[R] pmvt problem in multcomp

[Chihiro Kuroki]

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
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