logConDens: Compute log-concave density estimator and related quantities
In logcondens.mode: Compute MLE of Log-Concave Density on R with Fixed Mode, and Perform Inference for the Mode.

Description Usage Arguments Details Value Author(s) References Examples

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

This function is as it is in the logcondens package except we've added the 'prec' variable as an argument, and modified the values returned as output, to be in line with the activeSetLogCon.mode function.

1 2	logConDens(x, xgrid = NULL, smoothed = TRUE, print = FALSE, gam = NULL, xs = NULL, prec=10^-10)

`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, …, x_n and \hat 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.
`prec`	Governs precision of various subfunctions, e.g. the Newton-Raphson procedure.

See activeSetLogCon for details on the computations.

logConDens returns an object of class "dlc", a list containing the following components: xn, x, w, L, IsKnot, knots, phi, fhat, Fhat, H, n, m, mode, dlcMode, sig, phi.f, fhat.f, Fhat.f, E.f, phiPL, phiPR, phiPL.f, and phiPR.f, 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.

Kaspar Rufibach, kaspar.rufibach@gmail.com,
http://www.kasparrufibach.ch

Lutz Duembgen, duembgen@stat.unibe.ch,
http://www.staff.unibe.ch/duembgen

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 http://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. http://www.jstatsoft.org/v39/i06

## ===================================================
## 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()
## ===================================================

Loading required package: logcondens

Attaching package: 'logcondens.mode'

The following objects are masked from 'package:logcondens':

    activeSetLogCon, intF, logConDens

The following object is masked from 'package:base':

    dir.exists

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

Estimation of a log-concave density from i.i.d. data
 
Number of initial observations: n = 50
 
Number of unique observations (or grid points): m = 50
 
log-likelihood: -2.31
 
Maximum likelihood estimate:
Mode: x[17] = -0.43
Value of log-density at mode: -0.73
Value of density at mode: 0.48
 
Smoothed maximum likelihood estimate:
Mode: -0.32
Value of log-density at mode: -0.86
Value of density at mode: 0.42
 
Number of knots of the MLE: 6
 
Knots of the MLE:
x[1, 14, 17, 39, 44, 50] =
-1.71, -0.58, -0.43,  0.75,  1.25,  2.71

[1] "ASLC: Beginning"
[1] "iter1=2 / L=-6.7569 / max(H)=2.163 / #knots = 3"
[1] "iter1=3 / L=-6.7337 / max(H)=1.3981 / #knots = 4"
[1] "iter1=4 / L=-6.7266 / max(H)=0.4054 / #knots = 5"
[1] "iter1=5 / L=-6.7212 / max(H)=0.2512 / #knots = 6"
[1] "iter1=6 / L=-6.719 / max(H)=0.1588 / #knots = 7"
[1] "iter1=7 / L=-6.7177 / max(H)=0.0748 / #knots = 7"
[1] "iter1=7 / L=-6.7177 / max(H)=0.0748 / #knots = 7"
[1] "iter1=8 / L=-6.7176 / max(H)=0.0363 / #knots = 8"
[1] "iter1=9 / L=-6.7168 / max(H)=0.0321 / #knots = 8"
[1] "iter1=9 / L=-6.7168 / max(H)=0.0321 / #knots = 8"
[1] "iter1=10 / L=-6.7166 / max(H)=0.0207 / #knots = 9"
[1] "iter1=11 / L=-6.7165 / max(H)=0.0174 / #knots = 9"
[1] "iter1=11 / L=-6.7165 / max(H)=0.0174 / #knots = 9"
[1] "iter1=12 / L=-6.7164 / max(H)=0.0074 / #knots = 9"
[1] "iter1=12 / L=-6.7164 / max(H)=0.0074 / #knots = 9"
[1] "iter1=13 / L=-6.7163 / max(H)=0.005 / #knots = 9"
[1] "iter1=13 / L=-6.7163 / max(H)=0.005 / #knots = 9"
[1] "iter1=14 / L=-6.7163 / max(H)=2e-04 / #knots = 10"
[1] "iter1=15 / L=-6.7163 / max(H)=0 / #knots = 10"
[1] "iter1=15 / L=-6.7163 / max(H)=0 / #knots = 10"
[1] "iter1=16 / L=-6.7163 / max(H)=0 / #knots = 10"
[1] "iter1=16 / L=-6.7163 / max(H)=0 / #knots = 10"
[1] "ASLC: returning"
[1] "10% of computation of smooth estimates done"
[1] "20% of computation of smooth estimates done"
[1] "30% of computation of smooth estimates done"
[1] "40% of computation of smooth estimates done"
[1] "50% of computation of smooth estimates done"
[1] "60% of computation of smooth estimates done"
[1] "70% of computation of smooth estimates done"
[1] "80% of computation of smooth estimates done"
[1] "90% of computation of smooth estimates done"
[1] "100% of computation of smooth estimates done"