VGAM (version 0.9-6)

lms.yjn: LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Description

LMS quantile regression with the Yeo-Johnson transformation to normality.

Usage

lms.yjn(percentiles = c(25, 50, 75), zero = c(1,3),
        llambda = "identitylink", lsigma = "loge",
        idf.mu = 4, idf.sigma = 2,
        ilambda = 1, isigma = NULL, rule = c(10, 5),
        yoffset = NULL, diagW = FALSE, iters.diagW = 6)
lms.yjn2(percentiles=c(25,50,75), zero=c(1,3),
         llambda = "identitylink", lmu = "identitylink", lsigma = "loge",
         idf.mu = 4, idf.sigma = 2, ilambda = 1.0,
         isigma = NULL, yoffset = NULL, nsimEIM = 250)

Arguments

percentiles

A numerical vector containing values between 0 and 100, which are the quantiles. They will be returned as `fitted values'.

zero

See lms.bcn.

llambda, lmu, lsigma

See lms.bcn.

idf.mu, idf.sigma

See lms.bcn.

ilambda, isigma

See lms.bcn.

rule

Number of abscissae used in the Gaussian integration scheme to work out elements of the weight matrices. The values given are the possible choices, with the first value being the default. The larger the value, the more accurate the approximation

yoffset

A value to be added to the response y, for the purpose of centering the response before fitting the model to the data. The default value, NULL, means -median(y) is used, so that the response actually used has median zero. T

diagW

Logical. This argument is offered because the expected information matrix may not be positive-definite. Using the diagonal elements of this matrix results in a higher chance of it being positive-definite, however convergence will be very slow. I

iters.diagW

Integer. Number of iterations in which the diagonal elements of the expected information matrix are used. Only used if diagW = TRUE.

nsimEIM

See CommonVGAMffArguments for more information.

Value

• An object of class "vglmff" (see vglmff-class). The object is used by modelling functions such as vglm and vgam.

Warning

The computations are not simple, therefore convergence may fail. In that case, try different starting values.

The generic function predict, when applied to a lms.yjn fit, does not add back the yoffset value.

Details

Given a value of the covariate, this function applies a Yeo-Johnson transformation to the response to best obtain normality. The parameters chosen to do this are estimated by maximum likelihood or penalized maximum likelihood. The function lms.yjn2() estimates the expected information matrices using simulation (and is consequently slower) while lms.yjn() uses numerical integration. Try the other if one function fails.

References

Yeo, I.-K. and Johnson, R. A. (2000) A new family of power transformations to improve normality or symmetry. Biometrika, 87, 954--959.

Yee, T. W. (2004) Quantile regression via vector generalized additive models. Statistics in Medicine, 23, 2295--2315.

Yee, T. W. (2002) An Implementation for Regression Quantile Estimation. Pages 3--14. In: Haerdle, W. and Ronz, B., Proceedings in Computational Statistics COMPSTAT 2002. Heidelberg: Physica-Verlag.

Documentation accompanying the VGAM package at http://www.stat.auckland.ac.nz/~yee contains further information and examples.

See Also

lms.bcn, lms.bcg, qtplot.lmscreg, deplot.lmscreg, cdf.lmscreg, bmi.nz, amlnormal.

Examples

fit <- vgam(BMI ~ s(age, df = 4), lms.yjn, bmi.nz, trace = TRUE)
head(predict(fit))
head(fitted(fit))
head(bmi.nz)
# Person 1 is near the lower quartile of BMI amongst people his age
head(cdf(fit))

# Quantile plot
par(bty = "l", mar = c(5, 4, 4, 3) + 0.1, xpd = TRUE)
qtplot(fit, percentiles = c(5, 50, 90, 99), main = "Quantiles",
       xlim = c(15, 90), las = 1, ylab = "BMI", lwd = 2, lcol = 4)

# Density plot
ygrid <- seq(15, 43, len = 100)  # BMI ranges
par(mfrow = c(1, 1), lwd = 2)
(aa <- deplot(fit, x0 = 20, y = ygrid, xlab = "BMI", col = "black",
    main = "Density functions at Age = 20 (black), 42 (red) and 55 (blue)"))
aa <- deplot(fit, x0 = 42, y = ygrid, add = TRUE, llty = 2, col = "red")
aa <- deplot(fit, x0 = 55, y = ygrid, add = TRUE, llty = 4, col = "blue",
             Attach = TRUE)
with(aa@post, deplot)  # Contains density function values; == a@post$deplot