expr.dev.test: Deviance Test

In GlobalDeviance: Global Deviance Permutation Tests

Description

Deviance permuation test.

Usage

expr.dev.test(xx, formula.full, formula.red = NULL, D.red = NULL, model.dat, 
	test.vars, glm.family, perm = 100, method = c("chisqstat", "permutation"), 
	cf="fisher", adjust=FALSE, snowfall.args=list(parallel=FALSE), 
	snowfall.seed, save.stat.data = FALSE, 
	file.save = "GlobalDeviance_statistic_Tperm_and_Tobs.Rdata",
	use.save.stat.data = FALSE, 
	file.use = "GlobalDeviance_statistic_Tperm_and_Tobs.Rdata")

Arguments

xx	Dataset (variables x observations/patients).
formula.full	Formula from the full model.
formula.red	Formula from the reduced model.
D.red	Designmatrix of the reduced model.
model.dat	Dataset with covariables (observations/patients x covariables).
test.vars	Variables or groups of variables to test.
glm.family	Family for the regression.
perm	Number of permutations.
method	Method for the calculation of the p-value.
cf	Combining function for the partial tests.
adjust	Method for p-value adjustment. Not implemented.
snowfall.args	A list with parameters for the initialisation of parallelizing with package snowfall.
snowfall.seed	Start seed.
save.stat.data	Logical value, default is FALSE. Save the permutation and original test statistic.
file.save	File name for saving.
use.save.stat.data	Logical value, default is FALSE. Use the saved permutation and original test statistic.
file.use	File name for data loading.

Value

A list

method	Method for the calculation of the p-value.
number.of.variables	Number of variables.
number.of.permutations	Number of permutations.
formula.full	Formula from the full model.
formula.red	Formula from the reduced model.
test	Test results.
data.perm	Permutation test statistic.
data.original	Original test statistic.
test.vars	Variables or groups of variables to test.

Author(s)

Frederike Fuhlbrueck [e-mail]

See Also

See PermTest, varwiselogLik and Rossi.

Examples

## Not run: 
### Example 1: poisson random data 
set.seed(6666)
n<-100
Y1<-c(rpois(n, 1))
Y2<-c(rpois(n/2, 1), rpois(n/2, 10))
A<-rnorm(n)
B<-c(rep(1, n/2), rep(0, n/2))       # group variable
C<-rpois(n, 1)

test.variables<-list("Y1", "Y2", c("Y1", "Y2"))
names(test.variables)<-c("Y1", "Y2", "Y1, Y2")

t.random<-expr.dev.test(xx=t(data.frame(Y1, Y2)), formula.full=~ A + B + C, 
	formula.red=~ A + C, model.dat=data.frame(A, B, C), test.vars=test.variables, 
	glm.family=poisson(link="log"), perm=1000, method="permutation", cf="fisher", 
	snowfall.args=list(parallel=TRUE), snowfall.seed=54321)

summary(t.random, digits=3)



### Example 2:  data set Rossi
data(Rossi)

# Covariables (patients x covariables)
model.dat<-Rossi[, c("arrest", "fin", "wexp")]
str(model.dat)

# data (variables/genes x patients)
xx<-rbind(t(t(t(Rossi[, c("prio", "n.work.weeks")]))), rpois(432, 1))
rownames(xx)<-c("prio", "n.work.weeks", "random")

formula.full<- ~ arrest + fin + wexp
formula.red<- ~ arrest + fin

test.vars<-list("prio", "n.work.weeks", "random", c("prio", "n.work.weeks"), 
	c("prio", "n.work.weeks", "random"))
names(test.vars)<-c("prio", "n.work.weeks", "random", "prio+n.work.weeks", 
	"prio+n.work.weeks+random")

set.seed(54321)

t.rossi1<-expr.dev.test(xx=xx, formula.full=formula.full, formula.red=formula.red, 
	D.red=NULL, model.dat, test.vars=test.vars, glm.family=poisson(link="log"), 
	perm=100, method="permutation", cf="fisher")

t.rossi2<-expr.dev.test(xx=xx, formula.full=formula.full, formula.red=formula.red, 
	D.red=NULL, model.dat, test.vars=test.vars, glm.family=poisson(link="log"), 
	perm=100, method="chisqstat", cf="fisher")

summary(t.rossi1, digits=2)

summary(t.rossi2, digits=3)


## End(Not run)

GlobalDeviance documentation built on May 2, 2019, 11:32 a.m.