logcondens (version 2.1.8)

logConDens: Compute log-concave density estimator and related quantities

Description

Compute the log-concave and smoothed log-concave density estimator.

Usage

logConDens(x, xgrid = NULL, smoothed = TRUE, print = FALSE, 
    gam = NULL, xs = NULL)

Value

logConDens returns an object of class "dlc", a list containing the following components: xn, x, w, phi, IsKnot, L, Fhat, H, n, m, knots, mode, and sig as generated by activeSetLogCon. If smoothed = TRUE, then the returned object additionally contains f.smoothed, F.smoothed, gam, and xs as generated by evaluateLogConDens. Finally, the entry smoothed of type "logical" returnes the value of smoothed.

The methods summary.dlc and plot.dlc are used to obtain a summary and generate plots of the estimated density.

Arguments

x

Vector of independent and identically distributed numbers, not necessarily unique.

xgrid

Governs the generation of weights for observations. See preProcess for details.

smoothed

If TRUE, the smoothed version of the log-concave density estimator is also computed.

print

print = TRUE outputs the log-likelihood in every loop, print = FALSE does not. Make sure to tell R to output (press CTRL+W).

gam

Only necessary if smoothed = TRUE. The standard deviation of the normal kernel. If equal to NULL, gam is chosen such that the variances of the original sample \(x_1, \ldots, x_n\) and \(\widehat f_n^*\) coincide.

xs

Only necessary if smoothed = TRUE. Either provide a vector of support points where the smoothed estimator should be computed at, or leave as NULL. Then, a sufficiently width equidistant grid of points will be used.

Author

Kaspar Rufibach, ,
http://www.kasparrufibach.ch

Lutz Duembgen, ,
https://www.imsv.unibe.ch/about_us/staff/prof_dr_duembgen_lutz/index_eng.html

Details

See activeSetLogCon for details on the computations.

References

Duembgen, L, Huesler, A. and Rufibach, K. (2010). Active set and EM algorithms for log-concave densities based on complete and censored data. Technical report 61, IMSV, Univ. of Bern, available at https://arxiv.org/abs/0707.4643.

Duembgen, L. and Rufibach, K. (2009). Maximum likelihood estimation of a log--concave density and its distribution function: basic properties and uniform consistency. Bernoulli, 15(1), 40--68.

Duembgen, L. and Rufibach, K. (2011). logcondens: Computations Related to Univariate Log-Concave Density Estimation. Journal of Statistical Software, 39(6), 1--28. tools:::Rd_expr_doi("https://doi.org/10.18637/jss.v039.i06")

Examples

## ===================================================
## Illustrate on simulated data
## ===================================================

## Set parameters
n <- 50
x <- rnorm(n)

res <- logConDens(x, smoothed = TRUE, print = FALSE, gam = NULL, 
    xs = NULL)
summary(res)
plot(res, which = "density", legend.pos = "topright")
plot(res, which = "log-density")
plot(res, which = "CDF")

## Compute slopes and intercepts of the linear functions that 
## compose phi
slopes <- diff(res$phi) / diff(res$x)
intercepts <- -slopes * res$x[-n] + res$phi[-n]


## ===================================================
## Illustrate method on reliability data
## Reproduce Fig. 2 in Duembgen & Rufibach (2009)
## ===================================================

## Set parameters
data(reliability)
x <- reliability
n <- length(x)
res <- logConDens(x, smooth = TRUE, print = TRUE)
phi <- res$phi
f <- exp(phi)

## smoothed log-concave PDF
f.smoothed <- res$f.smoothed
xs <- res$xs

## compute kernel density
sig <- sd(x)
h <- sig / sqrt(n)
f.kernel <- rep(NA, length(xs))
for (i in 1:length(xs)){
    xi <- xs[i]
    f.kernel[i] <- mean(dnorm(xi, mean = x, sd = h))
}

## compute normal density
mu <- mean(x)
f.normal <- dnorm(xs, mean = mu, sd = sig)

## ===================================================
## Plot resulting densities, i.e. reproduce Fig. 2
## in Duembgen and Rufibach (2009)
## ===================================================
plot(0, 0, type = 'n', xlim = range(xs), ylim = c(0, 6.5 * 10^-3))
rug(res$x)
lines(res$x, f, col = 2)
lines(xs, f.normal, col = 3)
lines(xs, f.kernel, col = 4)
lines(xs, f.smoothed, lwd = 3, col = 5)
legend("topleft", c("log-concave", "normal", "kernel", 
    "log-concave smoothed"), lty = 1, col = 2:5, bty = "n")


## ===================================================
## Plot log-densities
## ===================================================
plot(0, 0, type = 'n', xlim = range(xs), ylim = c(-20, -5))
legend("bottomright", c("log-concave", "normal", "kernel", 
    "log-concave smoothed"), lty = 1, col = 2:5, bty = "n")
rug(res$x)
lines(res$x, phi, col = 2)
lines(xs, log(f.normal), col = 3)
lines(xs, log(f.kernel), col = 4)
lines(xs, log(f.smoothed), lwd = 3, col = 5)


## ===================================================
## Confidence intervals at a fixed point for the density
## see help file for logConCI()
## ===================================================