ordAOV: ANOVA for factors with ordered levels

In ahoshiyar/ordPens: Selection, Fusion, Smoothing and Principal Components Analysis for Ordinal Variables

ANOVA for factors with ordered levels

Description

This function performs analysis of variance when the factor(s) of interest has/have ordinal scale level. For testing, values from the null distribution are simulated.

Usage

ordAOV(x, y, type = c("RLRT", "LRT"), nsim = 10000,
null.sample = NULL, ...)

Arguments

x	a vector or matrix of integers 1,2,... giving the observed levels of the ordinal factor(s). If x is a matrix, it is assumed that each column corresponds to one ordinal factor.
y	the vector of response values.
type	the type of test to carry out: likelihood ratio ("LRT") or restricted likelihood ratio ("RLRT").
nsim	number of values to simulate from the null distribution.
null.sample	a vector, or a list of vectors (in case of multi-factorial ANOVA) containing values already simulated from the null distribution (overrides nsim)
...	additional arguments to LRTSim and RLRTSim, respectively.

Details

The method assumes that ordinal factor levels (contained in vector/columns of matrix x) take values 1,2,...,max, where max denotes the highest level of the respective factor observed in the data. Every level between 1 and max has to be observed at least once.

The method uses a mixed effects formulation of the usual one- or multi-factorial ANOVA model (with main effects only) while penalizing (squared) differences of adjacent means. Testing for equal means across factor levels is done by (restricted) likelihood ratio testing for a zero variance component in a linear mixed model. For simulating values from the finite sample null distribution of the (restricted) likelihood ratio statistic, the algorithms implemented in Package RLRsim are used. See LRTSim and RLRTSim for further information.

If x is a vector (or one-column matrix), one-factorial ANOVA is applied, and it is simulated from the exact finite sample null distribution as derived by Crainiceanu & Ruppert (2004). If x is a matrix, multi-factorial ANOVA (with main effects only) is done, and the approximation of the finite sample null distribution proposed by Greven et al. (2008) is used. Simulation studies by Gertheiss (2014) suggest that for ANOVA with ordinal factors RLRT should rather be used than LRT.

Value

In case of one-factorial ANOVA, a list of class htest containing the following components (see also exactLRT and exactRLRT):

statistic	the observed (restricted) likelihood ratio.
p	p-value for the observed test statistic.
method	a character string indicating what type of test was performed and how many values were simulated to determine the critical value.
sample	the samples from the null distribution returned by LRTSim and RLRTSim, respectively.

In case of multi-factorial ANOVA, a list (of lists) with the jth component giving the results above when testing the main effect of factor j.

Author(s)

Jan Gertheiss

References

Crainiceanu, C. and D. Ruppert (2004). Likelihood ratio tests in linear mixed models with one variance component, Journal of the Royal Statistical Society B, 66, 165-185.

Gertheiss, J. (2014). ANOVA for factors with ordered levels, Journal of Agricultural, Biological and Environmental Statistics, 19, 258-277.

Gertheiss, J. and F. Oehrlein (2011). Testing relevance and linearity of ordinal predictors, Electronic Journal of Statistics, 5, 1935-1959.

Greven, S., C. Crainiceanu, H. Kuechenhoff, and A. Peters (2008). Restricted likelihood ratio testing for zero variance components in linear mixed models, Journal of Computational and Graphical Statistics, 17, 870-891.

Scheipl, F., S. Greven, and H. Kuechenhoff (2008). Size and power of tests for a zero random effect variance or polynomial regression in additive and linear mixed models, Computational Statistics & Data Analysis, 52, 3283-3299.

See Also

LRTSim, RLRTSim

Examples

# load some data
data(ICFCoreSetCWP)

# the pysical health component summary
y <- ICFCoreSetCWP$phcs

# consider the first ordinal factor
x <- ICFCoreSetCWP[,1]

# adequate coding
x <- as.integer(x - min(x) + 1)

# ANOVA
ordAOV(x, y, type = "RLRT", nsim=1000000)

ahoshiyar/ordPens documentation built on May 7, 2024, 5:43 a.m.