Hi, Dennis,
Thanks for the reply. I tried to upgrade to R 2.13.0. Then when I tried to
load the library(nparcomp), I got an error
Error: package 'mvtnorm' is not installed for 'arch=i386'
What does that mean? Thanks.
Jun
On Fri, Apr 29, 2011 at 5:49 PM, Dennis Murphy <djmu...@gmail.com> wrote:
> Hi:
>
> Is this the function nparcomp() in the nparcomp package or the one
> from the mutoss package? When using functions from packages, it is
> useful to indicate the package name. I'm assuming you're using the
> nparcomp package, because your code worked for me when that package
> was loaded:
>
> > library(nparcomp)
> Loading required package: multcomp
> Loading required package: mvtnorm
> Loading required package: survival
> Loading required package: splines
> > nparcomp(Ulceration~Group,data=test,type='Dunnett',control='Non-treated')
>
> Nonparametric Multiple Comparison Procedure based on relative
> contrast effects , Type of Contrast : Dunnett
> NOTE:
> *-------------------Weight Matrix------------------*
> - Weight matrix for choosen contrast based on all-pairs comparisons
>
> *-----------Analysis of relative effects-----------*
> - Simultaneous Confidence Intervals for relative effects p(i,j)
> with confidence level 0.95
> - Method = Multivariate Delta-Method (Logit)
> - p-Values for H_0: p(i,j)=1/2
>
> *----------------Interpretation--------------------*
> p(a,b) > 1/2 : b tends to be larger than a
> *--------------Mult.Distribution-------------------*
> - Equicoordinate Quantile
> - Global p-Value
> *--------------------------------------------------*
> $weight.matrix
>
> < snipped for brevity - all zeros >
>
> $Data.Info
> Sample Size
> 1 Duoderm 24
> 2 Fibrase 24
> 3 Kollagenase 24
> 4 Non-treated 24
> 5 Stimulen 24
> 6 Vehicle 24
>
> $Analysis.of.relative.effects
> Comparison rel.effect confidence.interval t.value
> 1 p(Non-treated,Duoderm) 0.5 [ 0.499 ; 0.501 ] 0
> 2 p(Non-treated,Fibrase) 0.5 [ 0.499 ; 0.501 ] 0
> 3 p(Non-treated,Kollagenase) 0.5 [ 0.499 ; 0.501 ] 0
> 4 p(Non-treated,Stimulen) 0.5 [ 0.499 ; 0.501 ] 0
> 5 p(Non-treated,Vehicle) 0.5 [ 0.499 ; 0.501 ] 0
> p.value.adjusted p.value.unadjusted
> 1 1 1
> 2 1 1
> 3 1 1
> 4 1 1
> 5 1 1
>
> $Mult.Distribution
> Quantile p.Value.global
> 1 2.568766 1
>
> $Correlation
> [1] NA
>
> A graphic also appears indicating zero effect, which is what one would
> expect since Ulceration = 5 for every observation in the data frame.
>
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] nparcomp_1.0-1 multcomp_1.2-5 survival_2.36-9 mvtnorm_0.9-999
> [5] sos_1.3-0 brew_1.0-6 plyr_1.5.2
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.13.0 tools_2.13.0
>
> Check your version of R and the nparcomp package against this. If you
> have an older version of R or nparcomp, perhaps an upgrade is
> sufficient to fix the problem.
>
> HTH,
> Dennis
>
> On Fri, Apr 29, 2011 at 2:49 PM, Jun Shen <jun.shen...@gmail.com> wrote:
> > 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")
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
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