[R] Use nparcomp function from nparcomp library to run post hoc

From: Jun Shen <jun.shen.ut_at_gmail.com>
Date: Fri, 29 Apr 2011 16:49:00 -0500


Dear list,

I tried to use the nparcomp to run some post hoc non-parametric comparison and got and error.

Error in uniroot(pfct, interval = interval) :   f() values at end points not of opposite sign

 Appreciate any comments.

the command line:

>nparcomp(Ulceration~Group,data=test,type='Dunnett',control='Non-treated')

Jun



data as follows
structure(list(Group = c("Duoderm", "Duoderm", "Duoderm", "Duoderm",

"Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm",
"Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm",
"Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm",
"Duoderm", "Duoderm", "Fibrase", "Fibrase", "Fibrase", "Fibrase",
"Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase",
"Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase",
"Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase",
"Fibrase", "Fibrase", "Kollagenase", "Kollagenase", "Kollagenase",
"Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase",
"Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase",
"Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase",
"Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase",
"Kollagenase", "Non-treated", "Non-treated", "Non-treated", "Non-treated",
"Non-treated", "Non-treated", "Non-treated", "Non-treated", "Non-treated",
"Non-treated", "Non-treated", "Non-treated", "Non-treated", "Non-treated",
"Non-treated", "Non-treated", "Non-treated", "Non-treated", "Non-treated",
"Non-treated", "Non-treated", "Non-treated", "Non-treated", "Non-treated",
"Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen",
"Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen",
"Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen",
"Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen",
"Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle",
"Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle",
"Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle",
"Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle"
), Ulceration = c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5), Inflamation = c(3, 4, 3, 2, 3, 3, 4, 4, 2, 2, 3, 3,
3, 3, 3, 3, 3, 4, 3, 3, 3, 4, 3, 3, 2, 3, 3, 4, 3, 3, 2, 4, 4,
4, 4, 4, 4, 4, 3, 3, 4, 3, 5, 3, 3, 4, 4, 3, 3, 2, 4, 2, 3, 3,
4, 3, 4, 3, 3, 4, 3, 4, 2, 3, 3, 4, 2, 3, 4, 3, 2, 3, 3, 3, 2,
3, 2, 2, 2, 2, 4, 3, 2, 3, 3, 4, 3, 3, 4, 3, 4, 2, 4, 3, 4, 2,
4, 3, 4, 3, 2, 2, 2, 2, 3, 2, 3, 2, 4, 3, 2, 4, 4, 4, 2, 2, 3,
3, 2, 4, 3, 2, 3, 2, 2, 2, 4, 2, 3, 2, 3, 2, 3, 3, 3, 4, 3, 3,
4, 4, 2, 3, 2, 3), Fibroplasia = c(4, 4, 4, 4, 4, 3, 4, 4, 4,
3, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 2, 4, 4, 3,
2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 4, 3, 3, 3, 4, 3, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 3, 3, 3, 4, 4, 3, 4, 4, 4, 3, 4,
4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4,
4, 4, 3, 4, 4, 3, 4, 3, 2, 3, 3, 4, 3, 3, 4, 4, 3, 3, 3, 4, 3,
3, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 3, 4,
3, 4, 4, 4, 4, 4, 4, 4, 4), Fibrosis.and.Adexnal.Atrophy = c(4,
4, 4, 3, 4, 4, 4, 4, 4, 3, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 3, 4, 3, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 3, 4,
4, 4, 3, 4, 3, 3, 3, 3, 3, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 3, 3,
4, 4, 3, 3, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4,
4, 4, 3, 4, 4, 4, 3, 4, 3, 4, 3, 4, 4, 3, 4, 3, 2, 3, 3, 4, 4,
3, 4, 4, 3, 3, 3, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4,
3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4), Inflammation = c(2,
2, 2, 1, 1, 1, 2, 3, 1, 2, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 2, 1,
1, 1, 1, 1, 1, 1, 1, 2, NA, 1, 1, 1, 2, 2, 2, 1, 2, 1, 1, 2,
1, 1, 2, 1, 1, 2, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1,
1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, NA, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1,
2, 1, 2, 2, 1, 1, 2, 1, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 2,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2), Fibroplasia.1 =
c(4,
4, 4, 4, 4, 3, 4, 4, 4, 3, 4, 3, 3, 3, 4, 4, 4, 4, 3, 3, 3, 3,
4, 4, 4, 4, 3, 3, 4, 3, NA, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3,
3, 3, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 4, 3, 4, 3, 4, 4, 4, 4, 3,
3, 4, 4, 4, 3, 4, 3, 4, 4, 3, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4,
4, 3, 3, 3, NA, 4, 4, 4, 4, 3, 4, 3, 3, 3, 3, 3, 4, 2, 4, 3,
4, 4, 3, 4, 4, 2, 3, 2, 3, 3, 3, 3, 4, 4, 4, 4, 3, 3, 3, 3, 3,
4, 3, 3, 4, 4, 4, 4, 3, 3, 4, 3, 3, 4, 4, 4, 4, 3, 4, 4), Fibrosis = c(3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, NA, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3,
3, 3, 3, 3, NA, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 2, 3, 3,
3, 3, 3, 3, 3, 2, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3), Total = c(25,
26, 25, 22, 24, 22, 26, 27, 23, 21, 24, 21, 22, 23, 25, 24, 25,
26, 23, 23, 24, 24, 24, 24, 21, 24, 20, 24, 24, 22, 12, 25, 25,
25, 26, 26, 26, 24, 22, 21, 24, 22, 24, 22, 25, 23, 25, 24, 22,
21, 24, 21, 24, 24, 25, 23, 25, 23, 24, 24, 24, 24, 20, 21, 24,
26, 21, 22, 25, 23, 21, 24, 23, 24, 23, 22, 23, 23, 22, 23, 25,
23, 23, 24, 24, 24, 23, 22, 17, 25, 25, 21, 25, 22, 25, 19, 24,
23, 22, 23, 21, 16, 22, 20, 25, 22, 22, 24, 25, 19, 21, 20, 25,
23, 20, 22, 25, 24, 23, 25, 24, 22, 22, 21, 23, 23, 23, 20, 24, 23, 24, 23, 23, 22, 24, 23, 23, 24, 26, 25, 23, 23, 24, 25)), .Names =
c("Group",
"Ulceration", "Inflamation", "Fibroplasia", "Fibrosis.and.Adexnal.Atrophy",
"Inflammation", "Fibroplasia.1", "Fibrosis", "Total"), row.names = c(NA,
144L), class = "data.frame")

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