test.fixef: Perform t-Tests for Linear Contrasts on Fixed Effects

In VCA: Variance Component Analysis

Perform t-Tests for Linear Contrasts on Fixed Effects

Description

This function performs t-Tests for one or multiple linear combinations (contrasts) of estimated fixed effects.

Usage

test.fixef(
  obj,
  L,
  ddfm = c("contain", "residual", "satterthwaite"),
  method.grad = "simple",
  tol = 1e-12,
  quiet = FALSE,
  opt = TRUE,
  onlyDF = FALSE,
  ...
)

Arguments

obj	(VCA) object
L	(numeric) vector or matrix, specifying linear combinations of the fixed effects, in the latter case, each line represents a disctinct linear contrast
ddfm	(character) string specifying the method used for computing the denominator degrees of freedom for tests of fixed effects or LS Means. Available methods are "contain", "residual", and "satterthwaite".
method.grad	(character) string specifying the method to be used for approximating the gradient of the variance-covariance matrix of fixed effects at the estimated covariance parameter estimates (see function 'grad' (numDeriv) for details)
tol	(numeric) value specifying the numeric tolerance for testing equality to zero
quiet	(logical) TRUE = suppress warning messages, e.g. for non-estimable contrasts
opt	(logical) TRUE = tries to optimize computation time by avoiding unnecessary computations for balanced datasets (see details).
onlyDF	(logical) TRUE = only the specified type of degrees of freedom are determined without carrying out the actual hypothesis test(s)
...	further parameters (for internal use actually)

Details

Here, the same procedure as in SAS PROC MIXED ddfm=satterthwaite (sat) is implemented. This implementation was inspired by the code of function 'calcSatterth' of R-package 'lmerTest'. Thanks to the authors for this nice implementation.
Note, that approximated Satterthwaite degrees of freedom might differ from 'lmerTest' and SAS PROC MIXED. Both use the inverse Fisher-information matrix as approximation of the variance-covariance matrix of variance components (covariance parameters). Here, either the exact algorithm for ANOVA-estimators of variance components, described in Searle et. al (1992) p. 176, or the approximation presented in Giesbrecht and Burns (19985) are used. For balanced designs their will be no differences, usually. In case of balanced designs, the Satterthwaite approximation is equal to the degrees of freedom of the highest order random term in the model (see examples).

Value

(numeric) vector or matrix with 4 elements/columns corresponding to "Estimate", "t Value", "DF", and "Pr > |t|".

Author(s)

Andre Schuetzenmeister [e-mail] inspired by authors of R-package 'lmerTest'

References

Searle, S.R, Casella, G., McCulloch, C.E. (1992), Variance Components, Wiley New York

Giesbrecht, F.G. and Burns, J.C. (1985), Two-Stage Analysis Based on a Mixed Model: Large-Sample Asymptotic Theory and Small-Sample Simulation Results, Biometrics 41, p. 477-486

SAS Help and Documentation PROC MIXED (MODEL-statement, Option 'ddfm'), SAS Institute Inc., Cary, NC, USA

See Also

test.lsmeans, getL

Examples

## Not run: 
data(dataEP05A2_2)
ub.dat <- dataEP05A2_2[-c(11,12,23,32,40,41,42),]
fit1 <- anovaMM(y~day/(run), ub.dat)
fit2 <- remlMM(y~day/(run), ub.dat)
fe1 <- fixef(fit1)
fe1
fe2 <- fixef(fit2)
fe2
lc.mat <- getL( fit1, c("day1-day2", "day3-day6"))
lc.mat
test.fixef(fit1, lc.mat, ddfm="satt") 
test.fixef(fit2, lc.mat, ddfm="satt")

# some inferential statistics about fixed effects estimates
L <- diag(nrow(fe1))
rownames(L) <- colnames(L) <- rownames(fe1)
test.fixef(fit1, L)
test.fixef(fit2, L)

# using different "residual" method determining DFs
test.fixef(fit1, L, ddfm="res")
test.fixef(fit2, L, ddfm="res")  

# having 'opt=TRUE' is a good idea to save time 
# (in case of balanced designs)
data(VCAdata1)
datS3 <- VCAdata1[VCAdata1$sample==3,]
fit3 <- anovaMM(y~(lot+device)/(day)/run, datS3)
fit4 <- remlMM(y~(lot+device)/(day)/run, datS3)  
fit3$VarCov <- vcovVC(fit3)
fe3 <- fixef(fit3)
fe4 <- fixef(fit4)
L <- diag(nrow(fe3))
rownames(L) <- colnames(L) <- rownames(fe3)
system.time(tst1 <- test.fixef(fit3, L))
system.time(tst2 <- test.fixef(fit3, L, opt=FALSE))
system.time(tst3 <- test.fixef(fit4, L, opt=FALSE))
tst1
tst2
tst3

## End(Not run)

VCA documentation built on May 29, 2024, 1:48 a.m.