https://github.com/cran/bayestestR
Raw File
Tip revision: 645c10f110efae44c5ac60025664cd27f2b46a87 authored by Dominique Makowski on 26 March 2020, 05:10 UTC
version 0.5.3
Tip revision: 645c10f
estimate_density.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/estimate_density.R
\name{estimate_density}
\alias{estimate_density}
\alias{estimate_density.data.frame}
\title{Density Estimation}
\usage{
estimate_density(
  x,
  method = "kernel",
  precision = 2^10,
  extend = FALSE,
  extend_scale = 0.1,
  bw = "SJ",
  ...
)

\method{estimate_density}{data.frame}(
  x,
  method = "kernel",
  precision = 2^10,
  extend = FALSE,
  extend_scale = 0.1,
  bw = "SJ",
  group_by = NULL,
  ...
)
}
\arguments{
\item{x}{Vector representing a posterior distribution, or a data frame of such
vectors. Can also be a Bayesian model (\code{stanreg}, \code{brmsfit},
\code{MCMCglmm}, \code{mcmc} or \code{bcplm}) or a \code{BayesFactor} model.}

\item{method}{Density estimation method. Can be \code{"kernel"} (default), \code{"logspline"} or \code{"KernSmooth"}.}

\item{precision}{Number of points of density data. See the \code{n} parameter in \link[=density]{density}.}

\item{extend}{Extend the range of the x axis by a factor of \code{extend_scale}.}

\item{extend_scale}{Ratio of range by which to extend the x axis. A value of \code{0.1} means that the x axis will be extended by \code{1/10} of the range of the data.}

\item{bw}{the smoothing bandwidth to be used.  The kernels are scaled
    such that this is the standard deviation of the smoothing kernel.
    (Note this differs from the reference books cited below, and from S-PLUS.)

    \code{bw} can also be a character string giving a rule to choose the
    bandwidth.  See \code{\link[stats]{bw.nrd}}. \cr The default,
    \code{"nrd0"}, has remained the default for historical and
    compatibility reasons, rather than as a general recommendation,
    where e.g., \code{"SJ"} would rather fit, see also Venables and
    Ripley (2002).

    The specified (or computed) value of \code{bw} is multiplied by
    \code{adjust}.
  }

\item{...}{Currently not used.}

\item{group_by}{Optional character vector. If not \code{NULL} and \code{x} is a data frame, density estimation is performed for each group (subset) indicated by \code{group_by}.}
}
\description{
This function is a wrapper over different methods of density estimation. By default, it uses the base R \link{density} with by default uses a different smoothing bandwidth (\code{"SJ"}) from the legacy default implemented the base R \link{density} function (\code{"nrd0"}). However, Deng \& Wickham suggest that \code{method = "KernSmooth"} is the fastest and the most accurate.
}
\examples{
library(bayestestR)

set.seed(1)
x <- rnorm(250, 1)

# Methods
density_kernel <- estimate_density(x, method = "kernel")
density_logspline <- estimate_density(x, method = "logspline")
density_KernSmooth <- estimate_density(x, method = "KernSmooth")
density_mixture <- estimate_density(x, method = "mixture")

hist(x, prob = TRUE)
lines(density_kernel$x, density_kernel$y, col = "black", lwd = 2)
lines(density_logspline$x, density_logspline$y, col = "red", lwd = 2)
lines(density_KernSmooth$x, density_KernSmooth$y, col = "blue", lwd = 2)
lines(density_mixture$x, density_mixture$y, col = "green", lwd = 2)

# Extension
density_extended <- estimate_density(x, extend = TRUE)
density_default <- estimate_density(x, extend = FALSE)

hist(x, prob = TRUE)
lines(density_extended$x, density_extended$y, col = "red", lwd = 3)
lines(density_default$x, density_default$y, col = "black", lwd = 3)

df <- data.frame(replicate(4, rnorm(100)))
head(estimate_density(df))
\dontrun{
# rstanarm models
# -----------------------------------------------
library(rstanarm)
model <- stan_glm(mpg ~ wt + gear, data = mtcars, chains = 2, iter = 200, refresh = 0)
head(estimate_density(model))

library(emmeans)
head(estimate_density(emtrends(model, ~1, "wt")))

# brms models
# -----------------------------------------------
library(brms)
model <- brms::brm(mpg ~ wt + cyl, data = mtcars)
estimate_density(model)
}

}
\references{
Deng, H., & Wickham, H. (2011). Density estimation in R. Electronic publication.
}
back to top