat(count), colour = cat), distri = "nbinom",
#' geom = "step", position = position_nudge(x = -0.5)) +
#' stat_summary(aes(y = x, colour = cat, x = 1),
#' fun.data = function(x){data.frame(xintercept = mean(x))},
#' geom = "vline")
stat_theodensity <- function(
mapping = NULL, data = NULL,
geom = "line", position = "identity",
...,
distri = "norm", n = 512,
fix.arg = NULL,
start.arg = NULL,
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE
) {
if (!exists(paste0("d", distri), mode = "function")) {
cli::cli_abort(
"The {.arg distri} argument must have a valid density function called \\
{.fn d{distri}}."
)
}
if (distri %in% c("multinom", "hyper", "wilcox", "signrank")) {
cli::cli_abort(
"{.fn stat_theodensity} does not support the '{distri}' distribution."
)
}
layer(
data = data,
mapping = mapping,
stat = StatTheoDensity,
geom = geom,
position = position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params = list2(
distri = distri,
n = n,
fix.arg = fix.arg,
start.arg = start.arg,
na.rm = na.rm,
...
)
)
}
# ggproto -----------------------------------------------------------------
#' @usage NULL
#' @format NULL
#' @export
#' @rdname ggh4x_extensions
StatTheoDensity <- ggproto(
"StatTheoDensity",
StatDensity,
compute_group = function(
data, scales, distri = "norm", n = 512, distri_type = "continuous",
fix.arg = NULL, start.arg = NULL
) {
check_installed("fitdistrplus", "for `stat_theodensity()`.")
# Data to return upon failure
nulldata <- data.frame(
x = NA_real_,
density = NA_real_,
ndensity = NA_real_,
count = NA_real_,
n = NA_integer_
)
dfun <- get(paste0("d", distri), mode = "function")
x <- data$x
x <- x[!is.na(x)]
nx <- length(data$x)
if (nx < 2) {
cli::cli_warn("Groups with fewer than two data points have been dropped.")
return(nulldata)
}
range <- scales$x$dimension()
if (distri_type == "discrete") {
xseq <- seq(floor(range[1]), ceiling(range[2]), by = 1)
} else {
xseq <- seq(range[1], range[2], length.out = n)
}
par_est <- suppressWarnings(coef(fitdistrplus::fitdist(x, distri,
start = start.arg,
fix.arg = fix.arg)))
par_est <- c(par_est, unlist(fix.arg))
if (any(is.na(par_est) | is.nan(par_est) |
!is.finite(par_est) | is.null(par_est))) {
cli::cli_warn("Failed to estimate parameters of '{distri}' distribution.")
return(nulldata)
}
dens <- do.call(dfun, c(list(x = xseq), as.list(par_est)))
data.frame(
x = xseq,
density = dens,
scaled = dens / max(dens, na.rm = TRUE),
count = dens * nx,
n = nx
)
},
setup_params = function(data, params) {
dtype <- class_distri(params$distri)
if (dtype == "discrete") {
if (sum(abs(data$x %% 1)) > 0) {
cli::cli_abort(
"A discrete '{params$distri}' distribution cannot be fitted \\
to continuous data."
)
}
}
params <- c(params, distri_type = dtype)
# Chi square estimator causes trouble, estimate as gamma with rate = 0.5
if (params$distri == "chisq") {
params$distri <- "gamma"
if (is.null(params$fix.arg)) {
params$fix.arg <- list(rate = 0.5)
} else {
params$fix.arg <- list(shape = params$fix.arg$df / 2, rate = 0.5)
}
}
# Binom does not operate without size
if (params$distri == "binom") {
if (is.null(params$fix.arg)) {
params$fix.arg <- list(size = max(data$x))
cli::cli_inform(
"Estimating binomial PMF with {.field size} set to maximum data value."
)
}
params$start.arg <- list(prob = mean(data$x) / max(data$x))
}
params
}
)
# Helper functions --------------------------------------------------------
#' @keywords internal
class_distri <- function(distri) {
# Is distri discrete?
discrete_distris <- c("pois", "nbinom", "binom", "geom", "hyper",
"signrank", "multinom", "wilcox")
if (distri %in% discrete_distris) {
return("discrete")
}
# Is distri continuous?
conti_distris <- c("beta", "cauchy", "chisq", "exp", "f", "gamma",
"lnorm", "norm", "t", "unif", "weibull", "logis")
if (distri %in% conti_distris) {
return("continuous")
}
# Empirical test for functions outside the stats package
rfun <- dynGet(paste0("r", distri), inherits = TRUE)
# rfun <- get(paste0("r", distri), mode = "function")
routput <- tryCatch({
do.call(rfun, as.list(c(100, rep(1, length(formals(rfun)) - 1))))
},
warning = function(cond) {
},
error = function(cond) {
return(NULL)
})
if (is.integer(routput) | sum(routput %% 1) == 0) {
return("discrete")
} else if (is.numeric(routput)) {
return("continuous")
} else {
cli::cli_abort(
"{.fn stat_theodensity} failed to determine if the '{distri}' \\
distribution is discrete or continuous."
)
}
}
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