[R] pmvt problem in multcomp
Chihiro Kuroki
kuroki at oak.dti.ne.jp
Thu May 20 04:02:41 CEST 2004
Hi, all:
Two examples are shown below.
I want to use the multiple comparison of Dunnett.
It succeeded in upper case "example 1".
However, the lower case "example 2" went wrong.
In "example 2", the function pmvt return NaN, so I cannot show
this simtest result. Is there any solution?
(I changed the variable "maxpts" to a large number in front of
the function pmvt ... but, the function mvt returned an error. )
-- example 1 -------------------------------
require(multcomp)
Loading required package: multcomp
Loading required package: mvtnorm
[1] TRUE
y <- as.vector(t$int)
f <- as.factor(t$group1)
table(f)
f
1 2 3
20988 20988 20988
dat <- cbind(as.data.frame(y),f)
gc()
summary(simtest(y ~ f, data=dat, type="Dunnett"))
Simultaneous tests: Dunnett contrasts
Call:
simtest.formula(formula = y ~ f, data = dat, type = "Dunnett")
Dunnett contrasts for factor f
Contrast matrix:
f1 f2 f3
f2-f1 0 -1 1 0
f3-f1 0 -1 0 1
Absolute Error Tolerance: 0.001
Coefficients:
Estimate t value Std.Err. p raw p Bonf p adj
f2-f1 4.015 -0.677 5.934 0.499 0.997 0.722
f3-f1 2.486 -0.419 5.934 0.675 0.997 0.722
---------------------------------
-- example 2 -------------------------------
require(multcomp)
Loading required package: multcomp
Loading required package: mvtnorm
[1] TRUE
y <- as.vector(t$int)
f <- as.factor(t$group2)
table(f)
f
1 2 3 4 5
104940 104940 104940 104940 104940
dat <- cbind(as.data.frame(y),f)
gc()
summary(simtest(y ~ f, data=dat, type="Dunnett"))
[1] "des <- model.matrix(ff, mf)"
(Intercept) aaa1 aaa2 aaa3 aaa4
1 1 1 0 0 0
2 1 0 1 0 0
3 1 0 0 1 0
4 1 0 0 0 1
attr(,"assign")
[1] 0 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$aaa
[1] "ct"
[1] "gls <- rep(0,nrow(contonly))"
[1] 0 0 0 0
[1] "gls[i1] <- 1-prob"
[1] NaN 0 0 0
[1] "gls[i1] <- 1-prob"
[1] NaN NaN 0 0
[1] "gls[i1] <- 1-prob"
[1] NaN NaN -7.01661e-14 0.00000e+00
[1] "gls[i1] <- 1-prob"
[1] NaN NaN -7.016610e-14 3.362133e-11
[1] "glsbig"
aaa1 aaa2 aaa3 aaa4
1 NaN NaN NaN NaN
2 NaN NaN NaN NaN
3 0 0 -7.01661e-14 0.000000e+00
4 0 0 0.00000e+00 3.362133e-11
[1] "glsp"
aaa1 aaa2 aaa3 aaa4
NaN NaN NaN NaN
Error in if (glsp[i] < glsp[i - 1]) { : missing value where TRUE/FALSE needed
Execution halted
---------------------------------
--
kuroki at oak.dti.ne.jp
GnuPG fingerprint = 90FD FE79 905F 26F9 29C4 096F 8AA2 2C42 5130 1469
More information about the R-help
mailing list